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Jay Shendure, M.D./Ph.D. - Publications

Affiliations: 
Genome Sciences University of Washington, Seattle, Seattle, WA 
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371 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Barbosa K, Deshpande A, Perales ME, Xiang P, Murad R, Pramod AB, Minkina A, Robertson NA, Schischlik F, Lei X, Sun Y, Brown A, Amend D, Jeremias I, Doench JG, ... ... Shendure JA, et al. TRANSCRIPTIONAL CONTROL OF LEUKEMOGENESIS BY THE CHROMATIN READER SGF29. Blood. PMID 38048593 DOI: 10.1182/blood.2023021234  0.583
2023 Huang X, Henck J, Qiu C, Sreenivasan VKA, Balachandran S, Amarie OV, Hrabě de Angelis M, Behncke RY, Chan WL, Despang A, Dickel DE, Duran M, Feuchtinger A, Fuchs H, Gailus-Durner V, ... ... Shendure J, et al. Single-cell, whole-embryo phenotyping of mammalian developmental disorders. Nature. PMID 37968388 DOI: 10.1038/s41586-023-06548-w  0.721
2023 Chiou KL, Huang X, Bohlen MO, Tremblay S, DeCasien AR, O'Day DR, Spurrell CH, Gogate AA, Zintel TM, Andrews MG, Martínez MI, Starita LM, Montague MJ, Platt ML, Shendure J, et al. A single-cell multi-omic atlas spanning the adult rhesus macaque brain. Science Advances. 9: eadh1914. PMID 37824616 DOI: 10.1126/sciadv.adh1914  0.555
2023 Alghadeer A, Hanson-Drury S, Patni AP, Ehnes DD, Zhao YT, Li Z, Phal A, Vincent T, Lim YC, O'Day D, Spurrell CH, Gogate AA, Zhang H, Devi A, Wang Y, ... ... Shendure J, et al. Single-cell census of human tooth development enables generation of human enamel. Developmental Cell. PMID 37582367 DOI: 10.1016/j.devcel.2023.07.013  0.58
2023 Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, et al. GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3 (Bethesda, Md.). PMID 37552705 DOI: 10.1093/g3journal/jkad177  0.585
2023 Bennett JC, Emanuels A, Heimonen J, O'Hanlon J, Hughes JP, Han PD, Chow EJ, Ogokeh CE, Rolfes MA, Lockwood CM, Pfau B, Uyeki TM, Shendure J, Hoag S, Fay K, et al. nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic. Frontiers in Pediatrics. 11: 1198278. PMID 37484765 DOI: 10.3389/fped.2023.1198278  0.519
2023 Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, ... ... Shendure J, et al. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. PMID 37419111 DOI: 10.1016/j.molcel.2023.06.018  0.769
2023 McCulloch DJ, Rogers JH, Wang Y, Chow EJ, Link AC, Wolf CR, Uyeki TM, Rolfes MA, Mosites E, Sereewit J, Duchin JS, Sugg NK, Greninger AL, Boeckh MJ, Englund JA, ... Shendure J, et al. Respiratory syncytial virus and other respiratory virus infections in residents of homeless shelters - King County, Washington, 2019-2021. Influenza and Other Respiratory Viruses. 17: e13166. PMID 37346095 DOI: 10.1111/irv.13166  0.517
2023 Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid T, Kim H, Lalanne JB, Nathans JF, Shendure J. Chromatin context-dependent regulation and epigenetic manipulation of prime editing. Biorxiv : the Preprint Server For Biology. PMID 37090511 DOI: 10.1101/2023.04.12.536587  0.782
2023 Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, Oâ Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, ... ... Shendure J, et al. A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. Biorxiv : the Preprint Server For Biology. PMID 37066300 DOI: 10.1101/2023.04.05.535726  0.706
2023 Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, et al. GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse ( ). Biorxiv : the Preprint Server For Biology. PMID 37066261 DOI: 10.1101/2023.04.03.535372  0.585
2023 Chardon FM, McDiarmid TA, Page NF, Martin B, Domcke S, Regalado SG, Lalanne JÆ, Calderon D, Starita LM, Sanders SJ, Ahituv N, Shendure J. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. Biorxiv : the Preprint Server For Biology. PMID 37034704 DOI: 10.1101/2023.03.28.534017  0.604
2023 Agarwal V, Inoue F, Schubach M, Martin BK, Dash PM, Zhang Z, Sohota A, Noble WS, Yardimci GG, Kircher M, Shendure J, Ahituv N. Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types. Biorxiv : the Preprint Server For Biology. PMID 36945371 DOI: 10.1101/2023.03.05.531189  0.576
2023 Whalen S, Inoue F, Ryu H, Fair T, Markenscoff-Papadimitriou E, Keough K, Kircher M, Martin B, Alvarado B, Elor O, Laboy Cintron D, Williams A, Hassan Samee MA, Thomas S, Krencik R, ... ... Shendure J, et al. Machine learning dissection of human accelerated regions in primate neurodevelopment. Neuron. PMID 36640767 DOI: 10.1016/j.neuron.2022.12.026  0.511
2022 Paredes MI, Perofsky AC, Frisbie L, Moncla LH, Roychoudhury P, Xie H, Mohamed Bakhash SA, Kong K, Arnould I, Nguyen TV, Wendm ST, Hajian P, Ellis S, Mathias PC, Greninger AL, ... ... Shendure J, et al. Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county. Medrxiv : the Preprint Server For Health Sciences. PMID 36561171 DOI: 10.1101/2022.12.15.22283536  0.556
2022 Hansen C, Perofsky AC, Burstein R, Famulare M, Boyle S, Prentice R, Marshall C, McCormick BJJ, Reinhart D, Capodanno B, Truong M, Schwabe-Fry K, Kuchta K, Pfau B, Acker Z, ... ... Shendure J, et al. Trends in Risk Factors and Symptoms Associated With SARS-CoV-2 and Rhinovirus Test Positivity in King County, Washington, June 2020 to July 2022. Jama Network Open. 5: e2245861. PMID 36484987 DOI: 10.1001/jamanetworkopen.2022.45861  0.517
2022 Chiou KL, DeCasien AR, Rees KP, Testard C, Spurrell CH, Gogate AA, Pliner HA, Tremblay S, Mercer A, Whalen CJ, Negrón-Del Valle JE, Janiak MC, Bauman Surratt SE, González O, Compo NR, ... ... Shendure J, et al. Multiregion transcriptomic profiling of the primate brain reveals signatures of aging and the social environment. Nature Neuroscience. PMID 36424430 DOI: 10.1038/s41593-022-01197-0  0.533
2022 Martin BK, Qiu C, Nichols E, Phung M, Green-Gladden R, Srivatsan S, Blecher-Gonen R, Beliveau BJ, Trapnell C, Cao J, Shendure J. Optimized single-nucleus transcriptional profiling by combinatorial indexing. Nature Protocols. PMID 36261634 DOI: 10.1038/s41596-022-00752-0  0.692
2022 Pattwell SS, Arora S, Nuechterlein N, Zager M, Loeb KR, Cimino PJ, Holland NC, Reche-Ley N, Bolouri H, Almiron Bonnin DA, Szulzewsky F, Phadnis VV, Ozawa T, Wagner MJ, Haffner MC, ... ... Shendure J, et al. Oncogenic role of a developmentally regulated splice variant. Science Advances. 8: eabo6789. PMID 36206341 DOI: 10.1126/sciadv.abo6789  0.677
2022 Chung E, Magedson A, Emanuels A, Luiten K, Pfau B, Truong M, Chow EJ, Hughes JP, Uyeki TM, Englund JA, Nickerson DA, Lockwood CM, Shendure J, Starita LM, Chu HY. SARS-CoV-2 Screening Testing in Schools: A Comparison of School- vs Home-Based Collection Methods. Journal of the Pediatric Infectious Diseases Society. PMID 36082698 DOI: 10.1093/jpids/piac097  0.509
2022 Weil AA, Luiten KG, Casto AM, Bennett JC, O'Hanlon J, Han PD, Gamboa LS, McDermot E, Truong M, Gottlieb GS, Acker Z, Wolf CR, Magedson A, Chow EJ, Lo NK, ... ... Shendure J, et al. Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus. Nature Communications. 13: 5240. PMID 36068236 DOI: 10.1038/s41467-022-32786-z  0.63
2022 Johnsen JM, Fletcher SN, Dove A, McCracken H, Martin BK, Kircher M, Josephson NC, Shendure J, Ruuska SE, Valentino LA, Pierce GF, Watson C, Cheng D, Recht M, Konkle BA. Results of Genetic Analysis of 11,341 Participants Enrolled in the My Life, Our Future Hemophilia Genotyping Initiative in the United States. Journal of Thrombosis and Haemostasis : Jth. PMID 35770352 DOI: 10.1111/jth.15805  0.484
2022 Anderson DJ, Pauler FM, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. PMID 35452605 DOI: 10.1016/j.cels.2022.03.006  0.598
2022 Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nature Genetics. 54: 328-341. PMID 35288709 DOI: 10.1038/s41588-022-01018-x  0.706
2022 Burstein R, Althouse BM, Adler A, Akullian A, Brandstetter E, Cho S, Emanuels A, Fay K, Gamboa L, Han P, Huden K, Ilcisin M, Izzo M, Jackson ML, Kim AE, ... ... Shendure J, et al. Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data. Medrxiv : the Preprint Server For Health Sciences. PMID 35169816 DOI: 10.1101/2022.02.04.22270474  0.533
2022 Boeckh M, Chu HY, Englund JA, Lockwood CM, Nickerson DA, Shendure J, Starita L. The Seattle Flu Study: when regulations hinder pandemic surveillance. Nature Medicine. 28: 7-8. PMID 34937879 DOI: 10.1038/s41591-021-01587-0  0.507
2021 Weil AA, Sohlberg SL, O'Hanlon JA, Casto AM, Emanuels AW, Lo NK, Greismer EP, Magedson AM, Wilcox NC, Kim AE, Back L, Frazar CD, Pelle B, Sibley TR, Ilcisin M, ... ... Shendure JA, et al. SARS-CoV-2 Epidemiology on a Public University Campus in Washington State. Open Forum Infectious Diseases. 8: ofab464. PMID 34805425 DOI: 10.1093/ofid/ofab464  0.586
2021 Carroll PA, Freie BW, Cheng PF, Kasinathan S, Gu H, Hedrich T, Dowdle JA, Venkataramani V, Ramani V, Wu X, Raftery D, Shendure J, Ayer DE, Muller CH, Eisenman RN. The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. Plos Biology. 19: e3001085. PMID 34669700 DOI: 10.1371/journal.pbio.3001085  0.577
2021 Brewer CM, Nelson BR, Wakenight P, Collins SJ, Okamura DM, Dong XR, Mahoney WM, McKenna A, Shendure J, Timms A, Millen KJ, Majesky MW. Adaptations in Hippo-Yap signaling and myofibroblast fate underlie scar-free ear appendage wound healing in spiny mice. Developmental Cell. PMID 34610329 DOI: 10.1016/j.devcel.2021.09.008  0.464
2021 Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biology. 22: 279. PMID 34579774 DOI: 10.1186/s13059-021-02432-w  0.6
2021 Srivatsan S, Heidl S, Pfau B, Martin BK, Han PD, Zhong W, van Raay K, McDermot E, Opsahl J, Gamboa L, Smith N, Truong M, Cho S, Barrow KA, Rich LM, ... ... Shendure J, et al. SwabExpress: An end-to-end protocol for extraction-free covid-19 testing. Clinical Chemistry. PMID 34286830 DOI: 10.1093/clinchem/hvab132  0.729
2021 Simeonov KP, Byrns CN, Clark ML, Norgard RJ, Martin B, Stanger BZ, Shendure J, McKenna A, Lengner CJ. Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states. Cancer Cell. PMID 34115987 DOI: 10.1016/j.ccell.2021.05.005  0.512
2021 Chung E, Chow EJ, Wilcox NC, Burstein R, Brandstetter E, Han PD, Fay K, Pfau B, Adler A, Lacombe K, Lockwood CM, Uyeki TM, Shendure J, Duchin JS, Rieder MJ, et al. Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting. Jama Pediatrics. PMID 34115094 DOI: 10.1001/jamapediatrics.2021.2025  0.514
2021 Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, ... ... Shendure J, et al. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Science Translational Medicine. PMID 33941621 DOI: 10.1126/scitranslmed.abf0202  0.589
2021 Durham TJ, Daza RM, Gevirtzman L, Cusanovich D, Bolonduro O, Noble WS, Shendure J, Waterston RH. Comprehensive characterization of tissue-specific chromatin accessibility in L2 nematodes. Genome Research. PMID 33888511 DOI: 10.1101/gr.271791.120  0.73
2021 Rentzsch P, Schubach M, Shendure J, Kircher M. CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores. Genome Medicine. 13: 31. PMID 33618777 DOI: 10.1186/s13073-021-00835-9  0.552
2021 Truong M, Pfau B, McDermot E, Han PD, Brandstetter E, Richardson M, Kim AE, Rieder MJ, Chu HY, Englund JA, Nickerson DA, Shendure J, Lockwood CM, Konnick EQ, Starita LM, et al. Comparable specimen collection from both ends of at-home mid-turbinate swabs. Journal of Clinical Microbiology. PMID 33597259 DOI: 10.1128/JCM.03073-20  0.524
2020 Singh R, Demetci P, Bonora G, Ramani V, Lee C, Fang H, Duan Z, Deng X, Shendure J, Disteche C, Noble WS. Unsupervised manifold alignment for single-cell multi-omics data. Acm-Bcb ... ... : the ... Acm Conference On Bioinformatics, Computational Biology and Biomedicine. Acm Conference On Bioinformatics, Computational Biology and Biomedicine. 2020: 1-10. PMID 33954299 DOI: 10.1145/3388440.3412410  0.617
2020 Truong M, Pfau B, McDermot E, Han PD, Brandstetter E, Richardson M, Kim AE, Rieder MJ, Chu HY, Englund JA, Nickerson DA, Shendure J, Lockwood CM, Konnick EQ, Starita LM. Comparable specimen collection from both ends of at-home mid-turbinate swabs. Medrxiv : the Preprint Server For Health Sciences. PMID 33330895 DOI: 10.1101/2020.12.05.20244632  0.541
2020 Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, ... ... Shendure J, et al. A human cell atlas of fetal gene expression. Science (New York, N.Y.). 370. PMID 33184181 DOI: 10.1126/science.aba7721  0.701
2020 Domcke S, Hill AJ, Daza RM, Cao J, O'Day DR, Pliner HA, Aldinger KA, Pokholok D, Zhang F, Milbank JH, Zager MA, Glass IA, Steemers FJ, Doherty D, Trapnell C, ... ... Shendure J, et al. A human cell atlas of fetal chromatin accessibility. Science (New York, N.Y.). 370. PMID 33184180 DOI: 10.1126/science.aba7612  0.794
2020 Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, ... Shendure J, et al. Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature Protocols. PMID 33128032 DOI: 10.1038/s41596-020-00422-z  0.481
2020 Klein JC, Agarwal V, Inoue F, Keith A, Martin B, Kircher M, Ahituv N, Shendure J. A systematic evaluation of the design and context dependencies of massively parallel reporter assays. Nature Methods. PMID 33046894 DOI: 10.1038/s41592-020-0965-y  0.53
2020 Chu HY, Boeckh M, Englund JA, Famulare M, Lutz B, Nickerson DA, Rieder M, Starita LM, Adler A, Brandstetter E, Frazer CD, Han PD, Gulati RK, Hadfield J, Jackson M, ... ... Shendure J, et al. The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology. Bmj Open. 10: e037295. PMID 33033018 DOI: 10.1136/bmjopen-2020-037295  0.542
2020 Mueller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman N, Huang ML, ... ... Shendure J, et al. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Medrxiv : the Preprint Server For Health Sciences. PMID 33024981 DOI: 10.1101/2020.09.30.20204230  0.592
2020 Kim HJ, Yardımcı GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS. Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. Plos Computational Biology. 16: e1008173. PMID 32946435 DOI: 10.1371/Journal.Pcbi.1008173  0.645
2020 Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, ... ... Shendure J, et al. Cryptic transmission of SARS-CoV-2 in Washington state. Science (New York, N.Y.). PMID 32913002 DOI: 10.1126/Science.Abc0523  0.63
2020 Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulous-Soares I, Yosef N, Ye CJ, Pollard KS, ... Shendure J, et al. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature Protocols. PMID 32641802 DOI: 10.1038/S41596-020-0333-5  0.65
2020 Alexander J, LaPlant QC, Pattwell SS, Szulzewsky F, Cimino PJ, Caruso FP, Pugliese P, Chen Z, Chardon F, Hill AJ, Spurrell C, Ahrendsen D, Pietras A, Starita LM, Hambardzumyan D, ... ... Shendure J, et al. Multimodal single-cell analysis reveals distinct radioresistant stem-like and progenitor cell populations in murine glioma. Glia. PMID 32621641 DOI: 10.1002/Glia.23866  0.597
2020 Harrison JJ, Almblad H, Irie Y, Wolter DJ, Eggleston HC, Randall TE, Kitzman JO, Stackhouse B, Emerson JC, Mcnamara S, Larsen TJ, Shendure J, Hoffman LR, Wozniak DJ, Parsek MR. Elevated exopolysaccharide levels in Pseudomonas aeruginosa flagellar mutants have implications for biofilm growth and chronic infections. Plos Genetics. 16: e1008848. PMID 32530919 DOI: 10.1371/Journal.Pgen.1008848  0.753
2020 Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria N, Wang C, Yu G, Bushnell B, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, ... ... Shendure J, et al. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science (New York, N.Y.). PMID 32513865 DOI: 10.1126/Science.Abb9263  0.65
2020 Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, ... ... Shendure J, et al. Cryptic transmission of SARS-CoV-2 in Washington State. Medrxiv : the Preprint Server For Health Sciences. PMID 32511596 DOI: 10.1101/2020.04.02.20051417  0.608
2020 Deng X, Gu W, Federman S, Du Plessis L, Pybus O, Faria N, Wang C, Yu G, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, ... ... Shendure J, et al. A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage. Medrxiv : the Preprint Server For Health Sciences. PMID 32511579 DOI: 10.1101/2020.03.27.20044925  0.608
2020 Srivatsan S, Han PD, van Raay K, Wolf CR, McCulloch DJ, Kim AE, Brandstetter E, Martin B, Gehring J, Chen W, Kosuri S, Konnick EQ, Lockwood CM, Rieder MJ, ... ... Shendure J, et al. Preliminary support for a "dry swab, extraction free" protocol for SARS-CoV-2 testing via RT-qPCR. Biorxiv : the Preprint Server For Biology. PMID 32511368 DOI: 10.1101/2020.04.22.056283  0.739
2020 Jorden MA, Rudman SL, Villarino E, Hoferka S, Patel MT, Bemis K, Simmons CR, Jespersen M, Iberg Johnson J, Mytty E, Arends KD, Henderson JJ, Mathes RW, Weng CX, ... ... Shendure J, et al. Evidence for Limited Early Spread of COVID-19 Within the United States, January-February 2020. Mmwr. Morbidity and Mortality Weekly Report. 69: 680-684. PMID 32497028 DOI: 10.15585/Mmwr.Mm6922E1  0.588
2020 Agarwal V, Shendure J. Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks. Cell Reports. 31: 107663. PMID 32433972 DOI: 10.1016/J.Celrep.2020.107663  0.417
2020 Chu HY, Englund JA, Starita LM, Famulare M, Brandstetter E, Nickerson DA, Rieder MJ, Adler A, Lacombe K, Kim AE, Graham C, Logue J, Wolf CR, Heimonen J, McCulloch DJ, ... ... Shendure J, et al. Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform. The New England Journal of Medicine. PMID 32356944 DOI: 10.1056/Nejmc2008646  0.565
2020 Enikanolaiye A, Ruston J, Zeng R, Taylor C, Schrock M, Buchovecky CM, Shendure J, Acar E, Justice MJ. Suppressor mutations in -null mice implicate the DNA damage response in Rett syndrome pathology. Genome Research. PMID 32317254 DOI: 10.1101/Gr.258400.119  0.387
2020 Cao J, Zhou W, Steemers F, Trapnell C, Shendure J. Sci-fate characterizes the dynamics of gene expression in single cells. Nature Biotechnology. PMID 32284584 DOI: 10.1038/S41587-020-0480-9  0.715
2020 Rai V, Quang DX, Erdos MR, Cusanovich DA, Daza RM, Narisu N, Zou LS, Didion JP, Guan Y, Shendure J, Parker SCJ, Collins FS. Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures. Molecular Metabolism. 32: 109-121. PMID 32029221 DOI: 10.1016/J.Molmet.2019.12.006  0.728
2020 Gasperini M, Tome JM, Shendure J. Towards a comprehensive catalogue of validated and target-linked human enhancers. Nature Reviews. Genetics. PMID 31988385 DOI: 10.1038/S41576-019-0209-0  0.312
2020 Claussnitzer M, Cho JH, Collins R, Cox NJ, Dermitzakis ET, Hurles ME, Kathiresan S, Kenny EE, Lindgren CM, MacArthur DG, North KN, Plon SE, Rehm HL, Risch N, Rotimi CN, ... Shendure J, et al. A brief history of human disease genetics. Nature. 577: 179-189. PMID 31915397 DOI: 10.1038/S41586-019-1879-7  0.362
2020 Harrison JJ, Almblad H, Irie Y, Wolter DJ, Eggleston HC, Randall TE, Kitzman JO, Stackhouse B, Emerson JC, Mcnamara S, Larsen TJ, Shendure J, Hoffman LR, Wozniak DJ, Parsek MR. Supplementary materials and methods and supplementary references. Plos Genetics. DOI: 10.1371/Journal.Pgen.1008848.S001  0.716
2019 Gelman H, Dines JN, Berg J, Berger AH, Brnich S, Hisama FM, James RG, Rubin AF, Shendure J, Shirts B, Fowler DM, Starita LM. Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation. Genome Medicine. 11: 85. PMID 31862013 DOI: 10.1186/S13073-019-0698-7  0.646
2019 Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C. Massively multiplex chemical transcriptomics at single cell resolution. Science (New York, N.Y.). PMID 31806696 DOI: 10.1126/Science.Aax6234  0.783
2019 Alexander J, Findlay GM, Kircher M, Shendure J. Concurrent genome and epigenome editing by CRISPR-mediated sequence replacement. Bmc Biology. 17: 90. PMID 31739790 DOI: 10.1186/S12915-019-0711-Z  0.635
2019 Soza VL, Lindsley D, Waalkes A, Ramage E, Patwardhan RP, Burton JN, Adey A, Kumar A, Qiu R, Shendure J, Hall B. The Rhododendron genome and chromosomal organization provide insight into shared whole genome duplications across the heath family (Ericaceae). Genome Biology and Evolution. PMID 31702783 DOI: 10.1093/Gbe/Evz245  0.824
2019 Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biology. 20: 223. PMID 31679514 DOI: 10.1186/S13059-019-1845-6  0.729
2019 Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Methods (San Diego, Calif.). PMID 31536770 DOI: 10.1016/J.Ymeth.2019.09.012  0.653
2019 Kim S, Shendure J. Mechanisms of Interplay between Transcription Factors and the 3D Genome. Molecular Cell. PMID 31521504 DOI: 10.1016/J.Molcel.2019.08.010  0.382
2019 Pliner HA, Shendure J, Trapnell C. Supervised classification enables rapid annotation of cell atlases. Nature Methods. PMID 31501545 DOI: 10.1038/S41592-019-0535-3  0.321
2019 Yin Y, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure J. High-Throughput Single-Cell Sequencing with Linear Amplification. Molecular Cell. PMID 31495564 DOI: 10.1016/J.Molcel.2019.08.002  0.752
2019 McFaline-Figueroa JL, Hill AJ, Qiu X, Jackson D, Shendure J, Trapnell C. A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. Nature Genetics. 51: 1389-1398. PMID 31477929 DOI: 10.1038/S41588-019-0489-5  0.338
2019 Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N. Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nature Communications. 10: 3583. PMID 31395865 DOI: 10.1038/S41467-019-11526-W  0.595
2019 Bertero A, Fields PA, Smith AST, Leonard A, Beussman K, Sniadecki NJ, Kim DH, Tse HF, Pabon L, Shendure J, Noble WS, Murry CE. Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy. The Journal of Cell Biology. PMID 31395619 DOI: 10.1083/Jcb.201902117  0.346
2019 Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic Acids Research. PMID 31165867 DOI: 10.1093/Nar/Gkz487  0.706
2019 Klein JC, Keith A, Rice SJ, Shepherd C, Agarwal V, Loughlin J, Shendure J. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nature Communications. 10: 2434. PMID 31164647 DOI: 10.1038/S41467-019-10439-Y  0.337
2019 Minkina A, Shendure J. Expanding the single-cell genomics toolkit. Nature Genetics. 51: 931-932. PMID 31152159 DOI: 10.1038/S41588-019-0429-4  0.335
2019 Shigaki D, Adato O, Adhikar AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DP, Schubach M, Xiong C, Yan Z, Boyle AP, ... ... Shendure J, et al. Integration of Multiple Epigenomic Marks Improves Prediction of Variant Impact in Saturation Mutagenesis Reporter Assay. Human Mutation. PMID 31106481 DOI: 10.1002/Humu.23797  0.587
2019 Farhat MR, Freschi L, Calderon R, Ioerger T, Snyder M, Meehan CJ, de Jong B, Rigouts L, Sloutsky A, Kaur D, Sunyaev S, van Soolingen D, Shendure J, Sacchettini J, Murray M. GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nature Communications. 10: 2128. PMID 31086182 DOI: 10.1038/S41467-019-10110-6  0.576
2019 Kim S, Dunham MJ, Shendure J. A combination of transcription factors mediates inducible interchromosomal contacts. Elife. 8. PMID 31081754 DOI: 10.7554/Elife.42499  0.306
2019 Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH. Publisher Correction: DNA sequencing at 40: past, present and future. Nature. PMID 30948799 DOI: 10.1038/S41586-019-1120-8  0.622
2019 Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE. Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Nature Communications. 10: 1538. PMID 30948719 DOI: 10.1038/S41467-019-09483-5  0.678
2019 Ng BG, Lourenço CM, Losfeld ME, Buckingham KJ, Kircher M, Nickerson DA, Shendure J, Bamshad MJ, Freeze HH. Mutations in the translocon associated protein complex subunit SSR3 cause a novel Congenital Disorder of Glycosylation. Journal of Inherited Metabolic Disease. PMID 30945312 DOI: 10.1002/Jimd.12091  0.577
2019 Shendure J, Findlay GM, Snyder MW. Genomic Medicine-Progress, Pitfalls, and Promise. Cell. 177: 45-57. PMID 30901547 DOI: 10.1016/J.Cell.2019.02.003  0.602
2019 Ramani V, Qiu R, Shendure J. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Reports. 26: 2465-2476.e4. PMID 30811994 DOI: 10.1016/J.Celrep.2019.02.007  0.673
2019 Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J. The single-cell transcriptional landscape of mammalian organogenesis. Nature. PMID 30787437 DOI: 10.1038/S41586-019-0969-X  0.719
2019 Chu HY, Chu HY, Boeckh M, Boeckh M, Englund JA, Englund JA, Famulare M, Lutz BR, Lutz BR, Nickerson DA, Rieder M, Rieder M, Starita L, Starita L, Thompson M, ... ... Shendure J, et al. LB21. The Seattle Flu Study: A Community-Based Study of Influenza Open Forum Infectious Diseases. 6: S1002-S1002. DOI: 10.1093/Ofid/Ofz415.2504  0.581
2018 Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell. PMID 30612741 DOI: 10.1016/J.Cell.2018.11.029  0.425
2018 Swygert SG, Kim S, Wu X, Fu T, Hsieh TH, Rando OJ, Eisenman RN, Shendure J, McKnight JN, Tsukiyama T. Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence. Molecular Cell. PMID 30595435 DOI: 10.1016/J.Molcel.2018.11.020  0.319
2018 Sanchez C, Snyder MW, Tanos R, Shendure J, Thierry AR. New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis. Npj Genomic Medicine. 3: 31. PMID 30479833 DOI: 10.1038/S41525-018-0069-0  0.587
2018 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research. PMID 30371827 DOI: 10.1093/Nar/Gky1016  0.615
2018 Liu S, Huang S, Chen F, Zhao L, Yuan Y, Francis SS, Fang L, Li Z, Lin L, Liu R, Zhang Y, Xu H, Li S, Zhou Y, Davies RW, ... ... Shendure J, et al. Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. Cell. 175: 347-359.e14. PMID 30290141 DOI: 10.1016/J.Cell.2018.08.016  0.354
2018 Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, ... ... Shendure J, et al. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. The New England Journal of Medicine. 379: 1403-1415. PMID 30280646 DOI: 10.1056/Nejmoa1800474  0.53
2018 Starita LM, Islam MM, Banerjee T, Adamovich AI, Gullingsrud J, Fields S, Shendure J, Parvin JD. A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function. American Journal of Human Genetics. PMID 30219179 DOI: 10.1016/J.Ajhg.2018.07.016  0.646
2018 Findlay GM, Daza RM, Martin B, Zhang MD, Leith AP, Gasperini M, Janizek JD, Huang X, Starita LM, Shendure J. Accurate classification of BRCA1 variants with saturation genome editing. Nature. PMID 30209399 DOI: 10.1038/S41586-018-0461-Z  0.668
2018 Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science (New York, N.Y.). PMID 30166440 DOI: 10.1126/Science.Aau0730  0.791
2018 Ng BG, Underhill HR, Palm L, Bengtson P, Rozet JM, Gerber S, Munnich A, Zanlonghi X, Stevens CA, Kircher M, Nickerson DA, Buckingham KJ, Josephson KD, Shendure J, Bamshad MJ, et al. DPAGT1 Deficiency with Encephalopathy (DPAGT1-CDG): Clinical and Genetic Description of 11 New Patients. Jimd Reports. PMID 30117111 DOI: 10.1007/8904_2018_128  0.502
2018 Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. Molecular Cell. PMID 30078726 DOI: 10.1016/J.Molcel.2018.06.044  0.801
2018 Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, ... ... Shendure J, et al. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cell. PMID 30078704 DOI: 10.1016/J.Cell.2018.06.052  0.756
2018 Klein JC, Keith A, Agarwal V, Durham T, Shendure J. Functional characterization of enhancer evolution in the primate lineage. Genome Biology. 19: 99. PMID 30045748 DOI: 10.1186/S13059-018-1473-6  0.362
2018 McKenna A, Shendure J. FlashFry: a fast and flexible tool for large-scale CRISPR target design. Bmc Biology. 16: 74. PMID 29976198 DOI: 10.1186/S12915-018-0545-0  0.602
2018 Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, ... ... Shendure J, et al. High-resolution comparative analysis of great ape genomes. Science (New York, N.Y.). 360. PMID 29880660 DOI: 10.1126/Science.Aar6343  0.589
2018 Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, Kircher M, Khechaduri A, Dines JN, Hause RJ, Bhatia S, Evans WE, Relling MV, Yang W, Shendure J, et al. Multiplex assessment of protein variant abundance by massively parallel sequencing. Nature Genetics. PMID 29785012 DOI: 10.1038/S41588-018-0122-Z  0.742
2018 Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J. Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Research. 28: 766.3. PMID 29717003 DOI: 10.1101/gr.237321.118  0.471
2018 Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM. Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Nature Communications. 9: 1445. PMID 29654302 DOI: 10.1038/S41467-018-03694-Y  0.618
2018 Mulqueen RM, Pokholok D, Norberg SJ, Torkenczy KA, Fields AJ, Sun D, Sinnamon JR, Shendure J, Trapnell C, O'Roak BJ, Xia Z, Steemers FJ, Adey AC. Highly scalable generation of DNA methylation profiles in single cells. Nature Biotechnology. PMID 29644997 DOI: 10.1038/Nbt.4112  0.802
2018 Hause RJ, Pritchard CC, Shendure J, Salipante SJ. Corrigendum: Classification and characterization of microsatellite instability across 18 cancer types. Nature Medicine. 24: 525. PMID 29634692 DOI: 10.1038/nm0418-525a  0.478
2018 Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nature Biotechnology. PMID 29608178 DOI: 10.1038/Nbt.4103  0.601
2018 Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature. PMID 29539636 DOI: 10.1038/Nature25981  0.731
2018 Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C. On the design of CRISPR-based single-cell molecular screens. Nature Methods. PMID 29457792 DOI: 10.1038/Nmeth.4604  0.599
2018 Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z. Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Methods (San Diego, Calif.). PMID 29382556 DOI: 10.1016/J.Ymeth.2018.01.014  0.355
2018 Klein JC, Chen W, Gasperini M, Shendure J. Identifying novel enhancer elements with CRISPR-based screens. Acs Chemical Biology. PMID 29300083 DOI: 10.1021/Acschembio.7B00778  0.421
2018 Weichenhan D, Wang Q, Adey A, Wolf S, Shendure J, Eils R, Plass C. Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1708: 105-122. PMID 29224141 DOI: 10.1007/978-1-4939-7481-8_6  0.698
2017 Johnsen JM, Fletcher SN, Huston H, Roberge S, Martin BK, Kircher M, Josephson NC, Shendure J, Ruuska S, Koerper MA, Morales J, Pierce GF, Aschman DJ, Konkle BA. Novel approach to genetic analysis and results in 3000 hemophilia patients enrolled in the My Life, Our Future initiative. Blood Advances. 1: 824-834. PMID 29296726 DOI: 10.1182/Bloodadvances.2016002923  0.597
2017 Gray VE, Hause RJ, Luebeck J, Shendure J, Fowler DM. Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data. Cell Systems. PMID 29226803 DOI: 10.1016/J.Cels.2017.11.003  0.31
2017 Liu J, Halloran JT, Bilmes JA, Daza RM, Lee C, Mahen EM, Prunkard D, Song C, Blau S, Dorschner MO, Gadi VK, Shendure J, Blau CA, Noble WS. Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies. Scientific Reports. 7: 16943. PMID 29208983 DOI: 10.1038/S41598-017-16813-4  0.364
2017 Küry S, van Woerden GM, Besnard T, Proietti Onori M, Latypova X, Towne MC, Cho MT, Prescott TE, Ploeg MA, Sanders S, Stessman HAF, Pujol A, Distel B, Robak LA, Bernstein JA, ... ... Shendure J, et al. De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability. American Journal of Human Genetics. 101: 768-788. PMID 29100089 DOI: 10.1016/J.Ajhg.2017.10.003  0.652
2017 Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH. DNA sequencing at 40: past, present and future. Nature. PMID 29019985 DOI: 10.1038/Nature24286  0.673
2017 Hause RJ, Pritchard CC, Shendure J, Salipante SJ. Corrigendum: Classification and characterization of microsatellite instability across 18 cancer types. Nature Medicine. 23: 1241. PMID 28985213 DOI: 10.1038/Nm1017-1241A  0.53
2017 Cao J, Packer J, Waterston R, Trapnell C, Shendure J, Rajaram S, Wu LF, Altschuler SJ, Liang J, O'Brien LE, Eizenberg-Magar I, Rimer J, Friedman N, Metzl-Raz E, Kafri M, et al. Principles of Systems Biology, No. 21 : Editorial Cell Systems. 5: 158-160. PMID 28957648 DOI: 10.1016/J.Cels.2017.09.005  0.686
2017 Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature. 549: 219-226. PMID 28905911 DOI: 10.1038/Nature23884  0.379
2017 Heil CS, Burton JN, Liachko I, Friedrich A, Hanson NA, Morris CL, Schacherer J, Shendure J, Thomas JH, Dunham MJ. Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C. Yeast (Chichester, England). PMID 28892574 DOI: 10.1002/Yea.3280  0.722
2017 Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Variant Interpretation: Functional Assays to the Rescue. American Journal of Human Genetics. 101: 315-325. PMID 28886340 DOI: 10.1016/J.Ajhg.2017.07.014  0.799
2017 Ng BG, Asteggiano CG, Kircher M, Buckingham KJ, Raymond K, Nickerson DA, Shendure J, Bamshad MJ, Ensslen M, Freeze HH. Encephalopathy caused by novel mutations in the CMP-sialic acid transporter, SLC35A1. American Journal of Medical Genetics. Part A. PMID 28856833 DOI: 10.1002/Ajmg.A.38412  0.541
2017 Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science (New York, N.Y.). 357: 661-667. PMID 28818938 DOI: 10.1126/Science.Aam8940  0.79
2017 Gasperini M, Findlay GM, McKenna A, Milbank JH, Lee C, Zhang MD, Cusanovich DA, Shendure J. CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions. American Journal of Human Genetics. PMID 28712454 DOI: 10.1016/J.Ajhg.2017.06.010  0.809
2017 Zhang F, Christiansen L, Thomas J, Pokholok D, Jackson R, Morrell N, Zhao Y, Wiley M, Welch E, Jaeger E, Granat A, Norberg SJ, Halpern A, C Rogert M, Ronaghi M, ... Shendure J, et al. Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube. Nature Biotechnology. PMID 28650462 DOI: 10.1038/Nbt.3897  0.458
2017 Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, Shendure J, Dunham MJ. The dynamic three-dimensional organization of the diploid yeast genome. Elife. 6. PMID 28537556 DOI: 10.7554/Elife.23623  0.362
2017 Arts P, van der Raadt J, van Gestel SHC, Steehouwer M, Shendure J, Hoischen A, Albers CA. Quantification of differential gene expression by multiplexed targeted resequencing of cDNA. Nature Communications. 8: 15190. PMID 28474677 DOI: 10.1038/Ncomms15190  0.335
2017 Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, Shendure J, Salipante SJ. Correction: A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota. Plos Genetics. 13: e1006724. PMID 28410416 DOI: 10.1371/journal.pgen.1006724  0.753
2017 Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, ... ... Shendure J, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics. PMID 28263316 DOI: 10.1038/Ng.3802  0.712
2017 Simon MT, Ng BG, Friederich MW, Wang RY, Boyer M, Kircher M, Collard R, Buckingham KJ, Chang R, Shendure J, Nickerson DA, Bamshad MJ, Van Hove JL, Freeze HH, et al. Activation of a cryptic splice site in the mitochondrial elongation factor GFM1 causes combined OXPHOS deficiency. Mitochondrion. PMID 28216230 DOI: 10.1016/J.Mito.2017.02.004  0.57
2017 Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. Massively multiplex single-cell Hi-C. Nature Methods. PMID 28135255 DOI: 10.1038/Nmeth.4155  0.65
2017 Cantsilieris S, Stessman HA, Shendure J, Eichler EE. Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs). Methods in Molecular Biology (Clifton, N.J.). 1492: 95-106. PMID 27822858 DOI: 10.1007/978-1-4939-6442-0_6  0.578
2017 Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, Shendure J, Dunham MJ. Author response: The dynamic three-dimensional organization of the diploid yeast genome Elife. DOI: 10.7554/Elife.23623.031  0.319
2017 Ramani V, Duan Z, Shendure J. Massively multiplex single-cell Hi-C by combinatorial indexing Protocol Exchange. DOI: 10.1038/Protex.2017.005  0.607
2017 Kitzman JO, Starita LM, Lo RS, Fields S, Shendure J. Erratum: Corrigendum: Massively parallel single-amino-acid mutagenesis Nature Methods. 14: 540-540. DOI: 10.1038/Nmeth0517-540B  0.766
2016 Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, ... ... Shendure J, et al. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clinical Chemistry. PMID 27974384 DOI: 10.1373/Clinchem.2016.263897  0.317
2016 Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Research. PMID 27831498 DOI: 10.1101/Gr.212092.116  0.613
2016 Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, ... ... Shendure J, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 538: 336-343. PMID 27762356 DOI: 10.1038/Nature19840  0.823
2016 Hause RJ, Pritchard CC, Shendure J, Salipante SJ. Classification and characterization of microsatellite instability across 18 cancer types. Nature Medicine. PMID 27694933 DOI: 10.1038/Nm.4191  0.572
2016 Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z. Mapping 3D genome architecture through in situ DNase Hi-C. Nature Protocols. 11: 2104-2121. PMID 27685100 DOI: 10.1038/Nprot.2016.126  0.801
2016 Mirzaa G, Timms AE, Conti V, Boyle EA, Girisha KM, Martin B, Kircher M, Olds C, Juusola J, Collins S, Park K, Carter M, Glass I, Krägeloh-Mann I, Chitayat D, ... ... Shendure J, et al. PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution. Jci Insight. 1. PMID 27631024 DOI: 10.1172/Jci.Insight.87623  0.591
2016 Gasperini M, Starita L, Shendure J. The power of multiplexed functional analysis of genetic variants. Nature Protocols. 11: 1782-7. PMID 27583640 DOI: 10.1038/Nprot.2016.135  0.639
2016 Shendure J. Human genomics: A deep dive into genetic variation. Nature. 536: 277-8. PMID 27535530 DOI: 10.1038/536277A  0.417
2016 Wheeler PG, Ng BG, Sanford L, Sutton VR, Bartholomew DW, Pastore MT, Bamshad MJ, Kircher M, Buckingham KJ, Nickerson DA, Shendure J, Freeze HH. SRD5A3-CDG: Expanding the phenotype of a congenital disorder of glycosylation with emphasis on adult onset features. American Journal of Medical Genetics. Part A. PMID 27480077 DOI: 10.1002/Ajmg.A.37875  0.533
2016 Underhill HR, Kitzman JO, Hellwig S, Welker NC, Daza R, Baker DN, Gligorich KM, Rostomily RC, Bronner MP, Shendure J. Fragment Length of Circulating Tumor DNA. Plos Genetics. 12: e1006162. PMID 27428049 DOI: 10.1371/Journal.Pgen.1006162  0.76
2016 Burnicka-Turek O, Steimle JD, Huang W, Felker L, Kamp A, Kweon J, Peterson M, Reeves RH, Maslen CL, Gruber PJ, Yang XH, Shendure J, Moskowitz IP. Cilia Gene Mutations Cause Atrioventricular Septal Defects by Multiple Mechanisms. Human Molecular Genetics. PMID 27340223 DOI: 10.1093/Hmg/Ddw155  0.352
2016 Shendure J, Fields S. Massively Parallel Genetics. Genetics. 203: 617-9. PMID 27270695 DOI: 10.1534/Genetics.115.180562  0.304
2016 McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J. Whole organism lineage tracing by combinatorial and cumulative genome editing. Science (New York, N.Y.). PMID 27229144 DOI: 10.1126/Science.Aaf7907  0.626
2016 Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, ... Shendure J, et al. Long-read sequence assembly of the gorilla genome. Science (New York, N.Y.). 352: aae0344. PMID 27034376 DOI: 10.1126/Science.Aae0344  0.584
2016 Alazami AM, Al-Qattan SM, Faqeih E, Alhashem A, Alshammari M, Alzahrani F, Al-Dosari MS, Patel N, Alsagheir A, Binabbas B, Alzaidan H, Alsiddiky A, Alharbi N, Alfadhel M, Kentab A, ... ... Shendure J, et al. Expanding the clinical and genetic heterogeneity of hereditary disorders of connective tissue. Human Genetics. PMID 27023906 DOI: 10.1007/S00439-016-1660-Z  0.598
2016 Ramani V, Shendure J. Smash and DASH with Cas9. Genome Biology. 17: 42. PMID 26944856 DOI: 10.1186/S13059-016-0905-4  0.695
2016 Ng BG, Shiryaev SA, Rymen D, Eklund EA, Raymond K, Kircher M, Abdenur JE, Alehan F, Midro AT, Bamshad MJ, Barone R, Berry GT, Brumbaugh JE, Buckingham KJ, Clarkson K, ... ... Shendure J, et al. ALG1-CDG: Clinical and Molecular Characterization of 39 Unreported Patients. Human Mutation. PMID 26931382 DOI: 10.1002/Humu.22983  0.565
2016 Kumar A, Coleman I, Morrissey C, Zhang X, True LD, Gulati R, Etzioni R, Bolouri H, Montgomery B, White T, Lucas JM, Brown LG, Dumpit RF, DeSarkar N, Higano C, ... ... Shendure J, et al. Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer. Nature Medicine. PMID 26928463 DOI: 10.1038/Nm.4053  0.557
2016 Ramani V, Shendure J, Duan Z. Understanding Spatial Genome Organization: Methods and Insights. Genomics, Proteomics & Bioinformatics. PMID 26876719 DOI: 10.1016/J.Gpb.2016.01.002  0.669
2016 Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell. 164: 57-68. PMID 26771485 DOI: 10.1097/Tp.0000000000001176  0.706
2016 Kan M, Auer PL, Wang GT, Bucasas KL, Hooker S, Rodriguez A, Li B, Ellis J, Adrienne Cupples L, Ida Chen YD, Dupuis J, Fox CS, Gross MD, Smith JD, Heard-Costa N, ... ... Shendure J, et al. Rare variant associations with waist-to-hip ratio in European-American and African-American women from the NHLBI-Exome Sequencing Project. European Journal of Human Genetics : Ejhg. PMID 26757982 DOI: 10.1038/Ejhg.2015.272  0.333
2016 Johnsen J, Fletcher SN, Huston H, Roberge S, Martin BK, Kircher M, Josephson NC, Shendure J, Ruuska S, Koerper MA, Meltzer L, Pierce GF, Aschman D, Konkle B. Novel Approach to and Results of Genetic Analysis of 3000 Hemophilia Patients Enrolled in the MyLifeOurFuture Initiative Blood. 128: 205-205. DOI: 10.1182/Blood.V128.22.205.205  0.584
2015 Snyder MW, Gammill HS, Shendure J. Copy-Number Variation and False Positive Results of Prenatal Screening. The New England Journal of Medicine. 373: 2585. PMID 26699182 DOI: 10.1056/NEJMc1507106  0.448
2015 Ansar M, Jan A, Santos-Cortez RL, Wang X, Suliman M, Acharya A, Habib R, Abbe I, Ali G, Lee K, Smith JD, Nickerson DA, Shendure J, Bamshad MJ, et al. Expansion of the spectrum of ITGB6-related disorders to adolescent alopecia, dentogingival abnormalities and intellectual disability. European Journal of Human Genetics : Ejhg. PMID 26695873 DOI: 10.1038/Ejhg.2015.260  0.317
2015 Berletch JB, Ma W, Yang F, Shendure J, Noble WS, Disteche CM, Deng X. Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model. Data in Brief. 5: 761-9. PMID 26693509 DOI: 10.1016/J.Dib.2015.10.033  0.305
2015 Phadnis N, Baker EP, Cooper JC, Frizzell KA, Hsieh E, de la Cruz AF, Shendure J, Kitzman JO, Malik HS. An essential cell cycle regulation gene causes hybrid inviability in Drosophila. Science (New York, N.Y.). 350: 1552-5. PMID 26680200 DOI: 10.1126/Science.Aac7504  0.771
2015 Schueler M, Halbritter J, Phelps IG, Braun DA, Otto EA, Porath JD, Gee HY, Shendure J, O'Roak BJ, Lawson JA, Nabhan MM, Soliman NA, Nabhan MM, Doherty D, Hildebrandt F. Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies. Journal of Medical Genetics. PMID 26673778 DOI: 10.1136/Jmedgenet-2015-103304  0.681
2015 Salipante SJ, Adey A, Thomas A, Lee C, Liu YJ, Kumar A, Lewis AP, Wu D, Fromm JR, Shendure J. Recurrent somatic loss of TNFRSF14 in classical Hodgkin lymphoma. Genes, Chromosomes & Cancer. PMID 26650888 DOI: 10.1002/Gcc.22331  0.782
2015 Shaheen R, Patel N, Shamseldin H, Alzahrani F, Al-Yamany R, ALMoisheer A, Ewida N, Anazi S, Alnemer M, Elsheikh M, Alfaleh K, Alshammari M, Alhashem A, Alangari AA, Salih MA, ... ... Shendure J, et al. Accelerating matchmaking of novel dysmorphology syndromes through clinical and genomic characterization of a large cohort. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 26633546 DOI: 10.1038/Gim.2015.147  0.555
2015 Regalado ES, Guo DC, Santos-Cortez RL, Hostetler E, Bensend TA, Pannu H, Estrera A, Safi H, Mitchell AL, Evans JP, Leal SM, Bamshad M, Shendure J, Nickerson DA, et al. Pathogenic FBN1 Variants in Familial Thoracic Aortic Aneurysms and Dissections. Clinical Genetics. PMID 26621581 DOI: 10.1111/Cge.12702  0.312
2015 Klein JC, Lajoie MJ, Schwartz JJ, Strauch EM, Nelson J, Baker D, Shendure J. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Research. PMID 26553805 DOI: 10.1093/Nar/Gkv1177  0.771
2015 Mirzaa GM, Conti V, Timms AE, Smyser CD, Ahmed S, Carter M, Barnett S, Hufnagel RB, Goldstein A, Narumi-Kishimoto Y, Olds C, Collins S, Johnston K, Deleuze JF, Nitschké P, ... ... Shendure J, et al. Characterisation of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next-generation sequencing study. The Lancet. Neurology. PMID 26520804 DOI: 10.1016/S1474-4422(15)00278-1  0.327
2015 Rosenberg AB, Patwardhan RP, Shendure J, Seelig G. Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences. Cell. 163: 698-711. PMID 26496609 DOI: 10.1016/J.Cell.2015.09.054  0.721
2015 Shendure J, Akey JM. The origins, determinants, and consequences of human mutations. Science (New York, N.Y.). 349: 1478-83. PMID 26404824 DOI: 10.1126/Science.Aaa9119  0.333
2015 Jorth P, Staudinger BJ, Wu X, Hisert KB, Hayden H, Garudathri J, Harding CL, Radey MC, Rezayat A, Bautista G, Berrington WR, Goddard AF, Zheng C, Angermeyer A, Brittnacher MJ, ... ... Shendure J, et al. Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs. Cell Host & Microbe. 18: 307-19. PMID 26299432 DOI: 10.1016/J.Chom.2015.07.006  0.743
2015 Ng BG, Raymond K, Kircher M, Buckingham KJ, Wood T, Shendure J, Nickerson DA, Bamshad MJ, Wong JT, Monteiro FP, Graham BH, Jackson S, Sparkes R, Scheuerle AE, Cathey S, et al. Expanding the Molecular and Clinical Phenotype of SSR4-CDG. Human Mutation. PMID 26264460 DOI: 10.1002/Humu.22856  0.602
2015 Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. Bipartite structure of the inactive mouse X chromosome. Genome Biology. 16: 152. PMID 26248554 DOI: 10.1186/S13059-015-0728-8  0.638
2015 Carlson KD, Sudmant PH, Press MO, Eichler EE, Shendure J, Queitsch C. Corrigendum: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. Genome Research. 25: 1244. PMID 26240161  0.373
2015 Ramani V, Qiu R, Shendure J. High-throughput determination of RNA structure by proximity ligation. Nature Biotechnology. 33: 980-4. PMID 26237516 DOI: 10.1038/Nbt.3289  0.605
2015 Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, Shendure J, Salipante SJ. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota. Plos Genetics. 11: e1005413. PMID 26230489 DOI: 10.1371/Journal.Pgen.1005413  0.788
2015 Kircher M, Shendure J. Running spell-check to identify regulatory variants. Nature Genetics. 47: 853-5. PMID 26220134 DOI: 10.1038/Ng.3364  0.586
2015 Brennan G, Kitzman JO, Shendure J, Geballe AP. Experimental Evolution Identifies Vaccinia Virus Mutations in A24R and A35R That Antagonize the Protein Kinase R Pathway and Accompany Collapse of an Extragenic Gene Amplification. Journal of Virology. 89: 9986-97. PMID 26202237 DOI: 10.1128/Jvi.01233-15  0.762
2015 Wheway G, Schmidts M, Mans DA, Szymanska K, Nguyen TT, Racher H, Phelps IG, Toedt G, Kennedy J, Wunderlich KA, Sorusch N, Abdelhamed ZA, Natarajan S, Herridge W, van Reeuwijk J, ... ... Shendure J, et al. An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. Nature Cell Biology. PMID 26167768 DOI: 10.1038/Ncb3201  0.402
2015 Chong JX, Buckingham KJ, Jhangiani SN, Boehm C, Sobreira N, Smith JD, Harrell TM, McMillin MJ, Wiszniewski W, Gambin T, Coban Akdemir ZH, Doheny K, Scott AF, Avramopoulos D, Chakravarti A, ... ... Shendure J, et al. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. American Journal of Human Genetics. 97: 199-215. PMID 26166479 DOI: 10.1016/J.Ajhg.2015.06.009  0.625
2015 Bachmann-Gagescu R, Phelps IG, Dempsey JC, Sharma VA, Ishak GE, Boyle EA, Wilson M, Marques Lourenço C, Arslan M, Shendure J, Doherty D. KIAA0586 is Mutated in Joubert Syndrome. Human Mutation. PMID 26096313 DOI: 10.1002/Humu.22821  0.391
2015 Bachmann-Gagescu R, Dempsey JC, Phelps IG, O'Roak BJ, Knutzen DM, Rue TC, Ishak GE, Isabella CR, Gorden N, Adkins J, Boyle EA, de Lacy N, O'Day D, Alswaid A, Ramadevi A R, ... ... Shendure J, et al. Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity. Journal of Medical Genetics. PMID 26092869 DOI: 10.1136/Jmedgenet-2015-103087  0.646
2015 Ansar M, Santos-Cortez RL, Saqib MA, Zulfiqar F, Lee K, Ashraf NM, Ullah E, Wang X, Sajid S, Khan FS, Amin-Ud-Din M, Smith JD, Shendure J, Bamshad MJ, et al. Mutation of ATF6 causes autosomal recessive achromatopsia. Human Genetics. PMID 26063662 DOI: 10.1007/S00439-015-1571-4  0.35
2015 Kumar A, Ryan A, Kitzman JO, Wemmer N, Snyder MW, Sigurjonsson S, Lee C, Banjevic M, Zarutskie PW, Lewis AP, Shendure J, Rabinowitz M. Whole genome prediction for preimplantation genetic diagnosis. Genome Medicine. 7: 35. PMID 26019723 DOI: 10.1186/S13073-015-0160-4  0.821
2015 Chong JX, Burrage LC, Beck AE, Marvin CT, McMillin MJ, Shively KM, Harrell TM, Buckingham KJ, Bacino CA, Jain M, Alanay Y, Berry SA, Carey JC, Gibbs RA, Lee BH, ... ... Shendure J, et al. Autosomal-Dominant Multiple Pterygium Syndrome Is Caused by Mutations in MYH3. American Journal of Human Genetics. 96: 841-9. PMID 25957469 DOI: 10.1016/J.Ajhg.2015.04.004  0.333
2015 Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. Epigenetics. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science (New York, N.Y.). 348: 910-4. PMID 25953818 DOI: 10.1126/Science.Aab1601  0.797
2015 Snyder MW, Adey A, Kitzman JO, Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nature Reviews. Genetics. 16: 344-58. PMID 25948246 DOI: 10.1038/Nrg3903  0.826
2015 Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Research. 43: 5331-9. PMID 25940625 DOI: 10.1093/Nar/Gkv424  0.717
2015 Weren RDA, Ligtenberg MJL, Kets CM, De Voer RM, Verwiel ETP, Spruijt L, Van Zelst-Stams WAG, Jongmans MC, Gilissen C, Hehir-Kwa JY, Hoischen A, Shendure J, Boyle EA, Kamping EJ, Nagtegaal ID, et al. A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer Nature Genetics. 47: 668-671. PMID 25938944 DOI: 10.1038/Ng.3287  0.342
2015 Fairfield H, Srivastava A, Ananda G, Liu R, Kircher M, Lakshminarayana A, Harris BS, Karst SY, Dionne LA, Kane CC, Curtain M, Berry ML, Ward-Bailey PF, Greenstein I, Byers C, ... ... Shendure J, et al. Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders. Genome Research. 25: 948-57. PMID 25917818 DOI: 10.1101/Gr.186882.114  0.634
2015 Snyder MW, Simmons LE, Kitzman JO, Coe BP, Henson JM, Daza RM, Eichler EE, Shendure J, Gammill HS. Copy-number variation and false positive prenatal aneuploidy screening results. The New England Journal of Medicine. 372: 1639-45. PMID 25830323 DOI: 10.1056/Nejmoa1408408  0.783
2015 Starita LM, Young DL, Islam M, Kitzman JO, Gullingsrud J, Hause RJ, Fowler DM, Parvin JD, Shendure J, Fields S. Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. Genetics. 200: 413-22. PMID 25823446 DOI: 10.1534/Genetics.115.175802  0.795
2015 Berletch JB, Ma W, Yang F, Shendure J, Noble WS, Disteche CM, Deng X. Escape from X inactivation varies in mouse tissues. Plos Genetics. 11: e1005079. PMID 25785854 DOI: 10.1371/Journal.Pgen.1005079  0.333
2015 Jansen LA, Mirzaa GM, Ishak GE, O'Roak BJ, Hiatt JB, Roden WH, Gunter SA, Christian SL, Collins S, Adams C, Rivière JB, St-Onge J, Ojemann JG, Shendure J, Hevner RF, et al. PI3K/AKT pathway mutations cause a spectrum of brain malformations from megalencephaly to focal cortical dysplasia. Brain : a Journal of Neurology. 138: 1613-28. PMID 25722288 DOI: 10.1093/Brain/Awv045  0.775
2015 Chong JX, McMillin MJ, Shively KM, Beck AE, Marvin CT, Armenteros JR, Buckingham KJ, Nkinsi NT, Boyle EA, Berry MN, Bocian M, Foulds N, Uzielli ML, Haldeman-Englert C, Hennekam RC, ... ... Shendure J, et al. De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay. American Journal of Human Genetics. 96: 462-73. PMID 25683120 DOI: 10.1016/J.Ajhg.2015.01.003  0.333
2015 Carlson KD, Sudmant PH, Press MO, Eichler EE, Shendure J, Queitsch C. MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. Genome Research. 25: 750-61. PMID 25659649 DOI: 10.1101/Gr.182212.114  0.567
2015 Stitziel NO, Peloso GM, Abifadel M, Cefalu AB, Fouchier S, Motazacker MM, Tada H, Larach DB, Awan Z, Haller JF, Pullinger CR, Varret M, Rabès JP, Noto D, Tarugi P, ... ... Shendure J, et al. Exome sequencing in suspected monogenic dyslipidemias. Circulation. Cardiovascular Genetics. 8: 343-50. PMID 25632026 DOI: 10.1161/Circgenetics.114.000776  0.383
2015 D'Gama AM, Geng Y, Couto JA, Martin B, Boyle EA, LaCoursiere CM, Hossain A, Hatem NE, Barry BJ, Kwiatkowski DJ, Vinters HV, Barkovich AJ, Shendure J, Mathern GW, Walsh CA, et al. Mammalian target of rapamycin pathway mutations cause hemimegalencephaly and focal cortical dysplasia. Annals of Neurology. 77: 720-5. PMID 25599672 DOI: 10.1002/Ana.24357  0.336
2015 Kitzman JO, Starita LM, Lo RS, Fields S, Shendure J. Massively parallel single-amino-acid mutagenesis. Nature Methods. 12: 203-6, 4 p following. PMID 25559584 DOI: 10.1038/Nmeth.3223  0.808
2015 Guo DC, Gong L, Regalado ES, Santos-Cortez RL, Zhao R, Cai B, Veeraraghavan S, Prakash SK, Johnson RJ, Muilenburg A, Willing M, Jondeau G, Boileau C, Pannu H, Moran R, ... ... Shendure J, et al. MAT2A mutations predispose individuals to thoracic aortic aneurysms. American Journal of Human Genetics. 96: 170-7. PMID 25557781 DOI: 10.1016/J.Ajhg.2014.11.015  0.317
2015 Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nature Methods. 12: 71-8. PMID 25437436 DOI: 10.1038/Nmeth.3205  0.351
2015 Salipante SJ, Roach DJ, Kitzman JO, Snyder MW, Stackhouse B, Butler-Wu SM, Lee C, Cookson BT, Shendure J. Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains. Genome Research. 25: 119-28. PMID 25373147 DOI: 10.1101/Gr.180190.114  0.817
2015 Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, Shendure J, Salipante SJ. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota Plos Genetics. 11. DOI: 10.1371/journal.pgen.1005413  0.754
2015 Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. Bipartite structure of the inactive mouse X chromosome Genome Biology. 16. DOI: 10.1186/s13059-015-0728-8  0.546
2015 Bachmann-Gagescu R, Dempsey J, Phelps I, Isabella C, O'Day D, O'Roak B, Shendure J, Glass I, Doherty D. Genotype-Phenotype correlations in Joubert Syndrome in the Era of Next Generation Sequencing Cilia. 4. DOI: 10.1186/2046-2530-4-S1-P8  0.661
2015 Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing Science. 348: 910-914. DOI: 10.1126/science.aab1601  0.783
2015 Kitzman JO, Starita LM, Lo RS, Fields S, Shendure J. Massively parallel single-amino-acid mutagenesis Nature Methods. 12: 203-206. DOI: 10.1038/nmeth.3223  0.76
2015 Kircher M, Shendure J. Running spell-check to identify regulatory variants Nature Genetics. 47: 853-855. DOI: 10.1038/ng.3364  0.519
2015 Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey AC, Nova IC, Craig JM, Langford KW, Samson JM, Daza R, Doering K, Shendure J, Gundlach JH. Decoding Long Nanopore Reads of Bacteriophage Phi X 174 Biophysical Journal. 108: 630a. DOI: 10.1016/J.Bpj.2014.11.3425  0.69
2015 Chong JX, Buckingham KJ, Jhangiani SN, Boehm C, Sobreira N, Smith JD, Harrell TM, McMillin MJ, Wiszniewski W, Gambin T, CobanAkdemir ZH, Doheny K, Scott AF, Avramopoulos D, Chakravarti A, ... ... Shendure J, et al. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities American Journal of Human Genetics. DOI: 10.1016/j.ajhg.2015.06.009  0.488
2014 Kumar A, Boyle EA, Tokita M, Mikheev AM, Sanger MC, Girard E, Silber JR, Gonzalez-Cuyar LF, Hiatt JB, Adey A, Lee C, Kitzman JO, Born DE, Silbergeld DL, Olson JM, ... ... Shendure J, et al. Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes. Genome Biology. 15: 530. PMID 25608559 DOI: 10.1186/S13059-014-0530-Z  0.793
2014 Rehman AU, Santos-Cortez RL, Drummond MC, Shahzad M, Lee K, Morell RJ, Ansar M, Jan A, Wang X, Aziz A, Riazuddin S, Smith JD, Wang GT, Ahmed ZM, Gul K, ... ... Shendure J, et al. Challenges and solutions for gene identification in the presence of familial locus heterogeneity. European Journal of Human Genetics : Ejhg. PMID 25491636 DOI: 10.1038/Ejhg.2014.266  0.367
2014 O'Roak BJ, Stessman HA, Boyle EA, Witherspoon KT, Martin B, Lee C, Vives L, Baker C, Hiatt JB, Nickerson DA, Bernier R, Shendure J, Eichler EE. Recurrent de novo mutations implicate novel genes underlying simplex autism risk. Nature Communications. 5: 5595. PMID 25418537 DOI: 10.1038/Ncomms6595  0.794
2014 Hause RJ, Shendure J. Genetic variation meets replication origins. Cell. 159: 973-4. PMID 25416936 DOI: 10.1016/J.Cell.2014.11.009  0.435
2014 Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, ... ... Shendure J, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 515: 216-21. PMID 25363768 DOI: 10.1038/Nature13908  0.78
2014 Birnbaum RY, Patwardhan RP, Kim MJ, Findlay GM, Martin B, Zhao J, Bell RJ, Smith RP, Ku AA, Shendure J, Ahituv N. Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. Plos Genetics. 10: e1004592. PMID 25340400 DOI: 10.1371/Journal.Pgen.1004592  0.707
2014 Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Research. 24: 2041-9. PMID 25327137 DOI: 10.1101/Gr.178319.114  0.826
2014 Amini S, Pushkarev D, Christiansen L, Kostem E, Royce T, Turk C, Pignatelli N, Adey A, Kitzman JO, Vijayan K, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nature Genetics. 46: 1343-9. PMID 25326703 DOI: 10.1038/Ng.3119  0.834
2014 Pritchard CC, Morrissey C, Kumar A, Zhang X, Smith C, Coleman I, Salipante SJ, Milbank J, Yu M, Grady WM, Tait JF, Corey E, Vessella RL, Walsh T, Shendure J, et al. Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer. Nature Communications. 5: 4988. PMID 25255306 DOI: 10.1038/Ncomms5988  0.63
2014 Deriziotis P, O'Roak BJ, Graham SA, Estruch SB, Dimitropoulou D, Bernier RA, Gerdts J, Shendure J, Eichler EE, Fisher SE. De novo TBR1 mutations in sporadic autism disrupt protein functions. Nature Communications. 5: 4954. PMID 25232744 DOI: 10.1038/Ncomms5954  0.72
2014 Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C, Buono S, Vissers LE, Schuurs-Hoeijmakers JH, Hoischen A, Pfundt R, Krumm N, Carvill GL, ... ... Shendure J, et al. Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nature Genetics. 46: 1063-71. PMID 25217958 DOI: 10.1038/Ng.3092  0.728
2014 Kumar A, Dougherty M, Findlay GM, Geisheker M, Klein J, Lazar J, Machkovech H, Resnick J, Resnick R, Salter AI, Talebi-Liasi F, Arakawa C, Baudin J, Bogaard A, Salesky R, ... ... Shendure J, et al. Genome sequencing of idiopathic pulmonary fibrosis in conjunction with a medical school human anatomy course. Plos One. 9: e106744. PMID 25192356 DOI: 10.1371/Journal.Pone.0106744  0.581
2014 Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair. Nature. 513: 120-3. PMID 25141179 DOI: 10.1038/Nature13695  0.466
2014 Jamuar SS, Lam AT, Kircher M, D'Gama AM, Wang J, Barry BJ, Zhang X, Hill RS, Partlow JN, Rozzo A, Servattalab S, Mehta BK, Topcu M, Amrom D, Andermann E, ... ... Shendure J, et al. Somatic mutations in cerebral cortical malformations. The New England Journal of Medicine. 371: 733-43. PMID 25140959 DOI: 10.1056/Nejmoa1314432  0.622
2014 Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, ... ... Shendure J, et al. Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. Plos One. 9: e104396. PMID 25116239 DOI: 10.1371/Journal.Pone.0104396  0.748
2014 Schwartz JJ, Roach DJ, Thomas JH, Shendure J. Primate evolution of the recombination regulator PRDM9. Nature Communications. 5: 4370. PMID 25001002 DOI: 10.1038/Ncomms5370  0.612
2014 Bernier R, Golzio C, Xiong B, Stessman HA, Coe BP, Penn O, Witherspoon K, Gerdts J, Baker C, Vulto-van Silfhout AT, Schuurs-Hoeijmakers JH, Fichera M, Bosco P, Buono S, Alberti A, ... ... Shendure J, et al. Disruptive CHD8 mutations define a subtype of autism early in development. Cell. 158: 263-76. PMID 24998929 DOI: 10.1016/J.Cell.2014.06.017  0.713
2014 Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey A, Nova IC, Craig JM, Langford KW, Samson JM, Daza R, Doering K, Shendure J, Gundlach JH. Decoding long nanopore sequencing reads of natural DNA. Nature Biotechnology. 32: 829-33. PMID 24964173 DOI: 10.1038/Nbt.2950  0.698
2014 Nuttle X, Itsara A, Shendure J, Eichler EE. Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing. Nature Protocols. 9: 1496-513. PMID 24874815 DOI: 10.1038/Nprot.2014.096  0.611
2014 Boyle EA, O'Roak BJ, Martin BK, Kumar A, Shendure J. MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. Bioinformatics (Oxford, England). 30: 2670-2. PMID 24867941 DOI: 10.1093/Bioinformatics/Btu353  0.72
2014 Burton JN, Liachko I, Dunham MJ, Shendure J. Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps. G3 (Bethesda, Md.). 4: 1339-46. PMID 24855317 DOI: 10.1534/G3.114.011825  0.707
2014 SenGupta DJ, Cummings LA, Hoogestraat DR, Butler-Wu SM, Shendure J, Cookson BT, Salipante SJ. Whole-genome sequencing for high-resolution investigation of methicillin-resistant Staphylococcus aureus epidemiology and genome plasticity. Journal of Clinical Microbiology. 52: 2787-96. PMID 24850346 DOI: 10.1128/Jcm.00759-14  0.666
2014 MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, et al. Guidelines for investigating causality of sequence variants in human disease. Nature. 508: 469-76. PMID 24759409 DOI: 10.1038/Nature13127  0.426
2014 Salipante SJ, Fromm JR, Shendure J, Wood BL, Wu D. Detection of minimal residual disease in NPM1-mutated acute myeloid leukemia by next-generation sequencing. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. 27: 1438-46. PMID 24743218 DOI: 10.1038/Modpathol.2014.57  0.618
2014 McMillin MJ, Beck AE, Chong JX, Shively KM, Buckingham KJ, Gildersleeve HI, Aracena MI, Aylsworth AS, Bitoun P, Carey JC, Clericuzio CL, Crow YJ, Curry CJ, Devriendt K, Everman DB, ... ... Shendure J, et al. Mutations in PIEZO2 cause Gordon syndrome, Marden-Walker syndrome, and distal arthrogryposis type 5. American Journal of Human Genetics. 94: 734-44. PMID 24726473 DOI: 10.1016/J.Ajhg.2014.03.015  0.331
2014 Shinsky SA, Hu M, Vought VE, Ng SB, Bamshad MJ, Shendure J, Cosgrove MS. A non-active-site SET domain surface crucial for the interaction of MLL1 and the RbBP5/Ash2L heterodimer within MLL family core complexes. Journal of Molecular Biology. 426: 2283-99. PMID 24680668 DOI: 10.1016/J.Jmb.2014.03.011  0.516
2014 Brennan G, Kitzman JO, Rothenburg S, Shendure J, Geballe AP. Adaptive Gene Amplification As an Intermediate Step in the Expansion of Virus Host Range Plos Pathogens. 10. PMID 24626510 DOI: 10.1371/Journal.Ppat.1004002  0.75
2014 Carvill GL, Weckhuysen S, McMahon JM, Hartmann C, Møller RS, Hjalgrim H, Cook J, Geraghty E, O'Roak BJ, Petrou S, Clarke A, Gill D, Sadleir LG, Muhle H, von Spiczak S, ... ... Shendure J, et al. GABRA1 and STXBP1: novel genetic causes of Dravet syndrome. Neurology. 82: 1245-53. PMID 24623842 DOI: 10.1212/Wnl.0000000000000291  0.675
2014 Knowles MR, Ostrowski LE, Leigh MW, Sears PR, Davis SD, Wolf WE, Hazucha MJ, Carson JL, Olivier KN, Sagel SD, Rosenfeld M, Ferkol TW, Dell SD, Milla CE, Randell SH, ... ... Shendure J, et al. Mutations in RSPH1 cause primary ciliary dyskinesia with a unique clinical and ciliary phenotype. American Journal of Respiratory and Critical Care Medicine. 189: 707-17. PMID 24568568 DOI: 10.1164/Rccm.201311-2047Oc  0.597
2014 Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genetics. 46: 310-5. PMID 24487276 DOI: 10.1038/Ng.2892  0.759
2014 Santos-Cortez RL, Lee K, Giese AP, Ansar M, Amin-Ud-Din M, Rehn K, Wang X, Aziz A, Chiu I, Hussain Ali R, Smith JD, Shendure J, Bamshad M, Nickerson DA, et al. Adenylate cyclase 1 (ADCY1) mutations cause recessive hearing impairment in humans and defects in hair cell function and hearing in zebrafish. Human Molecular Genetics. 23: 3289-98. PMID 24482543 DOI: 10.1093/Hmg/Ddu042  0.323
2014 Rehman AU, Santos-Cortez RL, Morell RJ, Drummond MC, Ito T, Lee K, Khan AA, Basra MA, Wasif N, Ayub M, Ali RA, Raza SI, Nickerson DA, Shendure J, et al. Mutations in TBC1D24, a gene associated with epilepsy, also cause nonsyndromic deafness DFNB86. American Journal of Human Genetics. 94: 144-52. PMID 24387994 DOI: 10.1016/J.Ajhg.2013.12.004  0.367
2014 Krumm N, O'Roak BJ, Shendure J, Eichler EE. A de novo convergence of autism genetics and molecular neuroscience. Trends in Neurosciences. 37: 95-105. PMID 24387789 DOI: 10.1016/J.Tins.2013.11.005  0.723
2014 Tuz K, Bachmann-Gagescu R, O'Day DR, Hua K, Isabella CR, Phelps IG, Stolarski AE, O'Roak BJ, Dempsey JC, Lourenco C, Alswaid A, Bönnemann CG, Medne L, Nampoothiri S, Stark Z, ... ... Shendure J, et al. Mutations in CSPP1 cause primary cilia abnormalities and Joubert syndrome with or without Jeune asphyxiating thoracic dystrophy. American Journal of Human Genetics. 94: 62-72. PMID 24360808 DOI: 10.1016/J.Ajhg.2013.11.019  0.658
2014 He Z, O'Roak BJ, Smith JD, Wang G, Hooker S, Santos-Cortez RL, Li B, Kan M, Krumm N, Nickerson DA, Shendure J, Eichler EE, Leal SM. Rare-variant extensions of the transmission disequilibrium test: application to autism exome sequence data. American Journal of Human Genetics. 94: 33-46. PMID 24360806 DOI: 10.1016/J.Ajhg.2013.11.021  0.712
2014 Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, ... ... Shendure J, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 505: 43-9. PMID 24352235 DOI: 10.1038/Nature12886  0.826
2014 Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D, Scharenberg AM. MegaTALs: A rare-cleaving nuclease architecture for therapeutic genome engineering Nucleic Acids Research. 42: 2591-2601. PMID 24285304 DOI: 10.1093/Nar/Gkt1224  0.675
2014 Losfeld ME, Ng BG, Kircher M, Buckingham KJ, Turner EH, Eroshkin A, Smith JD, Shendure J, Nickerson DA, Bamshad MJ, Freeze HH. A new congenital disorder of glycosylation caused by a mutation in SSR4, the signal sequence receptor 4 protein of the TRAP complex. Human Molecular Genetics. 23: 1602-5. PMID 24218363 DOI: 10.1093/Hmg/Ddt550  0.675
2014 Milewicz DM, Regalado ES, Shendure J, Nickerson DA, Guo DC. Successes and challenges of using whole exome sequencing to identify novel genes underlying an inherited predisposition for thoracic aortic aneurysms and acute aortic dissections. Trends in Cardiovascular Medicine. 24: 53-60. PMID 23953976 DOI: 10.1016/J.Tcm.2013.06.004  0.334
2014 Taylor SD, Ericson NG, Burton JN, Prolla TA, Silber JR, Shendure J, Bielas JH. Targeted enrichment and high-resolution digital profiling of mitochondrial DNA deletions in human brain Aging Cell. 13: 29-38. PMID 23911137 DOI: 10.1111/Acel.12146  0.713
2014 SenGupta DJ, Cummings LA, Hoogestraat DR, Butler-Wu SM, Shendure J, Cookson BT, Salipante SJ. Whole-genome sequencing for high-resolution investigation of methicillin-resistant Staphylococcus aureus epidemiology and genome plasticity Journal of Clinical Microbiology. 52: 2787-2796. DOI: 10.1128/JCM.00759-14  0.599
2014 Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity Genome Research. 24: 2041-2049. DOI: 10.1101/gr.178319.114  0.814
2014 Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey A, Nova IC, Craig JM, Langford KW, Samson JM, Daza R, Doering K, Shendure J, Gundlach JH. Decoding long nanopore sequencing reads of natural DNA Nature Biotechnology. 32: 829-833. DOI: 10.1038/nbt.2950  0.645
2014 Salipante SJ, Fromm JR, Shendure J, Wood BL, Wu D. Detection of minimal residual disease in NPM1-mutated acute myeloid leukemia by next-generation sequencing Modern Pathology. 27: 1438-1446. DOI: 10.1038/modpathol.2014.57  0.561
2014 Shendure J, Eichler E, Tabor H, Bamshad M, Nickerson D, Murray J, Specker B, Swanson J, Faustman E. Results of whole-genome analysis from National Children's Study (NCS) Neurotoxicology and Teratology. 43: 78. DOI: 10.1016/J.Ntt.2014.04.011  0.415
2014 Tuz K, Bachmann-Gagescu R, O'Day DR, Hua K, Isabella CR, Phelps IG, Stolarski AE, O'Roak BJ, Dempsey JC, Lourenco C, Alswaid A, Bönnemann CG, Medne L, Nampoothiri S, Stark Z, ... ... Shendure J, et al. Erratum: Mutations in CSPP1 cause primary cilia abnormalities and Joubert syndrome with or without jeune asphyxiating thoracic dystrophy (American Journal of Human Genetics (2014) 94 (62-72)) American Journal of Human Genetics. 94. DOI: 10.1016/J.Ajhg.2014.01.003  0.65
2013 Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions Nature Biotechnology. 31: 1119-1125. PMID 24185095 DOI: 10.1038/Nbt.2727  0.809
2013 Wang Q, Gu L, Adey A, Radlwimmer B, Wang W, Hovestadt V, Bähr M, Wolf S, Shendure J, Eils R, Plass C, Weichenhan D. Tagmentation-based whole-genome bisulfite sequencing. Nature Protocols. 8: 2022-32. PMID 24071908 DOI: 10.1038/Nprot.2013.118  0.799
2013 Knowles MR, Ostrowski LE, Loges NT, Hurd T, Leigh MW, Huang L, Wolf WE, Carson JL, Hazucha MJ, Yin W, Davis SD, Dell SD, Ferkol TW, Sagel SD, Olivier KN, ... ... Shendure J, et al. Mutations in SPAG1 cause primary ciliary dyskinesia associated with defective outer and inner dynein arms. American Journal of Human Genetics. 93: 711-20. PMID 24055112 DOI: 10.1016/J.Ajhg.2013.07.025  0.591
2013 Carvill GL, Regan BM, Yendle SC, O'Roak BJ, Lozovaya N, Bruneau N, Burnashev N, Khan A, Cook J, Geraghty E, Sadleir LG, Turner SJ, Tsai MH, Webster R, Ouvrier R, ... ... Shendure J, et al. GRIN2A mutations cause epilepsy-aphasia spectrum disorders. Nature Genetics. 45: 1073-6. PMID 23933818 DOI: 10.1038/Ng.2727  0.645
2013 Laurie MT, Bertout JA, Taylor SD, Burton JN, Shendure JA, Bielas JH. Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries Biotechniques. 55: 61-67. PMID 23931593 DOI: 10.2144/000114063  0.682
2013 Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP, Martin BK, Qiu R, Lee C, Shendure J. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature. 500: 207-11. PMID 23925245 DOI: 10.1038/Nature12064  0.818
2013 Nuttle X, Huddleston J, O'Roak BJ, Antonacci F, Fichera M, Romano C, Shendure J, Eichler EE. Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions. Nature Methods. 10: 903-9. PMID 23892896 DOI: 10.1038/Nmeth.2572  0.756
2013 Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nature Genetics. 45: 1021-8. PMID 23892608 DOI: 10.1038/Ng.2713  0.676
2013 Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, ... ... Shendure J, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10  0.822
2013 Fitzgerald LM, Kumar A, Boyle EA, Zhang Y, McIntosh LM, Kolb S, Stott-Miller M, Smith T, Karyadi DM, Ostrander EA, Hsu L, Shendure J, Stanford JL. Germline missense variants in the BTNL2 gene are associated with prostate cancer susceptibility. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 22: 1520-8. PMID 23833122 DOI: 10.1158/1055-9965.Epi-13-0345  0.458
2013 Thompson O, Edgley M, Strasbourger P, Flibotte S, Ewing B, Adair R, Au V, Chaudhry I, Fernando L, Hutter H, Kieffer A, Lau J, Lee N, Miller A, Raymant G, ... ... Shendure J, et al. The million mutation project: a new approach to genetics in Caenorhabditis elegans. Genome Research. 23: 1749-62. PMID 23800452 DOI: 10.1101/Gr.157651.113  0.618
2013 Salipante SJ, Sengupta DJ, Rosenthal C, Costa G, Spangler J, Sims EH, Jacobs MA, Miller SI, Hoogestraat DR, Cookson BT, McCoy C, Matsen FA, Shendure J, Lee CC, Harkins TT, et al. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. Plos One. 8: e65226. PMID 23734239 DOI: 10.1371/Journal.Pone.0065226  0.617
2013 Carvill GL, Heavin SB, Yendle SC, McMahon JM, O'Roak BJ, Cook J, Khan A, Dorschner MO, Weaver M, Calvert S, Malone S, Wallace G, Stanley T, Bye AM, Bleasel A, ... ... Shendure J, et al. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1. Nature Genetics. 45: 825-30. PMID 23708187 DOI: 10.1038/Ng.2646  0.679
2013 Ng BG, Buckingham KJ, Raymond K, Kircher M, Turner EH, He M, Smith JD, Eroshkin A, Szybowska M, Losfeld ME, Chong JX, Kozenko M, Li C, Patterson MC, Gilbert RD, ... ... Shendure J, et al. Mosaicism of the UDP-galactose transporter SLC35A2 causes a congenital disorder of glycosylation. American Journal of Human Genetics. 92: 632-6. PMID 23561849 DOI: 10.1016/J.Ajhg.2013.03.012  0.689
2013 Snyder MW, Simmons LE, Kitzman JO, Santillan DA, Santillan MK, Gammill HS, Shendure J. Noninvasive fetal genome sequencing: A primer Prenatal Diagnosis. 33: 547-554. PMID 23553552 DOI: 10.1002/Pd.4097  0.829
2013 Marneros AG, Beck AE, Turner EH, McMillin MJ, Edwards MJ, Field M, de Macena Sobreira NL, Perez AB, Fortes JA, Lampe AK, Giovannucci Uzielli ML, Gordon CT, Plessis G, Le Merrer M, Amiel J, ... ... Shendure J, et al. Mutations in KCTD1 cause scalp-ear-nipple syndrome. American Journal of Human Genetics. 92: 621-6. PMID 23541344 DOI: 10.1016/J.Ajhg.2013.03.002  0.553
2013 Deng X, Berletch JB, Ma W, Nguyen DK, Hiatt JB, Noble WS, Shendure J, Disteche CM. Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation. Developmental Cell. 25: 55-68. PMID 23523075 DOI: 10.1016/J.Devcel.2013.01.028  0.652
2013 Starita LM, Pruneda JN, Lo RS, Fowler DM, Kim HJ, Hiatt JB, Shendure J, Brzovic PS, Fields S, Klevit RE. Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis. Proceedings of the National Academy of Sciences of the United States of America. 110: E1263-72. PMID 23509263 DOI: 10.1073/Pnas.1303309110  0.743
2013 Hiatt JB, Pritchard CC, Salipante SJ, O'Roak BJ, Shendure J. Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Research. 23: 843-54. PMID 23382536 DOI: 10.1101/Gr.147686.112  0.802
2013 Below JE, Earl DL, Shively KM, McMillin MJ, Smith JD, Turner EH, Stephan MJ, Al-Gazali LI, Hertecant JL, Chitayat D, Unger S, Cohn DH, Krakow D, Swanson JM, Faustman EM, ... Shendure J, et al. Whole-genome analysis reveals that mutations in inositol polyphosphate phosphatase-like 1 cause opsismodysplasia. American Journal of Human Genetics. 92: 137-43. PMID 23273567 DOI: 10.1016/J.Ajhg.2012.11.011  0.59
2013 Knowles MR, Leigh MW, Ostrowski LE, Huang L, Carson JL, Hazucha MJ, Yin W, Berg JS, Davis SD, Dell SD, Ferkol TW, Rosenfeld M, Sagel SD, Milla CE, Olivier KN, ... ... Shendure J, et al. Exome sequencing identifies mutations in CCDC114 as a cause of primary ciliary dyskinesia. American Journal of Human Genetics. 92: 99-106. PMID 23261302 DOI: 10.1016/J.Ajhg.2012.11.003  0.603
2013 McMillin MJ, Below JE, Shively KM, Beck AE, Gildersleeve HI, Pinner J, Gogola GR, Hecht JT, Grange DK, Harris DJ, Earl DL, Jagadeesh S, Mehta SG, Robertson SP, Swanson JM, ... ... Shendure J, et al. Mutations in ECEL1 cause distal arthrogryposis type 5D. American Journal of Human Genetics. 92: 150-6. PMID 23261301 DOI: 10.1016/J.Ajhg.2012.11.014  0.338
2013 Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Akey JM. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 493: 216-20. PMID 23201682 DOI: 10.1038/Nature11690  0.362
2013 Carvill GL, Heavin SB, Yendle SC, O'Roak BJ, Cook J, Khan A, Dorschner MO, Weaver MA, Calvert S, Malone S, Wallace G, Stanley T, Bye AM, Bleasel A, Howell KB, ... ... Shendure J, et al. Targeted resequencing in epileptic encephalopathies reveals marked genetic heterogeneity and novel genes Epilepsia. 54: 16-16. DOI: 10.1111/Epi.12228  0.659
2013 Fu W, O’Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Project NES, Akey JM. Erratum: Corrigendum: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants Nature. 495: 270-270. DOI: 10.1038/Nature12022  0.342
2012 O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, ... ... Shendure J, et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science (New York, N.Y.). 338: 1619-22. PMID 23160955 DOI: 10.1126/Science.1227764  0.809
2012 Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY. Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Molecular Cell. 48: 760-70. PMID 23142080 DOI: 10.1016/J.Molcel.2012.10.002  0.63
2012 Shendure J, Lieberman Aiden E. The expanding scope of DNA sequencing. Nature Biotechnology. 30: 1084-94. PMID 23138308 DOI: 10.1038/Nbt.2421  0.436
2012 Schwartz JJ, Lee C, Hiatt JB, Adey A, Shendure J. Capturing native long-range contiguity by in situ library construction and optical sequencing Proceedings of the National Academy of Sciences of the United States of America. 109: 18749-18754. PMID 23112150 DOI: 10.1073/Pnas.1202680109  0.824
2012 Horani A, Druley TE, Zariwala MA, Patel AC, Levinson BT, Van Arendonk LG, Thornton KC, Giacalone JC, Albee AJ, Wilson KS, Turner EH, Nickerson DA, Shendure J, Bayly PV, Leigh MW, et al. Whole-exome capture and sequencing identifies HEATR2 mutation as a cause of primary ciliary dyskinesia. American Journal of Human Genetics. 91: 685-93. PMID 23040496 DOI: 10.1016/J.Ajhg.2012.08.022  0.628
2012 Campbell CD, Chong JX, Malig M, Ko A, Dumont BL, Han L, Vives L, O'Roak BJ, Sudmant PH, Shendure J, Abney M, Ober C, Eichler EE. Estimating the human mutation rate using autozygosity in a founder population. Nature Genetics. 44: 1277-81. PMID 23001126 DOI: 10.1038/Ng.2418  0.731
2012 Peifer M, Fernández-Cuesta L, Sos ML, George J, Seidel D, Kasper LH, Plenker D, Leenders F, Sun R, Zander T, Menon R, Koker M, Dahmen I, Müller C, Di Cerbo V, ... ... Shendure J, et al. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nature Genetics. 44: 1104-10. PMID 22941188 DOI: 10.1038/Ng.2396  0.403
2012 Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, ... ... Shendure J, et al. A high-coverage genome sequence from an archaic Denisovan individual. Science (New York, N.Y.). 338: 222-6. PMID 22936568 DOI: 10.1126/Science.1224344  0.829
2012 Elde NC, Child SJ, Eickbush MT, Kitzman JO, Rogers KS, Shendure J, Geballe AP, Malik HS. Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell. 150: 831-41. PMID 22901812 DOI: 10.1016/J.Cell.2012.05.049  0.782
2012 Tabor HK, Murray JC, Gammill HS, Kitzman JO, Snyder MW, Ventura M, Lewis AP, Qiu R, Simmons LE, Rubens CE, Santillan MK, Eichler EE, Cheng EY, Bamshad MJ, Shendure J. Non-invasive fetal genome sequencing: opportunities and challenges. American Journal of Medical Genetics. Part A. 158: 2382-4. PMID 22887792 DOI: 10.1002/Ajmg.A.35545  0.801
2012 Schwartz JJ, Lee C, Shendure J. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nature Methods. 9: 913-5. PMID 22886093 DOI: 10.1038/Nmeth.2137  0.607
2012 Duan Z, Andronescu M, Schutz K, Lee C, Shendure J, Fields S, Noble WS, Anthony Blau C. A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes. Methods (San Diego, Calif.). 58: 277-88. PMID 22776363 DOI: 10.1016/J.Ymeth.2012.06.018  0.367
2012 Boileau C, Guo DC, Hanna N, Regalado ES, Detaint D, Gong L, Varret M, Prakash SK, Li AH, d'Indy H, Braverman AC, Grandchamp B, Kwartler CS, Gouya L, Santos-Cortez RL, ... ... Shendure J, et al. TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome. Nature Genetics. 44: 916-21. PMID 22772371 DOI: 10.1038/Ng.2348  0.313
2012 Rivière JB, Mirzaa GM, O'Roak BJ, Beddaoui M, Alcantara D, Conway RL, St-Onge J, Schwartzentruber JA, Gripp KW, Nikkel SM, Worthylake T, Sullivan CT, Ward TR, Butler HE, Kramer NA, ... ... Shendure J, et al. De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes. Nature Genetics. 44: 934-40. PMID 22729224 DOI: 10.1038/Ng.2331  0.694
2012 Kitzman JO, Snyder MW, Ventura M, Lewis AP, Qiu R, Simmons LE, Gammill HS, Rubens CE, Santillan DA, Murray JC, Tabor HK, Bamshad MJ, Eichler EE, Shendure J. Noninvasive whole-genome sequencing of a human fetus. Science Translational Medicine. 4: 137ra76. PMID 22674554 DOI: 10.1126/Scitranslmed.3004323  0.83
2012 Bamshad MJ, Shendure JA, Valle D, Hamosh A, Lupski JR, Gibbs RA, Boerwinkle E, Lifton RP, Gerstein M, Gunel M, Mane S, Nickerson DA. The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. American Journal of Medical Genetics. Part A. 158: 1523-5. PMID 22628075 DOI: 10.1002/Ajmg.A.35470  0.335
2012 Kohane IS, Shendure J. What's a Genome Worth? Science Translational Medicine. 4: 133fs13. PMID 22572879 DOI: 10.1126/Scitranslmed.3004208  0.372
2012 Bernier FP, Caluseriu O, Ng S, Schwartzentruber J, Buckingham KJ, Innes AM, Jabs EW, Innis JW, Schuette JL, Gorski JL, Byers PH, Andelfinger G, Siu V, Lauzon J, Fernandez BA, ... ... Shendure J, et al. Haploinsufficiency of SF3B4, a component of the pre-mRNA spliceosomal complex, causes Nager syndrome. American Journal of Human Genetics. 90: 925-33. PMID 22541558 DOI: 10.1016/J.Ajhg.2012.04.004  0.559
2012 O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, ... ... Shendure J, et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 485: 246-50. PMID 22495309 DOI: 10.1038/Nature10989  0.788
2012 Adey A, Shendure J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing Genome Research. 22: 1139-1143. PMID 22466172 DOI: 10.1101/Gr.136242.111  0.722
2012 Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, Ahituv N, Pennacchio LA, Shendure J. Massively parallel functional dissection of mammalian enhancers in vivo. Nature Biotechnology. 30: 265-70. PMID 22371081 DOI: 10.1038/Nbt.2136  0.812
2012 Rivière JB, van Bon BW, Hoischen A, Kholmanskikh SS, O'Roak BJ, Gilissen C, Gijsen S, Sullivan CT, Christian SL, Abdul-Rahman OA, Atkin JF, Chassaing N, Drouin-Garraud V, Fry AE, Fryns JP, ... ... Shendure J, et al. De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome. Nature Genetics. 44: 440-4, S1-2. PMID 22366783 DOI: 10.1038/Ng.1091  0.699
2012 Kumar A, MacKenzie AP, O'Roak BJ, Coleman I, Morrissey C, Lee C, White TA, Dumpit RF, True LD, Corey E, Vessella RL, Nelson PS, Shendure J. Abstract 5059: Exome and targeted sequencing to discover and validate candidate genes in advanced and lethal prostate cancer Cancer Research. 72: 5059-5059. DOI: 10.1158/1538-7445.Am2012-5059  0.747
2012 O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, Karakoc E, MacKenzie AP, Ng SB, Baker C, Rieder MJ, Nickerson DA, Bernier R, Fisher SE, Shendure J, et al. Corrigendum: Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations (Nature Genetics (2011) 43, (585-589)) Nature Genetics. 44: 471. DOI: 10.1038/Ng0412-471  0.806
2011 Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nature Genetics. 43: 1179-85. PMID 22019781 DOI: 10.1038/Ng.948  0.674
2011 Shendure JA, Porreca GJ, Church GM, Gardner AF, Hendrickson CL, Kieleczawa J, Slatko BE. Overview of DNA sequencing strategies. Current Protocols in Molecular Biology. Unit7.1. PMID 21987056 DOI: 10.1002/0471142727.Mb0701S96  0.815
2011 Kumar A, White TA, MacKenzie AP, Clegg N, Lee C, Dumpit RF, Coleman I, Ng SB, Salipante SJ, Rieder MJ, Nickerson DA, Corey E, Lange PH, Morrissey C, Vessella RL, ... ... Shendure J, et al. Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proceedings of the National Academy of Sciences of the United States of America. 108: 17087-92. PMID 21949389 DOI: 10.1073/Pnas.1108745108  0.73
2011 Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nature Reviews. Genetics. 12: 745-55. PMID 21946919 DOI: 10.1038/Nrg3031  0.615
2011 Shendure J. Next-generation human genetics. Genome Biology. 12: 408. PMID 21920048 DOI: 10.1186/Gb-2011-12-9-408  0.358
2011 Fairfield H, Gilbert GJ, Barter M, Corrigan RR, Curtain M, Ding Y, D'Ascenzo M, Gerhardt DJ, He C, Huang W, Richmond T, Rowe L, Probst FJ, Bergstrom DE, Murray SA, ... ... Shendure J, et al. Mutation discovery in mice by whole exome sequencing. Genome Biology. 12: R86. PMID 21917142 DOI: 10.1186/Gb-2011-12-9-R86  0.362
2011 Cooper GM, Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews. Genetics. 12: 628-40. PMID 21850043 DOI: 10.1038/Nrg3046  0.441
2011 George RD, McVicker G, Diederich R, Ng SB, MacKenzie AP, Swanson WJ, Shendure J, Thomas JH. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Research. 21: 1686-94. PMID 21795384 DOI: 10.1101/Gr.121327.111  0.627
2011 Cosart T, Beja-Pereira A, Chen S, Ng SB, Shendure J, Luikart G. Exome-wide DNA capture and next generation sequencing in domestic and wild species. Bmc Genomics. 12: 347. PMID 21729323 DOI: 10.1186/1471-2164-12-347  0.641
2011 Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, Lee C, Turner EH, Chen L, Kidd JM, Archidiacono N, ... Shendure J, et al. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Research. 21: 1640-9. PMID 21685127 DOI: 10.1101/Gr.124461.111  0.696
2011 Hannibal MC, Buckingham KJ, Ng SB, Ming JE, Beck AE, McMillin MJ, Gildersleeve HI, Bigham AW, Tabor HK, Mefford HC, Cook J, Yoshiura K, Matsumoto T, Matsumoto N, Miyake N, ... ... Shendure J, et al. Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome. American Journal of Medical Genetics. Part A. 155: 1511-6. PMID 21671394 DOI: 10.1002/Ajmg.A.34074  0.52
2011 O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, Karakoc E, Mackenzie AP, Ng SB, Baker C, Rieder MJ, Nickerson DA, Bernier R, Fisher SE, Shendure J, et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nature Genetics. 43: 585-9. PMID 21572417 DOI: 10.1038/Ng.835  0.81
2011 Kumar A, Shendure J, Nelson PS. Genome interrupted: sequencing of prostate cancer reveals the importance of chromosomal rearrangements. Genome Medicine. 3: 23. PMID 21542879 DOI: 10.1186/Gm237  0.561
2011 Muthappan V, Lee AY, Lamprecht TL, Akileswaran L, Dintzis SM, Lee C, Magrini V, Mardis ER, Shendure J, Van Gelder RN. Biome representational in silico karyotyping. Genome Research. 21: 626-33. PMID 21324882 DOI: 10.1101/Gr.115758.110  0.394
2011 Gallagher LA, Shendure J, Manoil C. Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq. Mbio. 2: e00315-10. PMID 21253457 DOI: 10.1128/Mbio.00315-10  0.383
2011 Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnology. 29: 59-63. PMID 21170042 DOI: 10.1038/Nbt.1740  0.825
2011 Kitzman JO, MacKenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J. Erratum: Haplotype-resolved genome sequencing of a Gujarati Indian individual Nature Biotechnology. 29: 459-459. DOI: 10.1038/Nbt0511-459C  0.79
2011 Nelson FK, Snyder M, Gardner AF, Hendrickson CL, Shendure JA, Porreca GJ, Church GM, Ausubel FM, Ju J, Kieleczawa J, Slatko BE. Introduction and historical overview of DNA sequencing Current Protocols in Molecular Biology. DOI: 10.1002/0471142727.mb0700s96  0.802
2010 Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X, Shendure J. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition Genome Biology. 11. PMID 21143862 DOI: 10.1186/Gb-2010-11-12-R119  0.808
2010 Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE. Diversity of human copy number variation and multicopy genes. Science (New York, N.Y.). 330: 641-6. PMID 21030649 DOI: 10.1126/Science.1197005  0.815
2010 Ng SB, Nickerson DA, Bamshad MJ, Shendure J. Massively parallel sequencing and rare disease. Human Molecular Genetics. 19: R119-24. PMID 20846941 DOI: 10.1093/Hmg/Ddq390  0.615
2010 Rios J, Stein E, Shendure J, Hobbs HH, Cohen JC. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Human Molecular Genetics. 19: 4313-8. PMID 20719861 DOI: 10.1093/Hmg/Ddq352  0.459
2010 Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, ... ... Shendure J, et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nature Genetics. 42: 790-3. PMID 20711175 DOI: 10.1038/Ng.646  0.704
2010 Igartua C, Turner EH, Ng SB, Hodges E, Hannon GJ, Bhattacharjee A, Rieder MJ, Nickerson DA, Shendure J. Targeted enrichment of specific regions in the human genome by array hybridization. Current Protocols in Human Genetics / Editorial Board, Jonathan L. Haines ... [Et Al.]. Unit 18.3. PMID 20582915 DOI: 10.1002/0471142905.Hg1803S66  0.71
2010 Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. A three-dimensional model of the yeast genome. Nature. 465: 363-7. PMID 20436457 DOI: 10.1038/Nature08973  0.376
2010 Yang F, Babak T, Shendure J, Disteche CM. Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Research. 20: 614-22. PMID 20363980 DOI: 10.1101/Gr.103200.109  0.325
2010 Cooper GM, Goode DL, Ng SB, Sidow A, Bamshad MJ, Shendure J, Nickerson DA. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nature Methods. 7: 250-1. PMID 20354513 DOI: 10.1038/Nmeth0410-250  0.603
2010 Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (New York, N.Y.). 328: 636-9. PMID 20220176 DOI: 10.1126/Science.1186802  0.446
2010 Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generation sequencing. Nature Methods. 7: 111-8. PMID 20111037 DOI: 10.1038/Nmeth.1419  0.693
2010 Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J. Parallel, tag-directed assembly of locally derived short sequence reads Nature Methods. 7: 119-122. PMID 20081835 DOI: 10.1038/Nmeth.1416  0.814
2010 Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics. 42: 30-5. PMID 19915526 DOI: 10.1038/Ng.499  0.608
2010 Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Erratum: Target-enrichment strategies for next-generation sequencing Nature Methods. 7: 479-479. DOI: 10.1038/Nmeth0610-479C  0.468
2009 Thomas JH, Emerson RO, Shendure J. Extraordinary molecular evolution in the PRDM9 fertility gene. Plos One. 4: e8505. PMID 20041164 DOI: 10.1371/Journal.Pone.0008505  0.329
2009 Patwardhan RP, Lee C, Litvin O, Young DL, Pe'Er D, Shendure J. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis Nature Biotechnology. 27: 1173-1175. PMID 19915551 DOI: 10.1038/Nbt.1589  0.788
2009 Vasta V, Ng SB, Turner EH, Shendure J, Hahn SH. Next generation sequence analysis for mitochondrial disorders. Genome Medicine. 1: 100. PMID 19852779 DOI: 10.1186/Gm100  0.705
2009 Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 461: 272-6. PMID 19684571 DOI: 10.1038/Nature08250  0.772
2009 Turner EH, Ng SB, Nickerson DA, Shendure J. Methods for genomic partitioning. Annual Review of Genomics and Human Genetics. 10: 263-84. PMID 19630561 DOI: 10.1146/Annurev-Genom-082908-150112  0.729
2009 Shendure J, Stewart CJ. Cancer genomes on a shoestring budget. The New England Journal of Medicine. 360: 2781-3. PMID 19516026 DOI: 10.1056/Nejme0903433  0.438
2009 Brkanac Z, Spencer D, Shendure J, Robertson PD, Matsushita M, Vu T, Bird TD, Olson MV, Raskind WH. IFRD1 is a candidate gene for SMNA on chromosome 7q22-q23. American Journal of Human Genetics. 84: 692-7. PMID 19409521 DOI: 10.1016/J.Ajhg.2009.04.008  0.405
2009 Turner EH, Lee C, Ng SB, Nickerson DA, Shendure J. Massively parallel exon capture and library-free resequencing across 16 genomes. Nature Methods. 6: 315-6. PMID 19349981 DOI: 10.1038/Nmeth.F.248  0.726
2008 Shendure J, Ji H. Next-generation DNA sequencing. Nature Biotechnology. 26: 1135-45. PMID 18846087 DOI: 10.1038/Nbt1486  0.44
2008 Shendure J. The beginning of the end for microarrays? Nature Methods. 5: 585-7. PMID 18587314 DOI: 10.1038/Nmeth0708-585  0.357
2008 Higgins AW, Alkuraya FS, Bosco AF, Brown KK, Bruns GA, Donovan DJ, Eisenman R, Fan Y, Farra CG, Ferguson HL, Gusella JF, Harris DJ, Herrick SR, Kelly C, Kim HG, ... ... Shendure J, et al. Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project. American Journal of Human Genetics. 82: 712-22. PMID 18319076 DOI: 10.1016/J.Ajhg.2008.01.011  0.392
2008 Shendure JA, Porreca GJ, Church GM. Overview of DNA sequencing strategies. Current Protocols in Molecular Biology. Unit 7.1. PMID 18231983 DOI: 10.1002/0471142727.mb0701s81  0.814
2008 Higgins AW, Alkuraya FS, Bosco AF, Brown KK, Bruns GAP, Donovan DJ, Eisenman R, Fan Y, Farra CG, Ferguson HL, Gusella JF, Harris DJ, Herrick SR, Kelly C, Kim HG, ... ... Shendure J, et al. Characterization of Apparently Balanced Chromosomal Rearrangements from the Developmental Genome Anatomy Project (DOI:10.1016/j.ajhg.2008.01.011) American Journal of Human Genetics. 83: 425-427. DOI: 10.1016/J.Ajhg.2008.08.011  0.328
2007 Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J. Multiplex amplification of large sets of human exons. Nature Methods. 4: 931-6. PMID 17934468 DOI: 10.1038/Nmeth1110  0.818
2006 Porreca GJ, Shendure J, Church GM. Polony DNA sequencing. Current Protocols in Molecular Biology. Unit 7.8. PMID 18265387 DOI: 10.1002/0471142727.Mb0708S76  0.831
2006 Turner DJ, Shendure J, Porreca G, Church G, Green P, Tyler-Smith C, Hurles ME. Assaying chromosomal inversions by single-molecule haplotyping. Nature Methods. 3: 439-45. PMID 16721377 DOI: 10.1038/Nmeth881  0.541
2006 Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. Long-range polony haplotyping of individual human chromosome molecules. Nature Genetics. 38: 382-7. PMID 16493423 DOI: 10.1038/Ng1741  0.795
2006 Church G, Shendure J, Porreca G. Sequencing thoroughbreds. Nature Biotechnology. 24: 139. PMID 16465149 DOI: 10.1038/Nbt0206-139B  0.529
2005 Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. Accurate multiplex polony sequencing of an evolved bacterial genome. Science (New York, N.Y.). 309: 1728-32. PMID 16081699 DOI: 10.1126/Science.1117389  0.807
2005 Zhu Z, Shendure J, Church GM. Discovering functional transcription-factor combinations in the human cell cycle. Genome Research. 15: 848-55. PMID 15930495 DOI: 10.1101/Gr.3394405  0.63
2004 Shendure J, Mitra RD, Varma C, Church GM. Advanced sequencing technologies: methods and goals. Nature Reviews. Genetics. 5: 335-44. PMID 15143316 DOI: 10.1038/Nrg1325  0.49
2004 Mitra RD, Shendure J, Olejnik J, Church GM. CorrigendumErratum to “Fluorescent in situ sequencing on polymerase colonies” [Anal. Biochem. 320 (2003) 55–65] Analytical Biochemistry. 328: 245. DOI: 10.1016/J.Ab.2004.03.002  0.523
2003 Zhu J, Shendure J, Mitra RD, Church GM. Single molecule profiling of alternative pre-mRNA splicing. Science (New York, N.Y.). 301: 836-8. PMID 12907803 DOI: 10.1126/Science.1085792  0.465
2003 Mitra RD, Shendure J, Olejnik J, Edyta-Krzymanska-Olejnik, Church GM. Fluorescent in situ sequencing on polymerase colonies. Analytical Biochemistry. 320: 55-65. PMID 12895469 DOI: 10.1016/S0003-2697(03)00291-4  0.551
2003 Mitra RD, Butty VL, Shendure J, Williams BR, Housman DE, Church GM. Digital genotyping and haplotyping with polymerase colonies. Proceedings of the National Academy of Sciences of the United States of America. 100: 5926-31. PMID 12730373 DOI: 10.1073/Pnas.0936399100  0.488
2002 Shendure J, Church GM. Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biology. 3: RESEARCH0044. PMID 12225583 DOI: 10.1186/Gb-2002-3-9-Research0044  0.542
2002 Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M. Identification of foreign gene sequences by transcript filtering against the human genome. Nature Genetics. 30: 141-2. PMID 11788827 DOI: 10.1038/Ng818  0.567
2001 Badarinarayana V, Estep PW, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM. Selection analyses of insertional mutants using subgenic-resolution arrays. Nature Biotechnology. 19: 1060-5. PMID 11689852 DOI: 10.1038/Nbt1101-1060  0.805
2001 Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J. Computational comparison of two draft sequences of the human genome. Nature. 409: 856-9. PMID 11237010 DOI: 10.1038/35057055  0.721
1998 Peirce JL, Derr R, Shendure J, Kolata T, Silver LM. A major influence of sex-specific loci on alcohol preference in C57Bl/6 and DBA/2 inbred mice. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 9: 942-8. PMID 9880657 DOI: 10.1007/S003359900904  0.482
1998 Shendure J, Melo JA, Pociask K, Derr R, Silver LM. Sex-restricted non-Mendelian inheritance of mouse chromosome 11 in the offspring of crosses between C57BL/6J and (C57BL/6J x DBA/2J)F1 mice. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 9: 812-5. PMID 9745035 DOI: 10.1007/S003359900872  0.494
1996 Melo JA, Shendure J, Pociask K, Silver LM. Identification of sex-specific quantitative trait loci controlling alcohol preference in C57BL/ 6 mice. Nature Genetics. 13: 147-53. PMID 8640219 DOI: 10.1038/Ng0696-147  0.477
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