Martin Kircher, Ph.D. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 

65 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
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  0.84
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, ... ... Kircher M, 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  0.84
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  0.84
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, ... ... Kircher M, 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  0.84
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  0.84
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  0.84
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, ... ... Kircher M, 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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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, 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  0.84
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  0.76
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, ... ... Kircher M, 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  0.76
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, et al. ALG1-CDG: Clinical and Molecular Characterization of 39 Unreported Patients. Human Mutation. PMID 26931382 DOI: 10.1002/Humu.22983  0.76
2016 Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Ž, Gušic I, et al. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature. PMID 26886800 DOI: 10.1038/Nature16544  0.76
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  0.76
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 Transplantation. 100: 698. DOI: 10.1097/TP.0000000000001176  0.76
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, ... Kircher M, 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  0.84
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  0.76
2015 Kircher M, Shendure J. Running spell-check to identify regulatory variants. Nature Genetics. 47: 853-5. PMID 26220134 DOI: 10.1038/Ng.3364  0.84
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, ... ... Kircher M, 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  0.84
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, 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  0.76
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, 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  0.76
2015 Garg A, Kircher M, Del Campo M, Amato RS, Agarwal AK. Whole exome sequencing identifies de novo heterozygous CAV1 mutations associated with a novel neonatal onset lipodystrophy syndrome. American Journal of Medical Genetics. Part A. PMID 25898808 DOI: 10.1002/Ajmg.A.37115  0.76
2015 Hughes DA, Kircher M, He Z, Guo S, Fairbrother GL, Moreno CS, Khaitovich P, Stoneking M. Evaluating intra- and inter-individual variation in the human placental transcriptome. Genome Biology. 16: 54. PMID 25887593 DOI: 10.1186/S13059-015-0627-Z  0.76
2015 Sawyer SL, Tian L, Kähkönen M, Schwartzentruber J, Kircher M, Majewski J, Dyment DA, Innes AM, Boycott KM, Moreau LA, Moilanen JS, Greenberg RA. Biallelic mutations in BRCA1 cause a new Fanconi anemia subtype. Cancer Discovery. 5: 135-42. PMID 25472942 DOI: 10.1158/2159-8290.CD-14-1156  0.76
2015 Kircher M, Shendure J. Running spell-check to identify regulatory variants Nature Genetics. 47: 853-855. DOI: 10.1038/ng.3364  0.76
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, ... ... Kircher M, 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  0.76
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, 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  0.76
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, et al. Somatic mutations in cerebral cortical malformations. The New England Journal of Medicine. 371: 733-43. PMID 25140959 DOI: 10.1056/Nejmoa1314432  0.76
2014 Castellano S, Parra G, Sánchez-Quinto FA, Racimo F, Kuhlwilm M, Kircher M, Sawyer S, Fu Q, Heinze A, Nickel B, Dabney J, Siebauer M, White L, Burbano HA, Renaud G, et al. Patterns of coding variation in the complete exomes of three Neandertals. Proceedings of the National Academy of Sciences of the United States of America. 111: 6666-71. PMID 24753607 DOI: 10.1073/Pnas.1405138111  0.76
2014 Schubert M, Ermini L, Der Sarkissian C, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nature Protocols. 9: 1056-82. PMID 24722405 DOI: 10.1038/Nprot.2014.063  0.76
2014 Wunderlich S, Kircher M, Vieth B, Haase A, Merkert S, Beier J, Göhring G, Glage S, Schambach A, Curnow EC, Pääbo S, Martin U, Enard W. Primate iPS cells as tools for evolutionary analyses. Stem Cell Research. 12: 622-9. PMID 24631741 DOI: 10.1016/J.Scr.2014.02.001  0.76
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, ... ... Kircher M, 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  0.76
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  0.76
2014 Heyn P, Kircher M, Dahl A, Kelso J, Tomancak P, Kalinka AT, Neugebauer KM. The earliest transcribed zygotic genes are short, newly evolved, and different across species. Cell Reports. 6: 285-92. PMID 24440719 DOI: 10.1016/J.Celrep.2013.12.030  0.76
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, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 505: 43-9. PMID 24352235 DOI: 10.1038/Nature12886  0.76
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  0.76
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, 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  0.76
2013 Renaud G, Kircher M, Stenzel U, Kelso J. freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics (Oxford, England). 29: 1208-1209. PMID 23471300 DOI: 10.1093/Bioinformatics/Btt117  0.76
2013 Good JM, Wiebe V, Albert FW, Burbano HA, Kircher M, Green RE, Halbwax M, André C, Atencia R, Fischer A, Pääbo S. Comparative population genomics of the ejaculate in humans and the great apes. Molecular Biology and Evolution. 30: 964-76. PMID 23329688 DOI: 10.1093/Molbev/Mst005  0.76
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, 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  0.76
2012 Fietz SA, Lachmann R, Brandl H, Kircher M, Samusik N, Schröder R, Lakshmanaperumal N, Henry I, Vogt J, Riehn A, Distler W, Nitsch R, Enard W, Pääbo S, Huttner WB. Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proceedings of the National Academy of Sciences of the United States of America. 109: 11836-41. PMID 22753484 DOI: 10.1073/Pnas.1209647109  0.76
2012 Hering L, Henze MJ, Kohler M, Kelber A, Bleidorn C, Leschke M, Nickel B, Meyer M, Kircher M, Sunnucks P, Mayer G. Opsins in onychophora (velvet worms) suggest a single origin and subsequent diversification of visual pigments in arthropods. Molecular Biology and Evolution. 29: 3451-8. PMID 22683812 DOI: 10.1093/Molbev/Mss148  0.76
2012 Kircher M. Analysis of high-throughput ancient DNA sequencing data Methods in Molecular Biology. 840: 197-228. PMID 22237537 DOI: 10.1007/978-1-61779-516-9_23  0.76
2012 Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research. 40: e3. PMID 22021376 DOI: 10.1093/Nar/Gkr771  0.76
2011 Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Pääbo S, Mann M. Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology. 7: 548. PMID 22068331 DOI: 10.1038/Msb.2011.81  0.76
2011 Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, et al. The evolution of gene expression levels in mammalian organs. Nature. 478: 343-8. PMID 22012392 DOI: 10.1038/Nature10532  0.76
2011 Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, Ko AM, Ko YC, Jinam TA, Phipps ME, Saitou N, Wollstein A, Kayser M, Pääbo S, Stoneking M. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. American Journal of Human Genetics. 89: 516-28. PMID 21944045 DOI: 10.1016/J.Ajhg.2011.09.005  0.76
2011 Kircher M, Heyn P, Kelso J. Addressing challenges in the production and analysis of illumina sequencing data Bmc Genomics. 12. PMID 21801405 DOI: 10.1186/1471-2164-12-382  0.76
2010 Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 468: 1053-60. PMID 21179161 DOI: 10.1038/Nature09710  0.76
2010 Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, Meyer M. Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA Nucleic Acids Research. 38: e161. PMID 20587499 DOI: 10.1093/Nar/Gkq572  0.76
2010 Kircher M, Kelso J. High-throughput DNA sequencing - Concepts and limitations Bioessays. 32: 524-536. PMID 20486139 DOI: 10.1002/Bies.200900181  0.76
2010 Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, et al. A draft sequence of the Neandertal genome. Science (New York, N.Y.). 328: 710-22. PMID 20448178 DOI: 10.1126/Science.1188021  0.76
2010 Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Pääbo S. A complete mtDNA genome of an early modern human from Kostenki, Russia. Current Biology : Cb. 20: 231-6. PMID 20045327 DOI: 10.1016/J.Cub.2009.11.068  0.76
2010 Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Research. 38: e87. PMID 20028723 DOI: 10.1093/Nar/Gkp1163  0.76
2010 Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5448  0.76
2009 Kircher M, Stenzel U, Kelso J. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biology. 10: R83. PMID 19682367 DOI: 10.1186/Gb-2009-10-8-R83  0.76
2008 Kircher M, Bock C, Paulsen M. Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. Bmc Genomics. 9: 346. PMID 18651963 DOI: 10.1186/1471-2164-9-346  0.76
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