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Benedict Paten, PhD - Publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 
 European Bioinformatics Institute University of Cambridge, Cambridge, England, United Kingdom 
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132 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
2024 Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, ... ... Paten B, et al. Structurally divergent and recurrently mutated regions of primate genomes. Cell. PMID 38428424 DOI: 10.1016/j.cell.2024.01.052  0.447
2023 Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, ... ... Paten B, et al. Identification of constrained sequence elements across 239 primate genomes. Nature. PMID 38030727 DOI: 10.1038/s41586-023-06798-8  0.426
2023 Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, Diekhans M, Fischer C, Navarro Gonzalez J, Hickey G, Hinrichs AS, Kuhn RM, Lee BT, Lee CM, Le Mercier P, ... ... Paten B, et al. The UCSC Genome Browser database: 2024 update. Nucleic Acids Research. PMID 37953330 DOI: 10.1093/nar/gkad987  0.494
2023 Kolesnikov A, Cook D, Nattestad M, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K. Local read haplotagging enables accurate long-read small variant calling. Biorxiv : the Preprint Server For Biology. PMID 37745389 DOI: 10.1101/2023.09.07.556731  0.375
2023 Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, ... ... Paten B, et al. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nature Methods. PMID 37710018 DOI: 10.1038/s41592-023-01993-x  0.366
2023 Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, ... ... Paten B, et al. A draft human pangenome reference. Nature. 617: 312-324. PMID 37165242 DOI: 10.1038/s41586-023-05896-x  0.384
2023 Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, et al. Increased mutation and gene conversion within human segmental duplications. Nature. 617: 325-334. PMID 37165237 DOI: 10.1038/s41586-023-05895-y  0.326
2023 Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Marschall T, Li H, Paten B. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology. PMID 37165083 DOI: 10.1038/s41587-023-01793-w  0.466
2023 Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C, Korbel JO, Paten B, Marschall T, Eichler EE. Gaps and complex structurally variant loci in phased genome assemblies. Genome Research. 33: 496-510. PMID 37164484 DOI: 10.1101/gr.277334.122  0.388
2023 Porubsky D, Harvey WT, Rozanski AN, Ebler J, Höps W, Ashraf H, Hasenfeld P, Paten B, Sanders AD, Marschall T, Korbel JO, Eichler EE. Inversion polymorphism in a complete human genome assembly. Genome Biology. 24: 100. PMID 37122002 DOI: 10.1186/s13059-023-02919-8  0.396
2023 Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, ... ... Paten B, ... ... Paten B, et al. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.). 380: eabn2937. PMID 37104612 DOI: 10.1126/science.abn2937  0.422
2023 Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, ... ... Paten B, ... ... Paten B, et al. Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.). 380: eabn3943. PMID 37104599 DOI: 10.1126/science.abn3943  0.44
2023 Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, ... ... Paten B, et al. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. Biorxiv : the Preprint Server For Biology. PMID 36945512 DOI: 10.1101/2023.03.10.531987  0.465
2023 Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Gordon DS, Wei X, Logsdon GA, Haukness M, Dishuck PC, ... ... Paten B, et al. Structurally divergent and recurrently mutated regions of primate genomes. Biorxiv : the Preprint Server For Biology. PMID 36945442 DOI: 10.1101/2023.03.07.531415  0.503
2023 Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga J, Juul S, McKenzie S, Simmonds SE, Park J, ... ... Paten B, et al. Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Biorxiv : the Preprint Server For Biology. PMID 36865218 DOI: 10.1101/2023.02.21.529152  0.321
2023 Marco-Sola S, Eizenga JM, Guarracino A, Paten B, Garrison E, Moreto M. Optimal gap-affine alignment in O(s) space. Bioinformatics (Oxford, England). PMID 36749013 DOI: 10.1093/bioinformatics/btad074  0.318
2023 Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PA, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, ... ... Paten B, et al. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Biorxiv : the Preprint Server For Biology. PMID 36711673 DOI: 10.1101/2023.01.12.523790  0.424
2023 Sibbesen JA, Eizenga JM, Novak AM, Sirén J, Chang X, Garrison E, Paten B. Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature Methods. 20: 239-247. PMID 36646895 DOI: 10.1038/s41592-022-01731-9  0.397
2022 Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, ... ... Paten B, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research. PMID 36420896 DOI: 10.1093/nar/gkac1071  0.496
2022 Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, ... ... Paten B, et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. PMID 36261518 DOI: 10.1038/s41586-022-05325-5  0.496
2022 Sirén J, Paten B. GBZ File Format for Pangenome Graphs. Bioinformatics (Oxford, England). PMID 36179091 DOI: 10.1093/bioinformatics/btac656  0.348
2022 Olson ND, Wagner J, McDaniel J, Stephens SH, Westreich ST, Prasanna AG, Johanson E, Boja E, Maier EJ, Serang O, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, ... ... Paten B, et al. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions. Cell Genomics. 2. PMID 35720974 DOI: 10.1016/j.xgen.2022.100129  0.469
2022 Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B. A complete pedigree-based graph workflow for rare candidate variant analysis. Genome Research. PMID 35483961 DOI: 10.1101/gr.276387.121  0.417
2022 Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, ... ... Paten B, et al. The Human Pangenome Project: a global resource to map genomic diversity. Nature. 604: 437-446. PMID 35444317 DOI: 10.1038/s41586-022-04601-8  0.506
2022 Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nature Methods. PMID 35361931 DOI: 10.1038/s41592-022-01440-3  0.424
2022 Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, ... ... Paten B, et al. A complete reference genome improves analysis of human genetic variation. Science (New York, N.Y.). 376: eabl3533. PMID 35357935 DOI: 10.1126/science.abl3533  0.478
2022 Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, ... ... Paten B, et al. The complete sequence of a human genome. Science (New York, N.Y.). 376: 44-53. PMID 35357919 DOI: 10.1126/science.abj6987  0.675
2022 Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, ... ... Paten B, et al. Complete genomic and epigenetic maps of human centromeres. Science (New York, N.Y.). 376: eabl4178. PMID 35357911 DOI: 10.1126/science.abl4178  0.465
2022 Goenka SD, Gorzynski JE, Shafin K, Fisk DG, Pesout T, Jensen TD, Monlong J, Chang PC, Baid G, Bernstein JA, Christle JW, Dalton KP, Garalde DR, Grove ME, Guillory J, ... ... Paten B, et al. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nature Biotechnology. PMID 35347328 DOI: 10.1038/s41587-022-01221-5  0.449
2022 Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, ... ... Paten B, et al. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genomics. 2. PMID 35199087 DOI: 10.1016/j.xgen.2021.100085  0.413
2022 Gorzynski JE, Goenka SD, Shafin K, Jensen TD, Fisk DG, Grove ME, Spiteri E, Pesout T, Monlong J, Baid G, Bernstein JA, Ceresnak S, Chang PC, Christle JW, Chubb H, ... ... Paten B, et al. Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. The New England Journal of Medicine. PMID 35020984 DOI: 10.1056/NEJMc2112090  0.412
2021 Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, ... ... Paten B, et al. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science (New York, N.Y.). 374: abg8871. PMID 34914532 DOI: 10.1126/science.abg8871  0.436
2021 Shafin K, Pesout T, Chang PC, Nattestad M, Kolesnikov A, Goel S, Baid G, Kolmogorov M, Eizenga JM, Miga KH, Carnevali P, Jain M, Carroll A, Paten B. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nature Methods. PMID 34725481 DOI: 10.1038/s41592-021-01299-w  0.406
2021 Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, ... Paten B, et al. Erratum to: Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 34015138 DOI: 10.1093/molbev/msab100  0.373
2021 Mao Y, Catacchio CR, Hillier LW, Porubsky D, Li R, Sulovari A, Fernandes JD, Montinaro F, Gordon DS, Storer JM, Haukness M, Fiddes IT, Murali SC, Dishuck PC, Hsieh P, ... ... Paten B, et al. A high-quality bonobo genome refines the analysis of hominid evolution. Nature. PMID 33953399 DOI: 10.1038/s41586-021-03519-x  0.524
2021 Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, ... ... Paten B, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0  0.683
2021 Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, ... ... Paten B, et al. Author Correction: Dense sampling of bird diversity increases power of comparative genomics. Nature. PMID 33833441 DOI: 10.1038/s41586-021-03473-8  0.317
2021 Garg P, Martin-Trujillo A, Rodriguez OL, Gies SJ, Hadelia E, Jadhav B, Jain M, Paten B, Sharp AJ. Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression. American Journal of Human Genetics. PMID 33794196 DOI: 10.1016/j.ajhg.2021.03.016  0.341
2020 Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, ... ... Paten B, et al. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science (New York, N.Y.). 370. PMID 33335035 DOI: 10.1126/science.abc6617  0.487
2020 Porubsky D, Ebert P, Audano PA, Vollger MR, Harvey WT, Marijon P, Ebler J, Munson KM, Sorensen M, Sulovari A, Haukness M, Ghareghani M, Lansdorp PM, Paten B, et al. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nature Biotechnology. PMID 33288906 DOI: 10.1038/s41587-020-0719-5  0.436
2020 Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, ... ... Paten B, et al. GENCODE 2021. Nucleic Acids Research. PMID 33270111 DOI: 10.1093/nar/gkaa1087  0.753
2020 Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, ... ... Paten B, et al. Dense sampling of bird diversity increases power of comparative genomics. Nature. 587: 252-257. PMID 33177665 DOI: 10.1038/s41586-020-2873-9  0.532
2020 Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, ... ... Paten B, et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 587: 246-251. PMID 33177663 DOI: 10.1038/s41586-020-2871-y  0.556
2020 Eizenga JM, Novak AM, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E. Efficient dynamic variation graphs. Bioinformatics (Oxford, England). PMID 33040146 DOI: 10.1093/Bioinformatics/Btaa640  0.468
2020 Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, ... Paten B, et al. Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 32946576 DOI: 10.1093/Molbev/Msaa240  0.479
2020 Garg P, Jadhav B, Rodriguez OL, Patel N, Martin-Trujillo A, Jain M, Metsu S, Olsen H, Paten B, Ritz B, Kooy RF, Gecz J, Sharp AJ. A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions. American Journal of Human Genetics. PMID 32937144 DOI: 10.1016/J.Ajhg.2020.08.019  0.46
2020 Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, ... ... Paten B, et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology. PMID 32686750 DOI: 10.1038/S41587-020-0503-6  0.564
2020 Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, ... ... Paten B, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. PMID 32663838 DOI: 10.1038/S41586-020-2547-7  0.502
2020 Chang X, Eizenga J, Novak AM, Sirén J, Paten B. Distance indexing and seed clustering in sequence graphs. Bioinformatics (Oxford, England). 36: i146-i153. PMID 32657356 DOI: 10.1093/Bioinformatics/Btaa446  0.562
2020 Ding H, Bailey AD, Jain M, Olsen H, Paten B. Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts. Bioinformatics (Oxford, England). PMID 32597959 DOI: 10.1093/Bioinformatics/Btaa601  0.39
2020 Krasheninnikova K, Diekhans M, Armstrong J, Dievskii A, Paten B, O'Brien S. halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments. Gigascience. 9. PMID 32463100 DOI: 10.1093/Gigascience/Giaa047  0.595
2020 Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, et al. Pangenome Graphs. Annual Review of Genomics and Human Genetics. PMID 32453966 DOI: 10.1146/annurev-genom-120219-080406  0.549
2020 Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, ... ... Paten B, et al. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000research. 9: 136. PMID 32308977 DOI: 10.12688/F1000Research.18236.1  0.341
2020 Hickey G, Heller D, Monlong J, Sibbesen JA, Sirén J, Eizenga J, Dawson ET, Garrison E, Novak AM, Paten B. Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biology. 21: 35. PMID 32051000 DOI: 10.1186/S13059-020-1941-7  0.418
2020 Burton AS, Stahl SE, John KK, Jain M, Juul S, Turner DJ, Harrington ED, Stoddart D, Paten B, Akeson M, Castro-Wallace SL. Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing. Genes. 11. PMID 31936690 DOI: 10.3390/Genes11010076  0.405
2019 Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, ... ... Paten B, et al. A strategy for building and using a human reference pangenome. F1000research. 8: 1751. PMID 34386196 DOI: 10.12688/f1000research.19630.1  0.366
2019 Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, ... ... Paten B, et al. Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods. PMID 31819268 DOI: 10.1038/S41592-019-0697-Z  0.327
2019 Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, ... ... Paten B, et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods. PMID 31740818 DOI: 10.1038/S41592-019-0617-2  0.376
2019 Sirén J, Garrison E, Novak AM, Paten B, Durbin R. Haplotype-aware graph indexes. Bioinformatics (Oxford, England). PMID 31406990 DOI: 10.1093/Bioinformatics/Btz575  0.515
2019 Beyer W, Novak AM, Hickey G, Chan J, Tan V, Paten B, Zerbino DR. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics (Oxford, England). PMID 31368484 DOI: 10.1093/Bioinformatics/Btz597  0.774
2019 Ebler J, Haukness M, Pesout T, Marschall T, Paten B. Haplotype-aware diplotyping from noisy long reads. Genome Biology. 20: 116. PMID 31159868 DOI: 10.1186/S13059-019-1709-0  0.439
2019 Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, et al. The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain. G3 (Bethesda, Md.). PMID 30996023 DOI: 10.1534/G3.119.400071  0.545
2019 Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin C, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, ... ... Paten B, et al. A strategy for building and using a human reference pangenome F1000research. 8: 1751. DOI: 10.12688/F1000Research.19630.1  0.468
2018 Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. Plos Genetics. 14: e1007752. PMID 30586411 DOI: 10.1371/Journal.Pgen.1007752  0.372
2018 Armstrong J, Fiddes IT, Diekhans M, Paten B. Whole-Genome Alignment and Comparative Annotation. Annual Review of Animal Biosciences. PMID 30379572 DOI: 10.1146/Annurev-Animal-020518-115005  0.614
2018 Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, ... ... Paten B, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/Nar/Gky955  0.754
2018 Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Chromosome assembly of large and complex genomes using multiple references. Genome Research. PMID 30341161 DOI: 10.1101/Gr.236273.118  0.563
2018 Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, ... ... Paten B, et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nature Genetics. PMID 30275530 DOI: 10.1038/S41588-018-0223-8  0.67
2018 Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology. PMID 30125266 DOI: 10.1038/Nbt.4227  0.682
2018 Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Research. PMID 29884752 DOI: 10.1101/Gr.233460.117  0.614
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, ... ... Paten B, et al. High-resolution comparative analysis of great ape genomes. Science (New York, N.Y.). 360. PMID 29880660 DOI: 10.1126/Science.Aar6343  0.552
2018 Tunstall T, Kock R, Vahala J, Diekhans M, Fiddes I, Armstrong J, Paten B, Ryder OA, Steiner CC. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Research. 28: 780-788. PMID 29798851 DOI: 10.1101/Gr.227603.117  0.392
2018 Haussler D, Smuga-Otto M, Eizenga JM, Paten B, Novak AM, Nikitin S, Zueva M, Miagkov D. A Flow Procedure for Linearization of Genome Sequence Graphs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 29792514 DOI: 10.1089/Cmb.2017.0248  0.51
2018 Dang LT, Tondl M, Chiu MHH, Revote J, Paten B, Tano V, Tokolyi A, Besse F, Quaife-Ryan G, Cumming H, Drvodelic MJ, Eichenlaub MP, Hallab JC, Stolper JS, Rossello FJ, et al. TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. Bmc Genomics. 19: 238. PMID 29621972 DOI: 10.1186/S12864-018-4630-0  0.545
2018 Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, ... ... Paten B, et al. Repeat associated mechanisms of genome evolution and function revealed by theandgenomes. Genome Research. PMID 29563166 DOI: 10.1101/Gr.234096.117  0.543
2018 Jain M, Olsen HE, Turner DJ, Stoddart D, Bulazel KV, Paten B, Haussler D, Willard HF, Akeson M, Miga KH. Linear assembly of a human centromere on the Y chromosome. Nature Biotechnology. PMID 29553574 DOI: 10.1038/Nbt.4109  0.429
2018 Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G. Superbubbles, Ultrabubbles, and Cacti. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 29461862 DOI: 10.1089/Cmb.2017.0251  0.539
2018 Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, ... ... Paten B, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology. PMID 29431738 DOI: 10.1038/Nbt.4060  0.545
2018 Marschall T, Marz M, Abeel T, Dijkstra L, Dutilh BE, Ghaffaari A, Kersey P, Kloosterman WP, Makinen V, Novak AM, Paten B, Porubsky D, Rivals E, Alkan C, Baaijens JA, et al. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics. 19: 118-135. PMID 27769991 DOI: 10.1093/Bib/Bbw089  0.579
2017 Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes I, Armstrong J, Laayouni H, Gordon D, Huddleston J, Perez RG, Povolotskaya I, Armero AS, Garrido JG, Ho D, Ribeca P, ... ... Paten B, et al. A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0). Gigascience. PMID 29092041 DOI: 10.1093/Gigascience/Gix098  0.594
2017 Rosen Y, Eizenga J, Paten B. Modelling haplotypes with respect to reference cohort variation graphs. Bioinformatics (Oxford, England). 33: i118-i123. PMID 28881971 DOI: 10.1093/Bioinformatics/Btx236  0.334
2017 Novak AM, Garrison E, Paten B. A graph extension of the positional Burrows-Wheeler transform and its applications. Algorithms For Molecular Biology : Amb. 12: 18. PMID 28702075 DOI: 10.1186/S13015-017-0109-9  0.501
2017 Jagodnik KM, Koplev S, Jenkins S, Ohno-Machado L, Paten B, Schurer SC, Dumontier M, Verborgh R, Bui A, Ping P, McKenna NJ, Madduri R, Pillai A, Ma'ayan A. Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop. Journal of Biomedical Informatics. PMID 28501646 DOI: 10.1016/J.Jbi.2017.05.006  0.324
2017 Paten B, Novak AM, Eizenga JM, Garrison E. Genome graphs and the evolution of genome inference. Genome Research. PMID 28360232 DOI: 10.1101/Gr.214155.116  0.577
2017 O'Connor BD, Yuen D, Chung V, Duncan AG, Liu XK, Patricia J, Paten B, Stein L, Ferretti V. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000research. 6: 52. PMID 28344774 DOI: 10.12688/F1000Research.10137.1  0.541
2017 Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B. Mapping DNA methylation with high-throughput nanopore sequencing. Nature Methods. PMID 28218897 DOI: 10.1038/Nmeth.4189  0.425
2017 Rice ES, Kohno S, St John J, Pham S, Howard J, Lareau L, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN, Gresham C, McCarthy F, Kern C, ... ... Paten B, et al. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Research. PMID 28137821 DOI: 10.1101/Gr.213595.116  0.438
2017 Dawson ET, Garrison E, Novak A, Paten B, Eizinga J, Hickey G, Chanock S, Durbin R. Abstract 3570: Germline structural variant detection with variation graphs Cancer Research. 77: 3570-3570. DOI: 10.1158/1538-7445.Am2017-3570  0.59
2016 Jain M, Olsen HE, Paten B, Akeson M. Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology. 17: 256. PMID 27964738 DOI: 10.1186/S13059-016-1122-X  0.505
2016 Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology. 17: 239. PMID 27887629 DOI: 10.1186/S13059-016-1103-0  0.494
2016 Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D. Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. Bmc Bioinformatics. 17: 400. PMID 27687569 DOI: 10.1186/S12859-016-1258-4  0.763
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, et al. Long-read sequence assembly of the gorilla genome. Science (New York, N.Y.). 352: aae0344. PMID 27034376 DOI: 10.1126/Science.Aae0344  0.607
2016 Lincoln SE, Cline M, Yang S, Kobayashi Y, Zhang M, O'Leary E, Topper S, Paten B, Nussbaum R. Variant classifications in BRCA1 and BRCA2: A systematic analysis of interlaboratory concordance Journal of Clinical Oncology. 34: 1592-1592. DOI: 10.1200/Jco.2016.34.15_Suppl.1592  0.388
2016 Novak AM, Garrison E, Paten B. A graph extension of the positional burrows-wheeler transform and its applications Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9838: 246-256. DOI: 10.1007/978-3-319-43681-4_20  0.406
2015 Ip CL, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, et al. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000research. 4: 1075. PMID 26834992 DOI: 10.12688/F1000Research.7201.1  0.577
2015 Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. PMID 26590259 DOI: 10.1093/Nar/Gkv1275  0.59
2015 Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, ... ... Paten B, et al. The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. Human Mutation. 36: 915-21. PMID 26295439 DOI: 10.1002/Humu.22858  0.354
2015 Novak AM, Rosen Y, Haussler D, Paten B. Canonical, stable, general mapping using context schemes. Bioinformatics (Oxford, England). 31: 3569-76. PMID 26220960 DOI: 10.1093/Bioinformatics/Btv435  0.426
2015 Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, James Kent W, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association : Jamia. PMID 26174866 DOI: 10.1093/Jamia/Ocv047  0.511
2015 Koepfli KP, Paten B, O'Brien SJ. The Genome 10K Project: a way forward. Annual Review of Animal Biosciences. 3: 57-111. PMID 25689317 DOI: 10.1146/Annurev-Animal-090414-014900  0.568
2015 Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nature Methods. 12: 351-6. PMID 25686389 DOI: 10.1038/Nmeth.3290  0.466
2015 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 387-401. PMID 25565268 DOI: 10.1089/Cmb.2014.0146  0.785
2015 Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, ... ... Paten B, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Research. 43: D670-81. PMID 25428374 DOI: 10.1093/Nar/Gku1177  0.624
2015 Ballinger TJ, Zerbino D, Paten B, Haussler D. Abstract B1-11: Application of the CN-AVG method to reconstruct the evolutionary history of glioblastoma multiforme Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-11  0.739
2015 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population Journal of Computational Biology. 22: 387-401. DOI: 10.1089/cmb.2014.0146  0.715
2014 Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, ... ... Paten B, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.). 346: 1254449. PMID 25504731 DOI: 10.1126/Science.1254449  0.576
2014 Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 516: 242-5. PMID 25274305 DOI: 10.1038/Nature13760  0.42
2014 Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, ... ... Paten B, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24: 2077-89. PMID 25273068 DOI: 10.1101/Gr.174920.114  0.505
2014 Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics (Oxford, England). 30: 3293-301. PMID 25138168 DOI: 10.1093/Bioinformatics/Btu534  0.557
2014 Paten B, Zerbino DR, Hickey G, Haussler D. A unifying model of genome evolution under parsimony Bmc Bioinformatics. 15. PMID 24946830 DOI: 10.1186/1471-2105-15-206  0.751
2014 Kolmogorov M, Raney B, Paten B, Pham S. Ragout - A reference-assisted assembly tool for bacterial genomes Bioinformatics. 30: I302-I309. PMID 24931998 DOI: 10.1093/bioinformatics/btu280  0.525
2014 Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser Bioinformatics. 30: 1003-1005. PMID 24227676 DOI: 10.1093/Bioinformatics/Btt637  0.537
2014 Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: Web-accessible browsers for comparative genomics Bioinformatics. 30: 3293-3301. DOI: 10.1093/bioinformatics/btu534  0.442
2014 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Haussler D, Paten B. Building a pangenome reference for a population Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8394: 207-221. DOI: 10.1007/978-3-319-05269-4-17  0.575
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, ... ... Paten B, 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  0.717
2013 Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: A hierarchical format for storing and analyzing multiple genome alignments Bioinformatics. 29: 1341-1342. PMID 23505295 DOI: 10.1093/Bioinformatics/Btt128  0.788
2012 Westesson O, Lunter G, Paten B, Holmes I. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. Plos One. 7: e34572. PMID 22536326 DOI: 10.1371/Journal.Pone.0034572  0.368
2012 Zerbino DR, Paten B, Haussler D. Integrating genomes Science. 336: 179-182. PMID 22499938 DOI: 10.1126/science.1216830  0.75
2011 Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, ... ... Paten B, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111  0.779
2011 Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment Genome Research. 21: 1512-1528. PMID 21665927 DOI: 10.1101/Gr.123356.111  0.753
2011 Roskin KM, Paten B, Haussler D. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization Bmc Bioinformatics. 12. PMID 21569267 DOI: 10.1186/1471-2105-12-144  0.353
2011 Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons Journal of Computational Biology. 18: 469-481. PMID 21385048 DOI: 10.1089/Cmb.2010.0252  0.518
2010 Haudry Y, Ramialison M, Paten B, Wittbrodt J, Ettwiller L. Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. Nature Protocols. 5: 323-34. PMID 20134431 DOI: 10.1038/Nprot.2009.158  0.706
2009 Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics (Oxford, England). 25: 295-301. PMID 19056777 DOI: 10.1093/Bioinformatics/Btn630  0.699
2008 Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research. 18: 1829-43. PMID 18849525 DOI: 10.1101/Gr.076521.108  0.69
2008 Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research. 18: 1814-28. PMID 18849524 DOI: 10.1101/Gr.076554.108  0.712
2007 Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Paten B, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340  0.481
2007 Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J. Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nature Methods. 4: 563-5. PMID 17589518 DOI: 10.1038/Nmeth1061  0.707
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Paten B, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.689
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Paten B, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  0.687
2005 Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biology. 6: R104. PMID 16356267 DOI: 10.1186/Gb-2005-6-12-R104  0.684
2004 Ettwiller L, Paten B. Guilt by multiple association Heredity. 92: 481-482. DOI: 10.1038/Sj.Hdy.6800452  0.756
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