Publications

2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 20132012 | 2011 | 2010 | 2009 | 20082007 | 2005

2020

Chang X, Eizenga J, Novak AM, Sirén J, Paten B. Distance indexing and seed clustering in sequence graphs. Bioinformatics. 2020;36:i146-i153. https://doi.org/10.1093/bioinformatics/btaa446

Eizenga J, et al. Pangenome Graphs. Annual Review of Genomics and Human Genetics. 2020;21. https://doi.org/10.1146/annurev-genom-120219-080406

Eizenga J, Novak A, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E. Succinct dynamic variation graphs. bioRxiv 056317. 2020. https://doi.org/10.1101/2020.04.23.056317

ENCODE Project Consortium, Snyder MP, Gingeras TR. Perspectives on ENCODE. Nature. 2020;583(7818):693-698. htps://doi.org/10.1038/s41586-020-2449-8

Hickey, G., Heller, D., Monlong, J., Sibbesen, J., Siren, J., Eizenga, J., Dawson, E., Garrison, E., Novak, A., Paten, B. Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biol. 2020;21:35. https://doi.org/10.1186/s13059-020-1941-7

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. 2020;9:6.  https://doi.org/10.1093/gigascience/giaa047

Salama, S. R., et al. Using great ape cerebral cortex organoids to study brain evolution and disease. American Journal of Physical Anthropology. 2020;171:245.

Sirén J, Garrison E, Novak A, Paten B, Durbin R. Haplotype-aware graph indexes. Bioinformatics. 2020;36(2):400-407. https://doi.org/10.1093/bioinformatics/btz575

Vivian J, Eizenga J, Beale H, Vaske O, Paten B. Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples. JCO Clinical Cancer Informatics. 2020;4:160-. https://doi.org/10.1200/CCI.19.00095

2019

Beyer W, Novak AM, Hickey G, Chan J, Tan V, Paten B, Zerbino D. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics. 2019;35(24):5318-5320. https://doi.org/10.1093/bioinformatics/btz597

Ebler, J., Haukness, M., Pesout, T., Marschall T, Paten B. Haplotype-aware diplotyping from noisy long reads. Genome Biol. 2019;20:116. https://doi.org/10.1186/s13059-019-1709-0 

Frankish A, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. 2019;47(D1):D766–D773. https://doi.org/10.1093/nar/gky955

Sweeney NT, James KN, Nistorica A, Lorig-Roach RM, Feldheim DA. Expression of transcription factors divides retinal ganglion cells into distinct classes. J Comp Neurol. 2019;527(1):225-235. https://doi.org/10.1002/cne.24172

Torkzadehmahani R, Kairouz P, Paten B. Dp-cgan: Differentially private synthetic data and label generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops. 2019;0-0. 

2018

Armstrong J, Fiddes I, Diekhans M, Paten B. Whole-genome alignment and comparative annotation. Annual Review of Animal Biosciences. 2018;7:41-64. https://doi.org/10.1146/annurev-animal-020518-115005

Haussler D, Smuga-Otto M, Eizenga J, Paten B, Novak A, Nikitin S, Zueva M, Miagkov. A flow procedure for linearization of genome sequence graphs. Journal of Computational Biology. 2018;25(7). https://doi.org/10.1089/cmb.2017.0248

Jain, M., Olsen, H., Turner, D., Stoddart, D., Bulazel, K., Paten, B., Haussler, D., Willard, H., Akeson, M., Miga, K. Linear assembly of a human centromere on the Y chromosome. Nat Biotechnol. 2018;36:321–323. https://doi.org/10.1038/nbt.4109

Lilue, J., et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet. 2018;50:1574–1583. https://doi.org/10.1038/s41588-018-0223-8

The Computational Pan-Genomics Consortium, Marschall T, Guryev V, Schonhuth A, Vandin F, Ye K. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics. 2018;19(1):118-135. https://doi.org/10.1093/bib/bbw089

Tunstall T, Kock R, Valhalla J, Diekhans M, Fiddes I, Armstrong J, Paten B, Ryder O, Steiner C. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Res. 2018;28:780-788. https://doi.org/10.1101/gr.227603.117

2017

Armstrong J, Hickey G, Diekhans M, Paten B. A comparative genomics multitool for scientific discovery and conservation. Manuscript number: 2017-06-07529. https://doi.org/10.1101/730531

Haussler D, Smuga-Otto M, Eizenga J, Paten B. A flow procedure for linearization of genome sequence graphs. Journal of Computational Biology. 2018;25(7). https://doi.org/10.1089/cmb.2017.0248

Lincoln S, Yang S, Cline M, Kobayashi Y, Zhang C, Topper S, Haussler D, Paten B, Nussbaum R. Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories. JCO Precision Oncology. 2017;1:1-10. https://doi.org/10.1200/PO.16.00020 

O’Connor BD, Yuen D, Chung V, Duncan A, Liu X, Patricia J, Paten B, Stein L, Ferretti V. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000Res. 2017;6:52. https://doi.org/10.12688/f1000research.10137.1

Paten B, Novak A, Eizenga J, Garrison E. Genome graphs and the evolution of genome inference. Genome Res. 2017;27:665-676. https://doi.org/10.1101/gr.214155.116 

Paten B., Novak A.M., Garrison E., Hickey G. (2017) Superbubbles, Ultrabubbles and Cacti. Research in Computational Molecular Biology. 2017;10229. https://doi.org/10.1007/978-3-319-56970-3_11 

Rand, A., Jain, M., Eizenga, J. Musselman-Brown A, Olsen H, Akeson M, Paten B. Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods. 2017;14:411–413. https://doi.org/10.1038/nmeth.4189

Regev A, et al. The human cell atlas white paper. HCA Consortium. 2017

Rosen Y., Eizenga J., Paten B. Describing the Local Structure of Sequence Graphs. Algorithms for Computational Biology. 2017;10252. https://doi.org/10.1007/978-3-319-58163-7_2 

Saha A, Kim Y, Gewirtz A, Jo B, Gao C, McDowell I, The GTEx Consortium, Engelhardt B, Battle A. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res. 2017;27:1843-1858. https://doi.org/10.1101/gr.216721.116

Yang F, Wang J, The GTEx Consortium, Pierce B, Chen L. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res. 2017;27:1859-1871. https://doi.org/10.1101/gr.216754.116

Zerbino D, Paten B, Haussler D. Integrating genomes. Science. 2012;336(6078):179-182. https://doi.org/10.1126/science.1216830

2015

Jain, M., Fiddes, I., Miga, K., Olsen, H., Paten, B., Akeson, M. Improved data analysis for the MinION nanopore sequencer.. Nature methods. 2015;12: 351–356. https://doi.org/10.1038/nmeth.3290

Koepfli K, Paten B, the Genome 10K Community of Scientists, O’Brien S. The Genome 10K Project: a way forward. Annual Review of Animal Biosciences. 2015;3:57-111. https://doi.org/10.1146/annurev-animal-090414-014900

Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, PatenB. Building a pan-genome reference for a population. J Comput Biol. 2015;22(5):387-401. https://doi.org/10.1089/cmb.2014.0146

Novak A, Rosen Y, Haussler D, Paten B. Canonical, stable, general mapping using context schemes. Bioinformatics. 2015; 31(22):3569–3576. https://doi.org/10.1093/bioinformatics/btv435

Paten B, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association. 2015;22(6):1143–1147. https://doi.org/10.1093/jamia/ocv047

Rosenbloom K, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Research. 2015;43(D1)D670–D681. https://doi.org/10.1093/nar/gku1177

Shafin MK, Kabir KL, Ridwan I, Anannya TT, Karim RS, Hoque MM, Rahman MS. Impact of heuristics in clustering large biological networks. Comput Biol Chem. 2015;59 Pt A:28-36. https://doi.org/10.1016/j.compbiolchem.2015.05.007

2012

Haussler D, et al. A million cancer genome warehouse. Defense Technical Information Center. 2012.

Westesson O, Lunter G, Paten B, Holmes I. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS One. 2012;7(4):e34572. https://doi.org/10.1371/journal.pone.0034572

Zerbino D, Paten B, Haussler D. Integrating genomes. Science. 2012;336(6078):179-182. https://doi.org/10.1126/science.1216830

2011

Paten B, Diekhans M, Earl D, St John J, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons. J Comput Biol. 2011;18(3):469-481. https://doi.org/10.1089/cmb.2010.0252

Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011;21(9):1512-1528. https://doi.org/10.1101/gr.123356.111

Westesson O, Lunter G, Paten B. Phylogenetic automata, pruning, and multiple alignment. 2011

2008

Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 2008;18(11):1814-1828. https://doi.org/10.1101/gr.076554.108

Paten B, Herrero J, Fitzgerald S, Beal K, Flicek, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res. 2008;18(11):1829-1843. https://doi.org/10.1101/gr.076521.108

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 Biol. 2005;6(12):R104. https://doi.org/10.1186/gb-2005-6-12-r104