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


Chang X, Eizenga J, Novak AM, Sirén J, Paten B. Distance indexing and seed clustering in sequence graphs. Bioinformatics. 2020;36:i146-i153.

Eizenga J, et al. Pangenome Graphs. Annual Review of Genomics and Human Genetics. 2020;21.

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.

ENCODE Project Consortium, Snyder MP, Gingeras TR. Perspectives on ENCODE. Nature. 2020;583(7818):693-698. htps://

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.

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.

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.

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-.


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.

Ebler, J., Haukness, M., Pesout, T., Marschall T, Paten B. Haplotype-aware diplotyping from noisy long reads. Genome Biol. 2019;20:116. 

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

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.

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. 


Armstrong J, Fiddes I, Diekhans M, Paten B. Whole-genome alignment and comparative annotation. Annual Review of Animal Biosciences. 2018;7:41-64.

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).

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.

Lilue, J., et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet. 2018;50:1574–1583.

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.

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.


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

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).

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. 

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.

Paten B, Novak A, Eizenga J, Garrison E. Genome graphs and the evolution of genome inference. Genome Res. 2017;27:665-676. 

Paten B., Novak A.M., Garrison E., Hickey G. (2017) Superbubbles, Ultrabubbles and Cacti. Research in Computational Molecular Biology. 2017;10229. 

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.

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. 

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.

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.

Zerbino D, Paten B, Haussler D. Integrating genomes. Science. 2012;336(6078):179-182.


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.

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.

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.

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

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.

Rosenbloom K, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Research. 2015;43(D1)D670–D681.

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.


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.

Zerbino D, Paten B, Haussler D. Integrating genomes. Science. 2012;336(6078):179-182.


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.

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.

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


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.

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.


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.