Publications

Benedict Paten’s publications from his Google Scholar

Jain, M., Koren, S., Miga, K. et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36:338–345. https://doi.org/10.1038/nbt.4060

Aguet, F., Brown, A., Castel, S. et al. Genetic effects on gene expression across human tissues. Nature. 2017;550: 204–213. https://doi.org/10.1038/nature24277 

Birney, E., Stamatoyannopoulos, J., Dutta, A. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447: 799–816. https://doi.org/10.1038/nature05874

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

The ENCODE Project Consortium (2011) A User’s Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9(4): e1001046. https://doi.org/10.1371/journal.pbio.1001046

Jain, M., Olsen, H.E., Paten, B. et al. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 2016;17(239). https://doi.org/10.1186/s13059-016-1103-0 

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

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

Speir M, Zweig A, Paten B. The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. 2016;44(D1):D717–D725. https://doi.org/10.1093/nar/gkv1275

Vivian, J., Rao, A., Nothaft, F. Toil enables reproducible, open source, big biomedical data analyses. Nat Biotechnol.  35, 314–316 (2017). https://doi.org/10.1038/nbt.3772

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

Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol. 2020;38:675–678. https://doi.org/10.1038/s41587-020-0546-8 

Goldman, M.J., Zhang, J., Fonseca, N.A. et al. A user guide for the online exploration and visualization of PCAWG data. Nat Commun. 2020;11:3400. https://doi.org/10.1038/s41467-020-16785-6 

Miga, K.H., Koren, S., Rhie, A. et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020. https://doi.org/10.1038/s41586-020-2547-7 

Tan, M., Li, Q., Shanmugam, R. et al. Dynamic landscape and regulation of RNA editing in mammals. Nature. 2017;550: 249–254. https://doi.org/10.1038/nature24041 

Koepfli K, Paten B, 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 

Tan, M., Li, Q., Shanmugam, R. et al. Dynamic landscape and regulation of RNA editing in mammals. Nature. 2017;550:249–254. https://doi.org/10.1038/nature24041 

Rand, A., Jain, M., Eizenga, J. et al. Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods. 2017;14:411–413. https://doi.org/10.1038/nmeth.4189 

Garrison, E., Sirén, J., Novak, A. et al. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol. 2018;36:875–879. https://doi.org/10.1038/nbt.4227 

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

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. doi: 10.1093/bib/bbw089 

Kronenberg Z, Fiddes I, Gordon D. High-resolution comparative analysis of great ape genomes. Science. 2018;360(6393). DOI: 10.1126/science.aar6343

Jain, M., Olsen, H., Turner, D. et al. Linear assembly of a human centromere on the Y chromosome. Nat Biotechnol. 2018;36:321–323. https://doi.org/10.1038/nbt.4109 

Saha A, Kim Y, Gewirtz A, Jo B. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res. 2017;27:1843-1858. Doi: 10.1101/gr.216721.116

Workman, R.E., Tang, A.D., Tang, P.S. et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat Methods. 2019;16:1297–1305. https://doi.org/10.1038/s41592-019-0617-2 

Lilue, J., Doran, A.G., Fiddes, I.T. 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 

Aguet, François et al. Genetic effects on gene expression across human tissues. Nature. 2017;550(767): 204–213

O’Connor BD, Yuen D, Chung V, Paten B. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000Res. 2017;6:52. doi:10.12688/f1000research.10137.1 

Novak, A.M., Garrison, E. & Paten, B. A graph extension of the positional Burrows–Wheeler transform and its applications. Algorithms Mol Biol. 2017;12:18. https://doi.org/10.1186/s13015-017-0109-9 

Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLOS Genetics. 2018;14(12):e1007752. https://doi.org/10.1371/journal.pgen.1007752 

Thybert D, Roller M, Navarro F, Paten B. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res. 2018;28:448-459. doi:10.1101/gr.234096.117

Paten B, Diekhans M, Druker B, Haussler D. 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 

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. doi:10.1101/gr.216754.116

HuBMAP Consortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 2019;547(7777):187-192. doi: 10.1038/s41586-019-1629-x 

Kolmogorov M, Armstrong J, Paten B. Chromosome assembly of large and complex genomes using multiple references. Genome Res. 2018;28:1720-1732. doi:

10.1101/gr.236273.118

Rice E, Kohno S, John J, Paten B. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res. 2017;27:686-696. Doi: 10.1101/gr.213595.116

Lincoln S, Cline M, Haussler D, Paten B. Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories. JCO Precision Oncology. 2017;1:1-10. DOI: 10.1200/PO.16.00020. 

Jagodnik K, Koplev S, Paten B. 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. 2017;71:49-57. https://doi.org/10.1016/j.jbi.2017.05.006 

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

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 

Miga, K.H., Koren, S., Rhie, A. et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020. https://doi.org/10.1038/s41586-020-2547-7 

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 

Fiddes I, Armstrong J, Paten B. Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation. Genome Res. 2018;28:1029-1038. Doi: 10.1101/gr.233460.117

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

Shafin, K., Pesout, T., Lorig-Roach, R. et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol. 2020. https://doi.org/10.1038/s41587-020-0503-6 

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, Patterson D, Paten B. A million cancer genome warehouse. Defense Technical Information Center. 2012. 

Tunstall T, Kock R, Paten B. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Res. 2018;28:780-788. Doi: 10.1101/gr.227603.117

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., Zerbino, D.R., Hickey, G. et al. A unifying model of genome evolution under parsimony. BMC Bioinformatics. 2014;15:206. https://doi.org/10.1186/1471-2105-15-206 

Roskin, K.M., Paten, B. & Haussler, D. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. BMC Bioinformatics. 2011;12:144. https://doi.org/10.1186/1471-2105-12-144 

Zerbino, D.R., Ballinger, T., Paten, B. et al. Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. BMC Bioinformatics. 2016;17:400. https://doi.org/10.1186/s12859-016-1258-4 

Yang S, Cline M, Zhang C, Paten B. Data sharing and reproducible clinical genetic testing: successes and challenges. Biocomputing. 2017;166-176. https://doi.org/10.1142/9789813207813_0017 

Hickey, G., Heller, D., Monlong, J. et al. Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biol. 2020;21:35. https://doi.org/10.1186/s13059-020-1941-7 

Regev A, Teichmann S, Rozenblatt-Rosen O, Paten B. The human cell atlas white paper. HCA Consortium. 2017

Sarsani V, Raghupathy N, Fiddes I, Paten B. The genome of C57BL/6J “Eve”, the mother of the laboratory mouse genome reference strain. G3: Genes, Genomes, Genetics. 2019;9(6):1795-1805. https://doi.org/10.1534/g3.119.400071 

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. 

Beyer W, Novak AM, Hickey G, Paten B, et al. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics. 2019;35(24):5318-5320. doi:10.1093/bioinformatics/btz597 

Rosen Y, Eizenga J, Paten B. Modelling haplotypes with respect to reference cohort variation graphs. Bioinformatics. 2017;33(14):i118–i123. https://doi.org/10.1093/bioinformatics/btx236 

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 

Armstrong J, Hickey G, Diekhans M, Paten B. Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era. BioRxiv 730531. 2019. https://doi.org/10.1101/730531 

Porubsky D, Ebert P, Audano P, Paten B. A fully phased accurate assembly of an individual human genome. BioRxiv 855049. 2019. https://doi.org/10.1101/855049 

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 

Llamas B, Narzisi G, Paten B. A strategy for building and using a human reference pangenome. Software Tool Article. 2019. 

Dang, L.T., Tondl, M., Chiu, M.H.H., Paten, B et al. TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. BMC Genomics. 2018;19:238. https://doi.org/10.1186/s12864-018-4630-0 

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

Burton, A., Stahl, S., John, K., Paten, B. Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing. Genes. 2020;11:76.  https://doi.org/10.3390/genes11010076 

Fernandes J, Haeussler M, Paten B, Haussler D. KRAB Zinc Finger Proteins coordinate across evolutionary time scales to battle retroelements. bioRxiv 429563. 2018. doi: https://doi.org/10.1101/429563 

Krasheninnikova K, Diekhans M, Armstrong J, Paten B. 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 

Eizenga J, Novak A,Sibbesen J, Paten B. Pangenome Graphs. Annual Review of Genomics and Human Genetics. 2020;21. https://doi.org/10.1146/annurev-genom-120219-080406 

Salama, S. R., Mantalas, G. L., Field, A. R., Paten, B. Using great ape cerebral cortex organoids to study brain evolution and disease. American Journal of Physical Anthropology. 2020;171:245.

Vos, R. A., Katayama, T., Mishima, H., Paten, B. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research. 2020;9:136. doi:10.12688/f1000research.18236.1 

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

Sun C, Huang J, Wang Y, Paten B. Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators. bioRxiv 122879. 2020. doi: https://doi.org/10.1101/2020.05.29.122879 

Rhie A, McCarthy S, Fedrigo O, Paten B. Towards complete and error-free genome assemblies of all vertebrate species. bioRxiv 110833. 2020. doi: https://doi.org/10.1101/2020.05.22.110833 

Eizenga J, Novak A, Kobayashi E, Paten B. Succinct dynamic variation graphs. bioRxiv 056317. 2020. doi: https://doi.org/10.1101/2020.04.23.056317 

Garg P, Jadhav B, Rodriguez O, Paten B. A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions. bioRxiv 007864. 2020. doi: https://doi.org/10.1101/2020.03.25.007864 

Birney, E., Stamatoyannopoulos, J., Dutta, A., Paten, B et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447:799–816. https://doi.org/10.1038/nature05874 

Armstrong J, Hickey G, Diekhans M, Paten B. A comparative genomics multitool for scientific discovery and conservation. Manuscript number: 2017-06-07529 (per your email, this is the preprint Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era). No publication dates scheduled. Coordinate with Broad and the Avian groups. UCSC is not planning on a release.

Abascal, F., Acosta, R., Addleman, N.J., Paten, B. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020;583:699–710. https://doi.org/10.1038/s41586-020-2493-4 

More Biomolecular Engineering (BME) publications

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. doi: 10.1002/cne.24172. 

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. doi: 10.1016/j.compbiolchem.2015.05.007. 

Heller P, Casaletto J, Ruiz G, Geller J. A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator. Sci Data. 2018;5:180156. doi:10.1038/sdata.2018.156