User profiles for B Paten

Benedict Paten

Associate Professor; Associate Director, UC Santa Cruz Genomics Institute, University of …
Verified email at ucsc.edu
Cited by 43894

[HTML][HTML] The Human Pangenome Project: a global resource to map genomic diversity

…, T Weissman, P Flicek, H Li, KH Miga, B Paten… - Nature, 2022 - nature.com
The human reference genome is the most widely used resource in human genetics and is
due for a major update. Its current structure is a linear composite of merged haplotypes from …

The Genome 10K Project: a way forward

KP Koepfli, B Paten… - Annu. Rev. Anim …, 2015 - annualreviews.org
… been prioritized to address such questions, including the following: (a) the evolution and
molecular mechanisms underlying genetic and temperature-dependent sex determination; (b) …

Genome graphs and the evolution of genome inference

B Paten, AM Novak, JM Eizenga, E Garrison - Genome research, 2017 - genome.cshlp.org
… Bidirected sequence graph (A) being unfolded into a directed acyclic graph (B), in preparation
for partial-order alignment. Node 6 is a reversed view of node 1, node 7 is a reversed view …

The complete sequence of a human genome

…, DE Miller, JC Mullikin, EW Myers, ND Olson, B Paten… - Science, 2022 - science.org
… (B) The ONT-assisted graph traversal for the 2p11 locus is given by numerical order. Based
on low … (B to D) Enlargements corresponding to regions of the genome featured in Fig. 2, …

[HTML][HTML] Towards complete and error-free genome assemblies of all vertebrate species

…, W Kwak, H Clawson, M Diekhans, L Nassar, B Paten… - Nature, 2021 - nature.com
High-quality and complete reference genome assemblies are fundamental for the application
of genomics to biology, disease, and biodiversity conservation. However, such assemblies …

GENCODE reference annotation for the human and mouse genomes

…, R Guigó, TJP Hubbard, M Kellis, B Paten… - Nucleic acids …, 2019 - academic.oup.com
The accurate identification and description of the genes in the human and mouse genomes
is a fundamental requirement for high quality analysis of data informing both genome biology …

[HTML][HTML] Nanopore sequencing and assembly of a human genome with ultra-long reads

…, AR Quinlan, TP Snutch, L Tee, B Paten… - Nature …, 2018 - nature.com
We report the sequencing and assembly of a reference genome for the human GM12878
Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. …

[HTML][HTML] A draft human pangenome reference

…, E Garrison, T Marschall, IM Hall, H Li, B Paten - Nature, 2023 - nature.com
Here the Human Pangenome Reference Consortium presents a first draft of the human
pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of …

The UCSC genome browser database: 2015 update

…, CH Li, KH Miga, N Nguyen, B Paten… - Nucleic acids …, 2015 - academic.oup.com
Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome
Browser database ( http://genome.ucsc.edu ) and associated tools continue to grow, providing a …

Toil enables reproducible, open source, big biomedical data analyses

…, J Zhu, S Zaranek, G Getz, D Haussler, B Paten - Nature …, 2017 - nature.com
… (b) Scatter plot showing the Pearson correlation between the results of the TCGA best-practices
pipeline and the CGL pipeline. 10,000 randomly selected sample and/or gene pairs …