Benedict Paten : rechercher sur Z-Library

Le plus grand référentiel d'articles scientifiques au monde. 70,000,000+ d'articles gratuitement.

Don't use scam websites

Livres
Articles (45)
Les plus populaires
Liste
- Liste
- Tableau

1

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

Jain, Miten, Olsen, Hugh E., Paten, Benedict, Akeson, Mark

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 921 KB

english, 2016

2

Variation graph toolkit improves read mapping by representing genetic variation in the reference

Garrison, Erik, Sirén, Jouni, Novak, Adam M, Hickey, Glenn, Eizenga, Jordan M, Dawson, Eric T, Jones, William, Garg, Shilpa, Markello, Charles, Lin, Michael F, Paten, Benedict, Durbin, Richard

Journal:

Nature Biotechnology

Année:

2018

Langue:

english

Fichier:

PDF, 2.56 MB

english, 2018

3

The Genome 10K Project: A Way Forward

Koepfli, Klaus-Peter, Paten, Benedict, O’Brien, Stephen J.

Journal:

Annual Review of Animal Biosciences

Année:

2015

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2015

4

Linear assembly of a human centromere on the Y chromosome

Jain, Miten, Olsen, Hugh E, Turner, Daniel J, Stoddart, David, Bulazel, Kira V, Paten, Benedict, Haussler, David, Willard, Huntington F, Akeson, Mark, Miga, Karen H

Journal:

Nature Biotechnology

Année:

2018

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2018

5

A Flow Procedure for Linearization of Genome Sequence Graphs

Haussler, David, Smuga-Otto, Maciej, Eizenga, Jordan M., Paten, Benedict, Novak, Adam M., Nikitin, Sergei, Zueva, Maria, Miagkov, Dmitrii

Journal:

Journal of Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 759 KB

english, 2018

6

Whole-Genome Alignment and Comparative Annotation

Armstrong, Joel, Fiddes, Ian T., Diekhans, Mark, Paten, Benedict

Journal:

Annual Review of Animal Biosciences

Année:

2019

Langue:

english

Fichier:

PDF, 949 KB

english, 2019

7

Sequence tube maps: making graph genomes intuitive to commuters

Beyer, Wolfgang, Novak, Adam M, Hickey, Glenn, Chan, Jeffrey, Tan, Vanessa, Paten, Benedict, Zerbino, Daniel R, Valencia, Alfonso

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 245 KB

english, 2019

8

Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization

Krishna M Roskin, Benedict Paten, David Haussler

Journal:

BMC Bioinformatics

Année:

2011

Langue:

english

Fichier:

PDF, 372 KB

english, 2011

9

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation

Ettwiller, Laurence, Paten, Benedict, Ramialison, Mirana, Birney, Ewan, Wittbrodt, Joachim

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 285 KB

english, 2007

10

Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation

Haudry, Yannick, Ramialison, Mirana, Paten, Benedict, Wittbrodt, Joachim, Ettwiller, Laurence

Journal:

Nature Protocols

Année:

2010

Langue:

english

Fichier:

PDF, 1.17 MB

english, 2010

11

The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates

Laurence Ettwiller, Benedict Paten, Marcel Souren, Felix Loosli…

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 2.45 MB

english, 2005

12

Cactus Graphs for Genome Comparisons

Paten, Benedict, Diekhans, Mark, Earl, Dent, John, John St., Ma, Jian, Suh, Bernard, Haussler, David

Journal:

Journal of Computational Biology

Année:

2011

Langue:

english

Fichier:

PDF, 644 KB

english, 2011

13

A unifying model of genome evolution under parsimony

Benedict Paten,Daniel R Zerbino,Glenn Hickey,David Haussler

Journal:

BMC Bioinformatics

Année:

2014

Langue:

english

Fichier:

PDF, 3.73 MB

english, 2014

14

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

Jacobs, Frank M. J., Greenberg, David, Nguyen, Ngan, Haeussler, Maximilian, Ewing, Adam D., Katzman, Sol, Paten, Benedict, Salama, Sofie R., Haussler, David

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 6.90 MB

english, 2014

15

Building a Pan-Genome Reference for a Population

Nguyen, Ngan, Hickey, Glenn, Zerbino, Daniel R., Raney, Brian, Earl, Dent, Armstrong, Joel, Kent, W. James, Haussler, David, Paten, Benedict

Journal:

Journal of Computational Biology

Année:

2015

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2015

16

Improved data analysis for the MinION nanopore sequencer

Jain, Miten, Fiddes, Ian T, Miga, Karen H, Olsen, Hugh E, Paten, Benedict, Akeson, Mark

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2015

17

The NIH BD2K center for big data in translational genomics

Paten, Benedict, Diekhans, Mark, Druker, Brian J., Friend, Stephen, Guinney, Justin, Gassner, Nadine, Guttman, Mitchell, James Kent, W, Mantey, Patrick, Margolin, Adam A, Massie, Matt, Novak, Adam M,

Journal:

Journal of the American Medical Informatics Association

Année:

2015

Langue:

english

Fichier:

PDF, 315 KB

english, 2015

18

Canonical, Stable, General Mapping using Context Schemes

Novak, Adam M, Rosen, Yohei, Haussler, David, Paten, Benedict

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 354 KB

english, 2015

19

The UCSC Genome Browser database: 2016 update

Speir, Matthew L., Zweig, Ann S., Rosenbloom, Kate R., Raney, Brian J., Paten, Benedict, Nejad, Parisa, Lee, Brian T., Learned, Katrina, Karolchik, Donna, Hinrichs, Angie S., Heitner, Steve, Harte, Ra

Journal:

Nucleic Acids Research

Année:

2016

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2016

20

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (4 – 8 January 2017)] Biocomputing 2017 - DATA SHARING AND REPRODUCIBLE CLINICAL GENETIC TESTING: SUCCESSES AND CHALLENGES

YANG, SHAN, CLINE, MELISSA, ZHANG, CAN, PATEN, BENEDICT, LINCOLN, STEPHEN E.

Langue:

english

Fichier:

PDF, 1.11 MB

english

21

Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

Jain, Miten, Olsen, Hugh E., Paten, Benedict, Akeson, Mark

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 226 KB

english, 2016

22

Mapping DNA methylation with high-throughput nanopore sequencing

Rand, Arthur C, Jain, Miten, Eizenga, Jordan M, Musselman-Brown, Audrey, Olsen, Hugh E, Akeson, Mark, Paten, Benedict

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 2.02 MB

english, 2017

23

Genome graphs and the evolution of genome inference

Paten, Benedict, Novak, Adam M., Eizenga, Jordan M., Garrison, Erik

Journal:

Genome Research

Année:

2017

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2017

24

Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop

Jagodnik, Kathleen M., Koplev, Simon, Jenkins, Sherry, Ohno-Machado, Lucila, Paten, Benedict, Schurer, Stephan C., Dumontier, Michel, Verborgh, Ruben, Bui, Alex, Ping, Peipei, McKenna, Neil J., Maddur

Journal:

Journal of Biomedical Informatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2017

25

Superbubbles, Ultrabubbles, and Cacti

Paten, Benedict, Eizenga, Jordan M., Rosen, Yohei M., Novak, Adam M., Garrison, Erik, Hickey, Glenn

Journal:

Journal of Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 808 KB

english, 2018

26

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs

Zerbino, Daniel R., Ballinger, Tracy, Paten, Benedict, Hickey, Glenn, Haussler, David

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2016

27

TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Dang, Louis T., Tondl, Markus, Chiu, Man Ho H., Revote, Jerico, Paten, Benedict, Tano, Vincent, Tokolyi, Alex, Besse, Florence, Quaife-Ryan, Greg, Cumming, Helen, Drvodelic, Mark J., Eichenlaub, Micha

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 1.39 MB

english, 2018

28

A graph extension of the positional Burrows–Wheeler transform and its applications

Novak, Adam M., Garrison, Erik, Paten, Benedict

Journal:

Algorithms for Molecular Biology

Année:

2017

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2017

29

Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells

Tunstall, Tate, Kock, Richard, Vahala, Jiri, Diekhans, Mark, Fiddes, Ian, Armstrong, Joel, Paten, Benedict, Ryder, Oliver A., Steiner, Cynthia C.

Journal:

Genome Research

Année:

2018

Langue:

english

Fichier:

PDF, 612 KB

english, 2018

30

Modelling haplotypes with respect to reference cohort variation graphs

Rosen, Yohei, Eizenga, Jordan, Paten, Benedict

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 505 KB

english, 2017

31

Chromosome assembly of large and complex genomes using multiple references

Kolmogorov, Mikhail, Armstrong, Joel, Raney, Brian J., Streeter, Ian, Dunn, Matthew, Yang, Fengtang, Odom, Duncan, Flicek, Paul, Keane, Thomas M., Thybert, David, Paten, Benedict, Pham, Son

Journal:

Genome Research

Année:

2018

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2018

32

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

Cline, Melissa S., Liao, Rachel G., Parsons, Michael T., Paten, Benedict, Alquaddoomi, Faisal, Antoniou, Antonis, Baxter, Samantha, Brody, Larry, Cook-Deegan, Robert, Coffin, Amy, Couch, Fergus J., Cr

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 3.04 MB

english, 2018

33

An average-case sublinear forward algorithm for the haploid Li and Stephens model

Rosen, Yohei M., Paten, Benedict J.

Journal:

Algorithms for Molecular Biology

Année:

2019

Langue:

english

Fichier:

PDF, 2.73 MB

english, 2019

34

Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories

Lincoln, Stephen E., Yang, Shan, Cline, Melissa S., Kobayashi, Yuya, Zhang, Can, Topper, Scott, Haussler, David, Paten, Benedict, Nussbaum, Robert L.

Journal:

JCO Precision Oncology

Année:

2017

Langue:

english

Fichier:

PDF, 677 KB

english, 2017

35

An average-case sublinear forward algorithm for the haploid Li and Stephens model

Rosen, Yohei M., Paten, Benedict J.

Journal:

Algorithms for Molecular Biology

Année:

2019

Fichier:

PDF, 2.73 MB

2019

36

Haplotype-aware diplotyping from noisy long reads

Ebler, Jana, Haukness, Marina, Pesout, Trevor, Marschall, Tobias, Paten, Benedict

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 2.05 MB

english, 2019

37

Haplotype-aware graph indexes

Sirén, Jouni, Garrison, Erik, Novak, Adam M, Paten, Benedict, Durbin, Richard, Valencia, Alfonso

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 281 KB

english, 2019

38

Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing

Burton, Aaron S., Stahl, Sarah E., John, Kristen K., Jain, Miten, Juul, Sissel, Turner, Daniel J., Harrington, Eoghan D., Stoddart, David, Paten, Benedict, Akeson, Mark, Castro-Wallace, Sarah L.

Journal:

Année:

2020

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2020

39

Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

Vivian, John, Eizenga, Jordan M., Beale, Holly C., Vaske, Olena M., Paten, Benedict

Journal:

JCO Clinical Cancer Informatics

Année:

2020

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2020

40

halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments

Krasheninnikova, Ksenia, Diekhans, Mark, Armstrong, Joel, Dievskii, Aleksei, Paten, Benedict, OâBrien, Stephen

Journal:

Année:

2020

Fichier:

PDF, 278 KB

2020

41

[IEEE 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) - Long Beach, CA, USA (2019.6.16-2019.6.17)] 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) - DP-CGAN: Differentially Private Synthetic Data and Label Generation

Torkzadehmahani, Reihaneh, Kairouz, Peter, Paten, Benedict

Année:

2019

Fichier:

PDF, 174 KB

2019

42

Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts

Ding, Hongxu, Bailey, Andrew D, Jain, Miten, Olsen, Hugh, Paten, Benedict, Wren, Jonathan

Journal:

Année:

2020

Fichier:

PDF, 229 KB

2020

43

Efficient dynamic variation graphs

Eizenga, Jordan M, Novak, Adam M, Kobayashi, Emily, Villani, Flavia, Cisar, Cecilia, Heumos, Simon, Hickey, Glenn, Colonna, Vincenza, Paten, Benedict, Garrison, Erik, Robinson, Peter

Journal:

Année:

2020

Fichier:

PDF, 862 KB

2020

44

A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions

Garg, Paras, Jadhav, Bharati, Rodriguez, Oscar L., Patel, Nihir, Martin-Trujillo, Alejandro, Jain, Miten, Metsu, Sofie, Olsen, Hugh, Paten, Benedict, Ritz, Beate, Kooy, R. Frank, Gecz, Jozef, Sharp, A

Journal:

The American Journal of Human Genetics

Année:

2020

Fichier:

PDF, 3.31 MB

2020

45

ProTECTâPrediction of T-Cell Epitopes for Cancer Therapy

Rao, Arjun A., Madejska, Ada A., Pfeil, Jacob, Paten, Benedict, Salama, Sofie R., Haussler, David

Journal:

Frontiers in Immunology

Année:

2020

Fichier:

PDF, 930 KB

2020