Pandemic-scale phylogenetics

por Ye, Cheng, Thornlow, Bryan, Kramer, Alexander, McBroome, Jakob, Hinrichs, Angie, Corbett-Detig, Russell, Turakhia, Yatish
Publicado 2021

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

por Lemay, Danielle G, Martin, William F, Hinrichs, Angie S, Rijnkels, Monique, German, J Bruce, Korf, Ian, Pollard, Katherine S
Publicado 2012

A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees

por McBroome, Jakob, Thornlow, Bryan, Hinrichs, Angie S., De Maio, Nicola, Goldman, Nick, Haussler, David, Corbett-Detig, Russell, Turakhia, Yatish
Publicado 2021

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2

por Ye, Cheng, Thornlow, Bryan, Hinrichs, Angie, Kramer, Alexander, Mirchandani, Cade, Torvi, Devika, Lanfear, Robert, Corbett-Detig, Russell, Turakhia, Yatish
Publicado 2022

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

por McBroome, Jakob, Thornlow, Bryan, Hinrichs, Angie S, Kramer, Alexander, De Maio, Nicola, Goldman, Nick, Haussler, David, Corbett-Detig, Russell, Turakhia, Yatish
Publicado 2021

Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approach...

por Thornlow, Bryan, Kramer, Alexander, Ye, Cheng, De Maio, Nicola, McBroome, Jakob, Hinrichs, Angie S., Lanfear, Robert, Turakhia, Yatish, Corbett-Detig, Russell
Publicado 2022

Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementati...

por Kramer, Alexander M, Thornlow, Bryan, Ye, Cheng, De Maio, Nicola, McBroome, Jakob, Hinrichs, Angie S, Lanfear, Robert, Turakhia, Yatish, Corbett-Detig, Russell
Publicado 2023

Navigating protected genomics data with UCSC Genome Browser in a Box

por Haeussler, Maximilian, Raney, Brian J., Hinrichs, Angie S., Clawson, Hiram, Zweig, Ann S., Karolchik, Donna, Casper, Jonathan, Speir, Matthew L., Haussler, David, Kent, W. James
Publicado 2015

Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape

por Turakhia, Yatish, Thornlow, Bryan, Hinrichs, Angie, McBroome, Jakob, Ayala, Nicolas, Ye, Cheng, Smith, Kyle, De Maio, Nicola, Haussler, David, Lanfear, Robert, Corbett-Detig, Russell
Publicado 2022

UCSC Data Integrator and Variant Annotation Integrator

por Hinrichs, Angie S., Raney, Brian J., Speir, Matthew L., Rhead, Brooke, Casper, Jonathan, Karolchik, Donna, Kuhn, Robert M., Rosenbloom, Kate R., Zweig, Ann S., Haussler, David, Kent, W. James
Publicado 2016

The UCSC Ebola Genome Portal

por Haeussler, Maximilian, Karolchik, Donna, Clawson, Hiram, Raney, Brian J, Rosenbloom, Kate R., Fujita, Pauline A., Hinrichs, Angie S., Speir, Matthew L, Eisenhart, Chris, Zweig, Ann S., Haussler, David, Kent, W. James
Publicado 2014

A lung-specific mutational signature enables inference of viral and bacterial respiratory niche

por Ruis, Christopher, Peacock, Thomas P., Polo, Luis M., Masone, Diego, Alvarez, Maria Soledad, Hinrichs, Angie S., Turakhia, Yatish, Cheng, Ye, McBroome, Jakob, Corbett-Detig, Russell, Parkhill, Julian, Floto, R. Andres
Publicado 2023

Stability of SARS-CoV-2 phylogenies

por Turakhia, Yatish, De Maio, Nicola, Thornlow, Bryan, Gozashti, Landen, Lanfear, Robert, Walker, Conor R., Hinrichs, Angie S., Fernandes, Jason D., Borges, Rui, Slodkowicz, Greg, Weilguny, Lukas, Haussler, David, Goldman, Nick, Corbett-Detig, Russell
Publicado 2020

The ENCODE Project at UC Santa Cruz

por Thomas, Daryl J., Rosenbloom, Kate R., Clawson, Hiram, Hinrichs, Angie S., Trumbower, Heather, Raney, Brian J., Karolchik, Donna, Barber, Galt P., Harte, Rachel A., Hillman-Jackson, Jennifer, Kuhn, Robert M., Rhead, Brooke L., Smith, Kayla E., Thakkapallayil, Archana, Zweig, Ann S., Haussler, David, Kent, W. James
Publicado 2007

ENCODE whole-genome data in the UCSC Genome Browser

por Rosenbloom, Kate R., Dreszer, Timothy R., Pheasant, Michael, Barber, Galt P., Meyer, Laurence R., Pohl, Andy, Raney, Brian J., Wang, Ting, Hinrichs, Angie S., Zweig, Ann S., Fujita, Pauline A., Learned, Katrina, Rhead, Brooke, Smith, Kayla E., Kuhn, Robert M., Karolchik, Donna, Haussler, David, Kent, W. James
Publicado 2010

The UCSC Genome Browser database: 2019 update

por Haeussler, Maximilian, Zweig, Ann S, Tyner, Cath, Speir, Matthew L, Rosenbloom, Kate R, Raney, Brian J, Lee, Christopher M, Lee, Brian T, Hinrichs, Angie S, Gonzalez, Jairo Navarro, Gibson, David, Diekhans, Mark, Clawson, Hiram, Casper, Jonathan, Barber, Galt P, Haussler, David, Kuhn, Robert M, Kent, W James
Publicado 2019

The UCSC SARS-CoV-2 Genome Browser

por Fernandes, Jason D., Hinrichs, Angie S., Clawson, Hiram, Gonzalez, Jairo Navarro, Lee, Brian T., Nassar, Luis R., Raney, Brian J., Rosenbloom, Kate R., Nerli, Santrupti, Rao, Arjun, Schmelter, Daniel, Zweig, Ann S., Lowe, Todd M., Ares, Manuel, Corbet-Detig, Russ, Kent, W. James, Haussler, David, Haeussler, Maximilian
Publicado 2020

UCSC Genome Browser enters 20th year

por Lee, Christopher M, Barber, Galt P, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Brian T, Nassar, Luis R, Powell, Conner C, Raney, Brian J, Rosenbloom, Kate R, Schmelter, Daniel, Speir, Matthew L, Zweig, Ann S, Haussler, David, Haeussler, Maximilian, Kuhn, Robert M, Kent, W James
Publicado 2020

The bovine lactation genome: insights into the evolution of mammalian milk

por Lemay, Danielle G, Lynn, David J, Martin, William F, Neville, Margaret C, Casey, Theresa M, Rincon, Gonzalo, Kriventseva, Evgenia V, Barris, Wesley C, Hinrichs, Angie S, Molenaar, Adrian J, Pollard, Katherine S, Maqbool, Nauman J, Singh, Kuljeet, Murney, Regan, Zdobnov, Evgeny M, Tellam, Ross L, Medrano, Juan F, German, J Bruce, Rijnkels, Monique
Publicado 2009

A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

por Thornlow, Bryan, Hinrichs, Angie S., Jain, Miten, Dhillon, Namrita, La, Scott, Kapp, Joshua D., Anigbogu, Ikenna, Cassatt-Johnstone, Molly, McBroome, Jakob, Haeussler, Maximilian, Turakhia, Yatish, Chang, Terren, Olsen, Hugh E, Sanford, Jeremy, Stone, Michael, Vaske, Olena, Bjork, Isabel, Akeson, Mark, Shapiro, Beth, Haussler, David, Kilpatrick, A. Marm, Corbett-Detig, Russell
Publicado 2021