Search | Genome Research

Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina

Meng Wang
Yumei Li
Jun Wang
Soo Hwan Oh
Yexuan Cao
Rui Chen

First Published March 6, 2025

Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding

Kai Li
Melissa L. Smith
J. Chris Blazier
Kelli J. Kochan
Jonathan M.D. Wood
Kerstin Howe Anne E. Kwitek Melinda R. Dwinell Hao Chen Julia L. Ciosek
... [+5 authors] ...,
Patrick Masterson
Terence D. Murphy
Theodore S. Kalbfleisch
Peter A. Doris

First Published November 8, 2024

CodonBERT large language model for mRNA vaccines

Sizhen Li
Saeed Moayedpour
Ruijiang Li
Michael Bailey
Saleh Riahi
Lorenzo Kogler-Anele Milad Miladi Jacob Miner Fabien Pertuy Dinghai Zheng Jun Wang Akshay Balsubramani Khang Tran Minnie Zacharia Monica Wu Xiaobo Gu Ryan Clinton Carla Asquith Joseph Skaleski Lianne Boeglin Sudha Chivukula Anusha Dias Tod Strugnell
... [+18 authors] ...,
Fernando Ulloa Montoya
Vikram Agarwal
Ziv Bar-Joseph
Sven Jager

First Published July 1, 2024

Gaps and complex structurally variant loci in phased genome assemblies

David Porubsky
Mitchell R. Vollger
William T. Harvey
Allison N. Rozanski
Peter Ebert
Glenn Hickey Patrick Hasenfeld Ashley D. Sanders Catherine Stober Jan O. Korbel Benedict Paten Tobias Marschall Evan E. Eichler Haley J. Abel Lucinda L. Antonacci-Fulton Mobin Asri Gunjan Baid Carl A. Baker Anastasiya Belyaeva Konstantinos Billis Guillaume Bourque Silvia Buonaiuto Andrew Carroll Mark J.P. Chaisson Pi-Chuan Chang Xian H. Chang Haoyu Cheng Justin Chu Sarah Cody Vincenza Colonna Daniel E. Cook Robert M. Cook-Deegan Omar E. Cornejo Mark Diekhans Daniel Doerr Peter Ebert Jana Ebler Evan E. Eichler Jordan M. Eizenga Susan Fairley Olivier Fedrigo Adam L. Felsenfeld Xiaowen Feng Christian Fischer Paul Flicek Giulio Formenti Adam Frankish Robert S. Fulton Yan Gao Shilpa Garg Erik Garrison Nanibaa’ A. Garrison Carlos Garcia Giron Richard E. Green Cristian Groza Andrea Guarracino Leanne Haggerty Ira M. Hall William T. Harvey Marina Haukness David Haussler Simon Heumos Glenn Hickey Kendra Hoekzema Thibaut Hourlier Kerstin Howe Miten Jain Erich D. Jarvis Hanlee P. Ji Eimear E. Kenny Barbara A. Koenig Alexey Kolesnikov Jan O. Korbel Jennifer Kordosky Sergey Koren HoJoon Lee Alexandra P. Lewis Heng Li Wen-Wei Liao Shuangjia Lu Tsung-Yu Lu Julian K. Lucas Hugo Magalhães Santiago Marco-Sola Pierre Marijon Charles Markello Tobias Marschall Fergal J. Martin Ann McCartney Jennifer McDaniel Karen H. Miga Matthew W. Mitchell Jean Monlong Jacquelyn Mountcastle Katherine M. Munson Moses Njagi Mwaniki Maria Nattestad Adam M. Novak Sergey Nurk Hugh E. Olsen Nathan D. Olson Benedict Paten Trevor Pesout Adam M. Phillippy Alice B. Popejoy David Porubsky Pjotr Prins Daniela Puiu Mikko Rautiainen Allison A. Regier Arang Rhie Samuel Sacco Ashley D. Sanders Valerie A. Schneider Baergen I. Schultz Kishwar Shafin Jonas A. Sibbesen Jouni Sirén Michael W. Smith Heidi J. Sofia Ahmad N. Abou Tayoun Françoise Thibaud-Nissen Chad Tomlinson Francesca Floriana Tricomi Flavia Villani Mitchell R. Vollger Justin Wagner Brian Walenz
... [+123 authors] ...,
Ting Wang
Jonathan M.D. Wood
Aleksey V. Zimin
Justin M. Zook

First Published May 10, 2023

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model

Li Tang
Matthew C. Hill
Jun Wang
Jianxin Wang
James F. Martin
Min Li

First Published November 12, 2020

Mus caroli and Mus pahari genomes" > Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

David Thybert
Maša Roller
Fábio C.P. Navarro
Ian Fiddes
Ian Streeter
Christine Feig David Martin-Galvez Mikhail Kolmogorov Václav Janoušek Wasiu Akanni Bronwen Aken Sarah Aldridge Varshith Chakrapani William Chow Laura Clarke Carla Cummins Anthony Doran Matthew Dunn Leo Goodstadt Kerstin Howe Matthew Howell Ambre-Aurore Josselin Robert C. Karn Christina M. Laukaitis Lilue Jingtao Fergal Martin Matthieu Muffato Stefanie Nachtweide Michael A. Quail Cristina Sisu Mario Stanke Klara Stefflova Cock Van Oosterhout Frederic Veyrunes Ben Ward Fengtang Yang Golbahar Yazdanifar Amonida Zadissa David J. Adams Alvis Brazma Mark Gerstein Benedict Paten
... [+37 authors] ...,
Son Pham
Thomas M. Keane
Duncan T. Odom
Paul Flicek

First Published March 21, 2018

Assembly and analysis of 100 full MHC haplotypes from the Danish population

Jacob M. Jensen
Palle Villesen
Rune M. Friborg
Thomas Mailund
Søren Besenbacher
Mikkel H. Schierup Lasse Maretty Jacob Malte Jensen Bent Petersen Jonas Andreas Sibbesen Siyang Liu Palle Villesen Laurits Skov Kirstine Belling Christian Theil Have Jose M.G. Izarzugaza Marie Grosjean Jette Bork-Jensen Jakob Grove Thomas D. Als Shujia Huang Yuqi Chang Ruiqi Xu Weijian Ye Junhua Rao Xiaosen Guo Jihua Sun Hongzhi Cao Chen Ye Johan v Beusekom Thomas Espeseth Esben Flindt Rune M. Friborg Anders E. Halager Stephanie Le Hellard Christina M. Hultman Francesco Lescai Shengting Li Ole Lund Peter Løngren Thomas Mailund Maria Luisa Matey-Hernandez Ole Mors Christian N.S. Pedersen Thomas Sicheritz-Pontén Patrick Sullivan Ali Syed David Westergaard Rachita Yadav Ning Li Xun Xu Torben Hansen Anders Krogh Lars Bolund Thorkild I.A. Sørensen Oluf Pedersen Ramneek Gupta Simon Rasmussen Søren Besenbacher Anders D. Børglum Jun Wang
... [+56 authors] ...,
Hans Eiberg
Karsten Kristiansen
Søren Brunak
Mikkel Heide Schierup

First Published August 3, 2017

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Valerie A. Schneider
Tina Graves-Lindsay
Kerstin Howe
Nathan Bouk
Hsiu-Chuan Chen
Paul A. Kitts Terence D. Murphy Kim D. Pruitt Françoise Thibaud-Nissen Derek Albracht Robert S. Fulton Milinn Kremitzki Vincent Magrini Chris Markovic Sean McGrath Karyn Meltz Steinberg Kate Auger William Chow Joanna Collins Glenn Harden Timothy Hubbard Sarah Pelan Jared T. Simpson Glen Threadgold James Torrance Jonathan M. Wood Laura Clarke Sergey Koren Matthew Boitano Paul Peluso Heng Li Chen-Shan Chin Adam M. Phillippy Richard Durbin
... [+29 authors] ...,
Richard K. Wilson
Paul Flicek
Evan E. Eichler
Deanna M. Church

First Published April 10, 2017

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Yue Shen
Giovanni Stracquadanio
Yun Wang
Kun Yang
Leslie A. Mitchell
Yaxin Xue Yizhi Cai Tai Chen Jessica S. Dymond Kang Kang Jianhui Gong Xiaofan Zeng Yongfen Zhang Yingrui Li Qiang Feng Xun Xu Jun Wang
... [+12 authors] ...,
Jian Wang
Huanming Yang
Jef D. Boeke
Joel S. Bader

First Published November 13, 2015

The pig X and Y Chromosomes: structure, sequence, and evolution

Benjamin M. Skinner
Carole A. Sargent
Carol Churcher
Toby Hunt
Javier Herrero
Jane E. Loveland Matt Dunn Sandra Louzada Beiyuan Fu William Chow James Gilbert Siobhan Austin-Guest Kathryn Beal Denise Carvalho-Silva William Cheng Daria Gordon Darren Grafham Matt Hardy Jo Harley Heidi Hauser Philip Howden Kerstin Howe Kim Lachani Peter J.I. Ellis Daniel Kelly Giselle Kerry James Kerwin Bee Ling Ng Glen Threadgold Thomas Wileman Jonathan M.D. Wood
... [+26 authors] ...,
Fengtang Yang
Jen Harrow
Nabeel A. Affara
Chris Tyler-Smith

First Published November 11, 2015

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Your search for returned 24 results

Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina

Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding

CodonBERT large language model for mRNA vaccines

Gaps and complex structurally variant loci in phased genome assemblies

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model

Mus caroli and Mus pahari genomes" > Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Assembly and analysis of 100 full MHC haplotypes from the Danish population

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

The pig X and Y Chromosomes: structure, sequence, and evolution

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Your search for returned 24 results