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spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model

  • Tianyu Liu
  • Tinglin Huang
  • Wengong Jin
  • Tinyi Chu
  • Rex Ying
  • Hongyu Zhao
  • First Published February 3, 2026

Epigenetic and evolutionary features of ape subterminal heterochromatin

  • DongAhn Yoo
  • Katherine M. Munson
  • Evan E. Eichler
  • First Published October 22, 2025

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

  • Chong Li
  • Marc Jan Bonder
  • Sabriya Syed
  • Matthew Jensen
  • Mark B. Gerstein
  • Michael C. Zody Mark J.P. Chaisson Michael E. Talkowski Tobias Marschall
  • ... [+4 authors] ...,
  • Jan O. Korbel
  • Evan E. Eichler
  • Charles Lee
  • Xinghua Shi
  • First Published December 5, 2024

High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation

  • Jonas A. Gustafson
  • Sophia B. Gibson
  • Nikhita Damaraju
  • Miranda P.G. Zalusky
  • Kendra Hoekzema
  • David Twesigomwe Lei Yang Anthony A. Snead Phillip A. Richmond Wouter De Coster Nathan D. Olson Andrea Guarracino Qiuhui Li Angela L. Miller Joy Goffena Zachary B. Anderson Sophie H.R. Storz Sydney A. Ward Maisha Sinha Claudia Gonzaga-Jauregui Wayne E. Clarke Anna O. Basile André Corvelo Catherine Reeves Adrienne Helland Rajeeva Lochan Musunuri Mahler Revsine Karynne E. Patterson Cate R. Paschal Christina Zakarian Sara Goodwin Tanner D. Jensen Esther Robb William Richard McCombie Fritz J. Sedlazeck Justin M. Zook Stephen B. Montgomery Erik Garrison Mikhail Kolmogorov Michael C. Schatz Richard N. McLaughlin Harriet Dashnow Michael C. Zody
  • ... [+38 authors] ...,
  • Matt Loose
  • Miten Jain
  • Evan E. Eichler
  • Danny E. Miller
  • First Published October 2, 2024

AGAP duplicons associate with structural diversity at Chromosome 10q11.22" > AGAP duplicons associate with structural diversity at Chromosome 10q11.22

  • Stefania Fornezza
  • Vincenza Simona Delvecchio
  • William T. Harvey
  • Philip C. Dishuck
  • Evan E. Eichler
  • Giuliana Giannuzzi
  • First Published September 25, 2024

TBC1D3 gene family in humans" > Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans

  • Xavi Guitart
  • David Porubsky
  • DongAhn Yoo
  • Max L. Dougherty
  • Philip C. Dishuck
  • Katherine M. Munson Alexandra P. Lewis Kendra Hoekzema
  • ... [+3 authors] ...,
  • Jordan Knuth
  • Stephen Chang
  • Tomi Pastinen
  • Evan E. Eichler
  • First Published August 6, 2024

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

  • Ryan Lorig-Roach
  • Melissa Meredith
  • Jean Monlong
  • Miten Jain
  • Hugh E. Olsen
  • Brandy McNulty David Porubsky Tessa G. Montague Julian K. Lucas Chris Condon Jordan M. Eizenga Sissel Juul Sean K. McKenzie Sara E. Simmonds Jimin Park Mobin Asri Sergey Koren Evan E. Eichler Richard Axel
  • ... [+14 authors] ...,
  • Bruce Martin
  • Paolo Carnevali
  • Karen H. Miga
  • Benedict Paten
  • First Published April 16, 2024

Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall

  • William T. Harvey
  • Peter Ebert
  • Jana Ebler
  • Peter A. Audano
  • Katherine M. Munson
  • Kendra Hoekzema David Porubsky
  • ... [+2 authors] ...,
  • Christine R. Beck
  • Tobias Marschall
  • Kiran Garimella
  • Evan E. Eichler
  • First Published December 7, 2023

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

C. Thomas Caskey (1938–2022)

  • Richard A. Gibbs
  • Aravinda Chakravarti
  • Evan E. Eichler
  • Eric D. Green
  • Richard M. Myers
  • Anne C. Ferguson-Smith
  • Kateryna D. Makova
  • Hillary E. Sussman
  • First Published February 17, 2022
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