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Research

Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T

  • Luis F. Paulin
  • Jeremy Fan
  • Kieran O'Neill
  • Erin Pleasance
  • Vanessa L. Porter
  • Steven J.M. Jones
  • Fritz J. Sedlazeck
  • First Published March 17, 2025
Research

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

  • Vanessa L. Porter
  • Michelle Ng
  • Kieran O'Neill
  • Signe MacLennan
  • Richard D. Corbett
  • Luka Culibrk Zeid Hamadeh Marissa Iden Rachel Schmidt Shirng-Wern Tsaih Carolyn Nakisige Martin Origa Jackson Orem Glenn Chang Jeremy Fan Ka Ming Nip Vahid Akbari Simon K. Chan James Hopkins Richard A. Moore Eric Chuah Karen L. Mungall Andrew J. Mungall
  • ... [+18 authors] ...,
  • Inanc Birol
  • Steven J.M. Jones
  • Janet S. Rader
  • Marco A. Marra
  • First Published December 5, 2024
In memoriam

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
In memoriam

Deborah A. Nickerson (1954 –2021)

  • Aravinda Chakravarti
  • Evan E. Eichler
  • Richard A. Gibbs
  • Eric D. Green
  • Richard M. Myers
  • Hillary E. Sussman
  • First Published January 24, 2022
Resource

D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation

  • Zhen-Xia Chen
  • David Sturgill
  • Jiaxin Qu
  • Huaiyang Jiang
  • Soo Park
  • Nathan Boley Ana Maria Suzuki Anthony R. Fletcher David C. Plachetzki Peter C. FitzGerald Carlo G. Artieri Joel Atallah Olga Barmina James B. Brown Kerstin P. Blankenburg Emily Clough Abhijit Dasgupta Sai Gubbala Yi Han Joy C. Jayaseelan Divya Kalra Yoo-Ah Kim Christie L. Kovar Sandra L. Lee Mingmei Li James D. Malley John H. Malone Tittu Mathew Nicolas R. Mattiuzzo Mala Munidasa Donna M. Muzny Fiona Ongeri Lora Perales Teresa M. Przytycka Ling-Ling Pu Garrett Robinson Rebecca L. Thornton Nehad Saada Steven E. Scherer Harold E. Smith Charles Vinson Crystal B. Warner Kim C. Worley Yuan-Qing Wu Xiaoyan Zou Peter Cherbas Manolis Kellis Michael B. Eisen Fabio Piano Karin Kionte David H. Fitch Paul W. Sternberg Asher D. Cutter Michael O. Duff Roger A. Hoskins Brenton R. Graveley Richard A. Gibbs Peter J. Bickel Artyom Kopp
  • ... [+54 authors] ...,
  • Piero Carninci
  • Susan E. Celniker
  • Brian Oliver
  • Stephen Richards
  • First Published July 1, 2014
Resource

Drosophila cell lines" > Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

  • Jiayu Wen
  • Jaaved Mohammed
  • Diane Bortolamiol-Becet
  • Harrison Tsai
  • Nicolas Robine
  • Jakub O. Westholm Erik Ladewig Qi Dai Katsutomo Okamura Alex S. Flynt Dayu Zhang Justen Andrews Lucy Cherbas
  • ... [+8 authors] ...,
  • Thomas C. Kaufman
  • Peter Cherbas
  • Adam Siepel
  • Eric C. Lai
  • First Published July 1, 2014
Method

Spark: A navigational paradigm for genomic data exploration

  • Cydney B. Nielsen
  • Hamid Younesy
  • Henriette O'Geen
  • Xiaoqin Xu
  • Andrew R. Jackson
  • Aleksandar Milosavljevic Ting Wang
  • ... [+2 authors] ...,
  • Joseph F. Costello
  • Martin Hirst
  • Peggy J. Farnham
  • Steven J.M. Jones
  • First Published September 7, 2012
Research

XIST locus" > Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus

  • Julie E. Horvath
  • Christina B. Sheedy
  • Stephanie L. Merrett
  • Abdoulaye Banire Diallo
  • David L. Swofford
  • NISC Comparative Sequencing Program
  • Eric D. Green
  • Huntington F. Willard
  • First Published April 25, 2011
Resource

Drosophila cell lines" > The transcriptional diversity of 25 Drosophila cell lines

  • Lucy Cherbas
  • Aarron Willingham
  • Dayu Zhang
  • Li Yang
  • Yi Zou
  • Brian D. Eads Joseph W. Carlson Jane M. Landolin Philipp Kapranov Jacqueline Dumais Anastasia Samsonova Jeong-Hyeon Choi Johnny Roberts Carrie A. Davis Haixu Tang Marijke J. van Baren Srinka Ghosh Alexander Dobin Kim Bell Wei Lin Laura Langton Michael O. Duff Aaron E. Tenney Chris Zaleski Michael R. Brent Roger A. Hoskins Thomas C. Kaufman Justen Andrews Brenton R. Graveley
  • ... [+24 authors] ...,
  • Norbert Perrimon
  • Susan E. Celniker
  • Thomas R. Gingeras
  • Peter Cherbas
  • First Published December 22, 2010
Method

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing

  • Jamie K. Teer
  • Lori L. Bonnycastle
  • Peter S. Chines
  • Nancy F. Hansen
  • Natsuyo Aoyama
  • Amy J. Swift Hatice Ozel Abaan Thomas J. Albert Elliott H. Margulies
  • ... [+4 authors] ...,
  • Eric D. Green
  • Francis S. Collins
  • James C. Mullikin
  • Leslie G. Biesecker
  • First Published September 1, 2010
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