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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
Research

RET regulatory code is disrupted in Hirschsprung disease" > A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease

  • Sumantra Chatterjee
  • Kameko M. Karasaki
  • Lauren E. Fries
  • Ashish Kapoor
  • Aravinda Chakravarti
  • First Published November 15, 2021
Method

Sequence-based correction of barcode bias in massively parallel reporter assays

  • Dongwon Lee
  • Ashish Kapoor
  • Changhee Lee
  • Michael Mudgett
  • Michael A. Beer
  • Aravinda Chakravarti
  • First Published July 20, 2021
Research

Complex mosaic structural variations in human fetal brains

  • Shobana Sekar
  • Livia Tomasini
  • Christos Proukakis
  • Taejeong Bae
  • Logan Manlove
  • Yeongjun Jang Soraya Scuderi Bo Zhou Maria Kalyva Anahita Amiri Jessica Mariani
  • ... [+6 authors] ...,
  • Fritz J. Sedlazeck
  • Alexander E. Urban
  • Flora M. Vaccarino
  • Alexej Abyzov
  • First Published October 29, 2020
Method

cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants" > Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants

  • Dongwon Lee
  • Ashish Kapoor
  • Alexias Safi
  • Lingyun Song
  • Marc K. Halushka
  • Gregory E. Crawford
  • Aravinda Chakravarti
  • First Published August 23, 2018
Research

TERT aberrations in acral melanoma" > Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma

  • Winnie S. Liang
  • William Hendricks
  • Jeffrey Kiefer
  • Jessica Schmidt
  • Shobana Sekar
  • John Carpten David W. Craig Jonathan Adkins Lori Cuyugan Zarko Manojlovic Rebecca F. Halperin Adrienne Helland Sara Nasser Christophe Legendre Laurence H. Hurley Karthigayini Sivaprakasam Douglas B. Johnson Holly Crandall Klaus J. Busam Victoria Zismann Valerie Deluca Jeeyun Lee
  • ... [+17 authors] ...,
  • Aleksandar Sekulic
  • Charlotte E. Ariyan
  • Jeffrey Sosman
  • Jeffrey Trent
  • First Published April 3, 2017
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
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