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Method

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

  • Jean Fan
  • Hae-Ock Lee
  • Soohyun Lee
  • Da-eun Ryu
  • Semin Lee
  • Catherine Xue Seok Jin Kim Kihyun Kim
  • ... [+3 authors] ...,
  • Nikolaos Barkas
  • Peter J. Park
  • Woong-Yang Park
  • Peter V. Kharchenko
  • First Published June 13, 2018
Research

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia

  • Lili Wang
  • Jean Fan
  • Joshua M. Francis
  • George Georghiou
  • Sarah Hergert
  • Shuqiang Li Rutendo Gambe Chensheng W. Zhou Chunxiao Yang Sheng Xiao Paola Dal Cin Michaela Bowden Dylan Kotliar Sachet A. Shukla Jennifer R. Brown Donna Neuberg Dario R. Alessi
  • ... [+12 authors] ...,
  • Cheng-Zhong Zhang
  • Peter V. Kharchenko
  • Kenneth J. Livak
  • Catherine J. Wu
  • First Published July 5, 2017
Resource

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

  • Stephen G. Landt
  • Georgi K. Marinov
  • Anshul Kundaje
  • Pouya Kheradpour
  • Florencia Pauli
  • Serafim Batzoglou Bradley E. Bernstein Peter Bickel James B. Brown Philip Cayting Yiwen Chen Gilberto DeSalvo Charles Epstein Katherine I. Fisher-Aylor Ghia Euskirchen Mark Gerstein Jason Gertz Alexander J. Hartemink Michael M. Hoffman Vishwanath R. Iyer Youngsook L. Jung Subhradip Karmakar Manolis Kellis Peter V. Kharchenko Qunhua Li Tao Liu X. Shirley Liu Lijia Ma Aleksandar Milosavljevic Richard M. Myers Peter J. Park Michael J. Pazin Marc D. Perry Debasish Raha Timothy E. Reddy Joel Rozowsky Noam Shoresh Arend Sidow Matthew Slattery John A. Stamatoyannopoulos Michael Y. Tolstorukov Kevin P. White Simon Xi
  • ... [+38 authors] ...,
  • Peggy J. Farnham
  • Jason D. Lieb
  • Barbara J. Wold
  • Michael Snyder
  • First Published September 5, 2012
Research

Drosophila genome" > Nature and function of insulator protein binding sites in the Drosophila genome

  • Yuri B. Schwartz
  • Daniela Linder-Basso
  • Peter V. Kharchenko
  • Michael Y. Tolstorukov
  • Maria Kim
  • Hua-Bing Li Andrey A. Gorchakov Aki Minoda Gregory Shanower Artyom A. Alekseyenko Nicole C. Riddle Youngsook L. Jung Tingting Gu Annette Plachetka Sarah C.R. Elgin Mitzi I. Kuroda
  • ... [+11 authors] ...,
  • Peter J. Park
  • Mikhail Savitsky
  • Gary H. Karpen
  • Vincenzo Pirrotta
  • First Published July 5, 2012
Research

Drosophila heterochromatin" > Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

  • Nicole C. Riddle
  • Aki Minoda
  • Peter V. Kharchenko
  • Artyom A. Alekseyenko
  • Yuri B. Schwartz
  • Michael Y. Tolstorukov Andrey A. Gorchakov Jacob D. Jaffe Cameron Kennedy Daniela Linder-Basso Sally E. Peach Gregory Shanower Haiyan Zheng Mitzi I. Kuroda
  • ... [+9 authors] ...,
  • Vincenzo Pirrotta
  • Peter J. Park
  • Sarah C.R. Elgin
  • Gary H. Karpen
  • First Published December 22, 2010
Research

Drosophila replication program" > Chromatin signatures of the Drosophila replication program

  • Matthew L. Eaton
  • Joseph A. Prinz
  • Heather K. MacAlpine
  • George Tretyakov
  • Peter V. Kharchenko
  • David M. MacAlpine
  • First Published December 22, 2010
Method

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

  • Lukas Chavez
  • Justyna Jozefczuk
  • Christina Grimm
  • Jörn Dietrich
  • Bernd Timmermann
  • Hans Lehrach
  • Ralf Herwig
  • James Adjaye
  • First Published August 27, 2010
Letter

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

  • Andrew L. Hufton
  • Susanne Mathia
  • Helene Braun
  • Udo Georgi
  • Hans Lehrach
  • Martin Vingron
  • Albert J. Poustka
  • Georgia Panopoulou
  • First Published August 24, 2009
Letter

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

  • Michael Y. Tolstorukov
  • Peter V. Kharchenko
  • Joseph A. Goldman
  • Robert E. Kingston
  • Peter J. Park
  • First Published February 26, 2009
LETTER

HOX gene clusters" > Nucleosome positioning in human HOX gene clusters

  • Peter V. Kharchenko
  • Caroline J. Woo
  • Michael Y. Tolstorukov
  • Robert E. Kingston
  • Peter J. Park
  • First Published August 22, 2008
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