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Resource

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

  • Guanjue Xiang
  • Xi He
  • Belinda M. Giardine
  • Kathryn J. Isaac
  • Dylan J. Taylor
  • Rajiv C. McCoy Camden Jansen Cheryl A. Keller Alexander Q. Wixom April Cockburn Amber Miller Qian Qi Yanghua He Yichao Li Jens Lichtenberg Elisabeth F. Heuston Stacie M. Anderson Jing Luan Marit W. Vermunt Feng Yue Michael E.G. Sauria Michael C. Schatz James Taylor Berthold Göttgens Jim R. Hughes Douglas R. Higgs Mitchell J. Weiss Yong Cheng Gerd A. Blobel David M. Bodine
  • ... [+25 authors] ...,
  • Yu Zhang
  • Qunhua Li
  • Shaun Mahony
  • Ross C. Hardison
  • First Published July 1, 2024
Research

Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling

  • Yichen Hu
  • Amnon Amir
  • Xiaochang Huang
  • Yan Li
  • Shi Huang
  • Elaine Wolfe
  • Sophie Weiss
  • Rob Knight
  • Zhenjiang Zech Xu
  • First Published June 10, 2022
Method

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

  • Kelly Cochran
  • Divyanshi Srivastava
  • Avanti Shrikumar
  • Akshay Balsubramani
  • Ross C. Hardison
  • Anshul Kundaje
  • Shaun Mahony
  • First Published January 18, 2022
Method

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

  • George Armstrong
  • Kalen Cantrell
  • Shi Huang
  • Daniel McDonald
  • Niina Haiminen
  • Anna Paola Carrieri Qiyun Zhu Antonio Gonzalez Imran McGrath Kristen L. Beck Daniel Hakim Aki S. Havulinna Guillaume Méric Teemu Niiranen Leo Lahti Veikko Salomaa Mohit Jain Michael Inouye Austin D. Swafford
  • ... [+14 authors] ...,
  • Ho-Cheol Kim
  • Laxmi Parida
  • Yoshiki Vázquez-Baeza
  • Rob Knight
  • First Published September 3, 2021
Erratum

Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

  • Zhoutao Chen
  • Long Pham
  • Tsai-Chin Wu
  • Guoya Mo
  • Yu Xia
  • Peter L. Chang Devin Porter Tan Phan Huu Che Hao Tran Vikas Bansal Justin Shaffer Pedro Belda-Ferre Greg Humphrey Rob Knight
  • ... [+10 authors] ...,
  • Pavel Pevzner
  • Son Pham
  • Yong Wang
  • Ming Lei
  • First Published May 3, 2021
Research

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

  • Jonathon L. Baker
  • James T. Morton
  • Márcia Dinis
  • Ruth Alvarez
  • Nini C. Tran
  • Rob Knight
  • Anna Edlund
  • First Published November 25, 2020
Method

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

  • Zhoutao Chen
  • Long Pham
  • Tsai-Chin Wu
  • Guoya Mo
  • Yu Xia
  • Peter L. Chang Devin Porter Tan Phan Huu Che Hao Tran Vikas Bansal Justin Shaffer Pedro Belda-Ferre Greg Humphrey Rob Knight
  • ... [+10 authors] ...,
  • Pavel Pevzner
  • Son Pham
  • Yong Wang
  • Ming Lei
  • First Published June 15, 2020
Resource

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

  • Guanjue Xiang
  • Cheryl A. Keller
  • Elisabeth Heuston
  • Belinda M. Giardine
  • Lin An
  • Alexander Q. Wixom Amber Miller April Cockburn Michael E.G. Sauria Kathryn Weaver Jens Lichtenberg Berthold Göttgens Qunhua Li David Bodine Shaun Mahony James Taylor Gerd A. Blobel Mitchell J. Weiss Yong Cheng Feng Yue
  • ... [+15 authors] ...,
  • Jim Hughes
  • Douglas R. Higgs
  • Yu Zhang
  • Ross C. Hardison
  • First Published March 4, 2020
Resource

Organ-level protein networks as a reference for the host effects of the microbiome

  • Robert H. Mills
  • Jacob M. Wozniak
  • Alison Vrbanac
  • Anaamika Campeau
  • Benoit Chassaing
  • Andrew Gewirtz
  • Rob Knight
  • David J. Gonzalez
  • First Published January 28, 2020
Method

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

  • Tao Yang
  • Feipeng Zhang
  • Galip Gürkan Yardımcı
  • Fan Song
  • Ross C. Hardison
  • William Stafford Noble
  • Feng Yue
  • Qunhua Li
  • First Published August 30, 2017
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