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Method

Multiplexed long-read plasmid validation and analysis using OnRamp

  • Camille Mumm
  • Melissa L. Drexel
  • Torrin L. McDonald
  • Adam G. Diehl
  • Jessica A. Switzenberg
  • Alan P. Boyle
  • First Published May 8, 2023
Method

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence

  • Ningxin Ouyang
  • Alan P. Boyle
  • First Published July 6, 2020
Resource

Toward the human cellular microRNAome

  • Matthew N. McCall
  • Min-Sik Kim
  • Mohammed Adil
  • Arun H. Patil
  • Yin Lu
  • Christopher J. Mitchell Pamela Leal-Rojas Jinchong Xu Manoj Kumar Valina L. Dawson Ted M. Dawson Alexander S. Baras Avi Z. Rosenberg
  • ... [+8 authors] ...,
  • Dan E. Arking
  • Kathleen H. Burns
  • Akhilesh Pandey
  • Marc K. Halushka
  • First Published September 6, 2017
Method

Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

  • T.S. Keshava Prasad
  • Ajeet Kumar Mohanty
  • Manish Kumar
  • Sreelakshmi K. Sreenivasamurthy
  • Gourav Dey
  • Raja Sekhar Nirujogi Sneha M. Pinto Anil K. Madugundu Arun H. Patil Jayshree Advani Srikanth S. Manda Manoj Kumar Gupta Sutopa B. Dwivedi Dhanashree S. Kelkar Brantley Hall Xiaofang Jiang Ashley Peery Pavithra Rajagopalan Soujanya D. Yelamanchi Hitendra S. Solanki Remya Raja Gajanan J. Sathe Sandip Chavan Renu Verma Krishna M. Patel Ankit P. Jain Nazia Syed Keshava K. Datta Aafaque Ahmed Khan Manjunath Dammalli Savita Jayaram Aneesha Radhakrishnan Christopher J. Mitchell Chan-Hyun Na Nirbhay Kumar Photini Sinnis Igor V. Sharakhov Charles Wang
  • ... [+33 authors] ...,
  • Harsha Gowda
  • Zhijian Tu
  • Ashwani Kumar
  • Akhilesh Pandey
  • First Published November 15, 2016
Resource

Annotation of functional variation in personal genomes using RegulomeDB

  • Alan P. Boyle
  • Eurie L. Hong
  • Manoj Hariharan
  • Yong Cheng
  • Marc A. Schaub
  • Maya Kasowski Konrad J. Karczewski Julie Park
  • ... [+3 authors] ...,
  • Benjamin C. Hitz
  • Shuai Weng
  • J. Michael Cherry
  • Michael Snyder
  • First Published September 5, 2012
Method

Linking disease associations with regulatory information in the human genome

  • Marc A. Schaub
  • Alan P. Boyle
  • Anshul Kundaje
  • Serafim Batzoglou
  • Michael Snyder
  • First Published September 5, 2012
Resource

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

  • Lingyun Song
  • Zhancheng Zhang
  • Linda L. Grasfeder
  • Alan P. Boyle
  • Paul G. Giresi
  • Bum-Kyu Lee Nathan C. Sheffield Stefan Gräf Mikael Huss Damian Keefe Zheng Liu Darin London Ryan M. McDaniell Yoichiro Shibata Kimberly A. Showers Jeremy M. Simon Teresa Vales Tianyuan Wang Deborah Winter Zhuzhu Zhang Neil D. Clarke Ewan Birney
  • ... [+17 authors] ...,
  • Vishwanath R. Iyer
  • Gregory E. Crawford
  • Jason D. Lieb
  • Terrence S. Furey
  • First Published July 12, 2011
Method

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

  • Alan P. Boyle
  • Lingyun Song
  • Bum-Kyu Lee
  • Darin London
  • Damian Keefe
  • Ewan Birney
  • Vishwanath R. Iyer
  • Gregory E. Crawford
  • Terrence S. Furey
  • First Published November 24, 2010
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