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Resource

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

  • Simon Bray
  • John Chilton
  • Matthias Bernt
  • Nicola Soranzo
  • Marius van den Beek
  • Bérénice Batut Helena Rasche
  • ... [+2 authors] ...,
  • Martin Čech
  • Peter J.A. Cock
  • Björn Grüning
  • Anton Nekrutenko
  • First Published February 24, 2023
Method

Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly

  • Ou Wang
  • Robert Chin
  • Xiaofang Cheng
  • Michelle Ka Yan Wu
  • Qing Mao
  • Jingbo Tang Yuhui Sun Ellis Anderson Han K. Lam Dan Chen Yujun Zhou Linying Wang Fei Fan Yan Zou Yinlong Xie Rebecca Yu Zhang Snezana Drmanac Darlene Nguyen Chongjun Xu Christian Villarosa Scott Gablenz Nina Barua Staci Nguyen Wenlan Tian Jia Sophie Liu Jingwan Wang Xiao Liu Xiaojuan Qi Ao Chen He Wang Yuliang Dong Wenwei Zhang Andrei Alexeev Huanming Yang Jian Wang
  • ... [+30 authors] ...,
  • Karsten Kristiansen
  • Xun Xu
  • Radoje Drmanac
  • Brock A. Peters
  • First Published April 2, 2019
Research

RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA

  • Dan Bar-Yaacov
  • Gal Avital
  • Liron Levin
  • Allison L. Richards
  • Naomi Hachen
  • Boris Rebolledo Jaramillo
  • Anton Nekrutenko
  • Raz Zarivach
  • Dan Mishmar
  • First Published August 2, 2013
Resource

Windshield splatter analysis with the Galaxy metagenomic pipeline

  • Sergei Kosakovsky Pond
  • Samir Wadhawan
  • Francesca Chiaromonte
  • Guruprasad Ananda
  • Wen-Yu Chung
  • James Taylor
  • Anton Nekrutenko
  • First Published October 9, 2009
RESOURCE

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

  • Webb Miller
  • Kate Rosenbloom
  • Ross C. Hardison
  • Minmei Hou
  • James Taylor
  • Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
  • ... [+17 authors] ...,
  • Eric S. Lander
  • Adam Siepel
  • David Haussler
  • W. James Kent
  • First Published November 5, 2007
RESOURCE

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

  • Daniel Blankenberg
  • James Taylor
  • Ian Schenck
  • Jianbin He
  • Yi Zhang
  • Matthew Ghent Narayanan Veeraraghavan Istvan Albert
  • ... [+3 authors] ...,
  • Webb Miller
  • Kateryna D. Makova
  • Ross C. Hardison
  • Anton Nekrutenko
  • First Published June 13, 2007
RESOURCE

Galaxy: A platform for interactive large-scale genome analysis

  • Belinda Giardine
  • Cathy Riemer
  • Ross C. Hardison
  • Richard Burhans
  • Laura Elnitski
  • Prachi Shah Yi Zhang Daniel Blankenberg Istvan Albert
  • ... [+4 authors] ...,
  • James Taylor
  • Webb Miller
  • W. James Kent
  • Anton Nekrutenko
  • First Published September 16, 2005
RESOURCE

High-Density Rat Radiation Hybrid Maps Containing Over 24,000 SSLPs, Genes, and ESTs Provide a Direct Link to the Rat Genome Sequence

  • Anne E. Kwitek
  • Jo Gullings-Handley
  • Jiaming Yu
  • Danilo C. Carlos
  • Kimberly Orlebeke
  • Jeff Nie Jeffrey Eckert Angela Lemke Jaime Wendt Andrae Susan Bromberg Dean Pasko Dan Chen Todd E. Scheetz Thomas L. Casavant
  • ... [+9 authors] ...,
  • M. Bento Soares
  • Val C. Sheffield
  • Peter J. Tonellato
  • Howard J. Jacob
  • First Published April 1, 2004
Methods

Integrative Genomics: In Silico Coupling of Rat Physiology and Complex Traits With Mouse and Human Data

  • Simon N. Twigger
  • Jeff Nie
  • Victor Ruotti
  • Jiaming Yu
  • Dan Chen
  • Dawei Li Jed Mathis Vijay Narayanasamy Gopal R. Gopinath Dean Pasko Mary Shimoyama Norberto de la Cruz
  • ... [+7 authors] ...,
  • Susan Bromberg
  • Anne E. Kwitek
  • Howard J. Jacob
  • Peter J. Tonellato
  • First Published April 1, 2004
LETTER

Signatures of Domain Shuffling in the Human Genome

  • Henrik Kaessmann
  • Sebastian Zöllner
  • Anton Nekrutenko
  • Wen-Hsiung Li
  • First Published November 1, 2002
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