Literature DB >> 22205509

GeneProf: analysis of high-throughput sequencing experiments.

Florian Halbritter, Harsh J Vaidya, Simon R Tomlinson.   

Abstract

Mesh：

Year:  2011        PMID： 22205509     DOI： 10.1038/nmeth.1809

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  8 in total

1.  Repeatability of published microarray gene expression analyses.

Authors:  John P A Ioannidis; David B Allison; Catherine A Ball; Issa Coulibaly; Xiangqin Cui; Aedín C Culhane; Mario Falchi; Cesare Furlanello; Laurence Game; Giuseppe Jurman; Jon Mangion; Tapan Mehta; Michael Nitzberg; Grier P Page; Enrico Petretto; Vera van Noort
Journal:  Nat Genet       Date:  2008-01-28       Impact factor: 38.330

2.  Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.

Authors:  Mitchell Guttman; Manuel Garber; Joshua Z Levin; Julie Donaghey; James Robinson; Xian Adiconis; Lin Fan; Magdalena J Koziol; Andreas Gnirke; Chad Nusbaum; John L Rinn; Eric S Lander; Aviv Regev
Journal:  Nat Biotechnol       Date:  2010-05-02       Impact factor: 54.908

3.  Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells.

Authors:  Alexander Marson; Stuart S Levine; Megan F Cole; Garrett M Frampton; Tobias Brambrink; Sarah Johnstone; Matthew G Guenther; Wendy K Johnston; Marius Wernig; Jamie Newman; J Mauro Calabrese; Lucas M Dennis; Thomas L Volkert; Sumeet Gupta; Jennifer Love; Nancy Hannett; Phillip A Sharp; David P Bartel; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2008-08-08       Impact factor: 41.582

4.  Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

Authors:  Xi Chen; Han Xu; Ping Yuan; Fang Fang; Mikael Huss; Vinsensius B Vega; Eleanor Wong; Yuriy L Orlov; Weiwei Zhang; Jianming Jiang; Yuin-Han Loh; Hock Chuan Yeo; Zhen Xuan Yeo; Vipin Narang; Kunde Ramamoorthy Govindarajan; Bernard Leong; Atif Shahab; Yijun Ruan; Guillaume Bourque; Wing-Kin Sung; Neil D Clarke; Chia-Lin Wei; Huck-Hui Ng
Journal:  Cell       Date:  2008-06-13       Impact factor: 41.582

5.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors:  Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal:  Genome Biol       Date:  2010-08-25       Impact factor: 13.583

6.  The $1,000 genome, the $100,000 analysis?

Authors:  Elaine R Mardis
Journal:  Genome Med       Date:  2010-11-26       Impact factor: 11.117

7.  Taverna: a tool for building and running workflows of services.

Authors:  Duncan Hull; Katy Wolstencroft; Robert Stevens; Carole Goble; Mathew R Pocock; Peter Li; Tom Oinn
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

8.  Sharing detailed research data is associated with increased citation rate.

Authors:  Heather A Piwowar; Roger S Day; Douglas B Fridsma
Journal:  PLoS One       Date:  2007-03-21       Impact factor: 3.240
  8 in total
  49 in total

1.  RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.

Authors:  Alessandro La Ferlita; Salvatore Alaimo; Sebastiano Di Bella; Emanuele Martorana; Georgios I Laliotis; Francesco Bertoni; Luciano Cascione; Philip N Tsichlis; Alfredo Ferro; Roberta Bosotti; Alfredo Pulvirenti
Journal:  BMC Bioinformatics       Date:  2021-06-03       Impact factor: 3.169

Review 2.  Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.

Authors:  Anton Nekrutenko; James Taylor
Journal:  Nat Rev Genet       Date:  2012-09       Impact factor: 53.242

3.  Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network.

Authors:  Nicola Festuccia; Agnès Dubois; Sandrine Vandormael-Pournin; Elena Gallego Tejeda; Adrien Mouren; Sylvain Bessonnard; Florian Mueller; Caroline Proux; Michel Cohen-Tannoudji; Pablo Navarro
Journal:  Nat Cell Biol       Date:  2016-10-10       Impact factor: 28.824

4.  Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure.

Authors:  Fayaz Seifuddin; Gary Wand; Olivia Cox; Mehdi Pirooznia; Laura Moody; Xiaoju Yang; Jonathan Tai; Gretha Boersma; Kellie Tamashiro; Peter Zandi; Richard Lee
Journal:  Epigenetics       Date:  2017-05-30       Impact factor: 4.528

5.  Circadian behavior is light-reprogrammed by plastic DNA methylation.

Authors:  Abdelhalim Azzi; Robert Dallmann; Alison Casserly; Hubert Rehrauer; Andrea Patrignani; Bert Maier; Achim Kramer; Steven A Brown
Journal:  Nat Neurosci       Date:  2014-02-16       Impact factor: 24.884

6.  Computational challenges in modeling gene regulatory events.

Authors:  Abhijeet Pataskar; Vijay K Tiwari
Journal:  Transcription       Date:  2016-07-08

7.  An interactive environment for agile analysis and visualization of ChIP-sequencing data.

Authors:  Mads Lerdrup; Jens Vilstrup Johansen; Shuchi Agrawal-Singh; Klaus Hansen
Journal:  Nat Struct Mol Biol       Date:  2016-02-29       Impact factor: 15.369

8.  Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain.

Authors:  Gonzalo H Villarino; Qiwen Hu; Silvia Manrique; Miguel Flores-Vergara; Bhupinder Sehra; Linda Robles; Javier Brumos; Anna N Stepanova; Lucia Colombo; Eva Sundberg; Steffen Heber; Robert G Franks
Journal:  Plant Physiol       Date:  2016-03-16       Impact factor: 8.340

9.  Cyclin-dependent kinase 8 module expression profiling reveals requirement of mediator subunits 12 and 13 for transcription of Serpent-dependent innate immunity genes in Drosophila.

Authors:  Emilia Kuuluvainen; Heini Hakala; Essi Havula; Michelle Sahal Estimé; Mika Rämet; Ville Hietakangas; Tomi P Mäkelä
Journal:  J Biol Chem       Date:  2014-04-28       Impact factor: 5.157

Review 10.  Defining the Clinical Value of a Genomic Diagnosis in the Era of Next-Generation Sequencing.

Authors:  Natasha T Strande; Jonathan S Berg
Journal:  Annu Rev Genomics Hum Genet       Date:  2016-05-26       Impact factor: 8.929
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