Literature DB >> 23929347

Network cleanup.

Babak Alipanahi1, Brendan J Frey.   

Abstract

Mesh：

Year:  2013        PMID： 23929347     DOI： 10.1038/nbt.2657

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  6 in total

1.  Deciphering the splicing code.

Authors:  Yoseph Barash; John A Calarco; Weijun Gao; Qun Pan; Xinchen Wang; Ofer Shai; Benjamin J Blencowe; Brendan J Frey
Journal:  Nature       Date:  2010-05-06       Impact factor: 49.962

2.  Cytoscape Web: an interactive web-based network browser.

Authors:  Christian T Lopes; Max Franz; Farzana Kazi; Sylva L Donaldson; Quaid Morris; Gary D Bader
Journal:  Bioinformatics       Date:  2010-07-23       Impact factor: 6.937

3.  A compendium of RNA-binding motifs for decoding gene regulation.

Authors:  Debashish Ray; Hilal Kazan; Kate B Cook; Matthew T Weirauch; Hamed S Najafabadi; Xiao Li; Serge Gueroussov; Mihai Albu; Hong Zheng; Ally Yang; Hong Na; Manuel Irimia; Leah H Matzat; Ryan K Dale; Sarah A Smith; Christopher A Yarosh; Seth M Kelly; Behnam Nabet; Desirea Mecenas; Weimin Li; Rakesh S Laishram; Mei Qiao; Howard D Lipshitz; Fabio Piano; Anita H Corbett; Russ P Carstens; Brendan J Frey; Richard A Anderson; Kristen W Lynch; Luiz O F Penalva; Elissa P Lei; Andrew G Fraser; Benjamin J Blencowe; Quaid D Morris; Timothy R Hughes
Journal:  Nature       Date:  2013-07-11       Impact factor: 49.962

4.  Network deconvolution as a general method to distinguish direct dependencies in networks.

Authors:  Soheil Feizi; Daniel Marbach; Muriel Médard; Manolis Kellis
Journal:  Nat Biotechnol       Date:  2013-07-14       Impact factor: 54.908

5.  Network link prediction by global silencing of indirect correlations.

Authors:  Baruch Barzel; Albert-László Barabási
Journal:  Nat Biotechnol       Date:  2013-07-14       Impact factor: 54.908

6.  Wisdom of crowds for robust gene network inference.

Authors:  Daniel Marbach; James C Costello; Robert Küffner; Nicole M Vega; Robert J Prill; Diogo M Camacho; Kyle R Allison; Manolis Kellis; James J Collins; Gustavo Stolovitzky
Journal:  Nat Methods       Date:  2012-07-15       Impact factor: 28.547
  6 in total
  11 in total

1.  Part mutual information for quantifying direct associations in networks.

Authors:  Juan Zhao; Yiwei Zhou; Xiujun Zhang; Luonan Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2016-04-18       Impact factor: 11.205

2.  Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks.

Authors:  Xiujun Zhang; Juan Zhao; Jin-Kao Hao; Xing-Ming Zhao; Luonan Chen
Journal:  Nucleic Acids Res       Date:  2014-12-24       Impact factor: 16.971

3.  Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis.

Authors:  Chuang Ma; Mingming Xin; Kenneth A Feldmann; Xiangfeng Wang
Journal:  Plant Cell       Date:  2014-02-11       Impact factor: 11.277

4.  Experimental noise cutoff boosts inferability of transcriptional networks in large-scale gene-deletion studies.

Authors:  C F Blum; N Heramvand; A S Khonsari; M Kollmann
Journal:  Nat Commun       Date:  2018-01-09       Impact factor: 14.919

5.  A two-step framework for inferring direct protein-protein interaction network from AP-MS data.

Authors:  Bo Tian; Can Zhao; Feiyang Gu; Zengyou He
Journal:  BMC Syst Biol       Date:  2017-09-21

6.  NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples.

Authors:  Hua Yu; Bingke Jiao; Lu Lu; Pengfei Wang; Shuangcheng Chen; Chengzhi Liang; Wei Liu
Journal:  PLoS One       Date:  2018-02-09       Impact factor: 3.240

7.  Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius.

Authors:  Shilai Xing; Chengcheng Tao; Zhihong Song; Wei Liu; Juan Yan; Lifang Kang; Cong Lin; Tao Sang
Journal:  Plant Mol Biol       Date:  2018-07-13       Impact factor: 4.076

8.  MIDER: network inference with mutual information distance and entropy reduction.

Authors:  Alejandro F Villaverde; John Ross; Federico Morán; Julio R Banga
Journal:  PLoS One       Date:  2014-05-07       Impact factor: 3.240

9.  Differential network analysis from cross-platform gene expression data.

Authors:  Xiao-Fei Zhang; Le Ou-Yang; Xing-Ming Zhao; Hong Yan
Journal:  Sci Rep       Date:  2016-09-28       Impact factor: 4.379

10.  The Distance Precision Matrix: computing networks from non-linear relationships.

Authors:  Mahsa Ghanbari; Julia Lasserre; Martin Vingron
Journal:  Bioinformatics       Date:  2019-03-15       Impact factor: 6.937
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