Literature DB >> 23594911

Computational solutions for omics data.

Bonnie Berger1, Jian Peng, Mona Singh.   

Abstract

High-throughput experimental technologies are generating increasingly massive and complex genomic data sets. The sheer enormity and heterogeneity of these data threaten to make the arising problems computationally infeasible. Fortunately, powerful algorithmic techniques lead to software that can answer important biomedical questions in practice. In this Review, we sample the algorithmic landscape, focusing on state-of-the-art techniques, the understanding of which will aid the bench biologist in analysing omics data. We spotlight specific examples that have facilitated and enriched analyses of sequence, transcriptomic and network data sets.

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Year:  2013        PMID: 23594911      PMCID: PMC3966295          DOI: 10.1038/nrg3433

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  163 in total

1.  Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data.

Authors:  Amos Tanay; Roded Sharan; Martin Kupiec; Ron Shamir
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-18       Impact factor: 11.205

Review 2.  Computational methods for transcriptome annotation and quantification using RNA-seq.

Authors:  Manuel Garber; Manfred G Grabherr; Mitchell Guttman; Cole Trapnell
Journal:  Nat Methods       Date:  2011-05-27       Impact factor: 28.547

3.  Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:  Mark B Gerstein; Zhi John Lu; Eric L Van Nostrand; Chao Cheng; Bradley I Arshinoff; Tao Liu; Kevin Y Yip; Rebecca Robilotto; Andreas Rechtsteiner; Kohta Ikegami; Pedro Alves; Aurelien Chateigner; Marc Perry; Mitzi Morris; Raymond K Auerbach; Xin Feng; Jing Leng; Anne Vielle; Wei Niu; Kahn Rhrissorrakrai; Ashish Agarwal; Roger P Alexander; Galt Barber; Cathleen M Brdlik; Jennifer Brennan; Jeremy Jean Brouillet; Adrian Carr; Ming-Sin Cheung; Hiram Clawson; Sergio Contrino; Luke O Dannenberg; Abby F Dernburg; Arshad Desai; Lindsay Dick; Andréa C Dosé; Jiang Du; Thea Egelhofer; Sevinc Ercan; Ghia Euskirchen; Brent Ewing; Elise A Feingold; Reto Gassmann; Peter J Good; Phil Green; Francois Gullier; Michelle Gutwein; Mark S Guyer; Lukas Habegger; Ting Han; Jorja G Henikoff; Stefan R Henz; Angie Hinrichs; Heather Holster; Tony Hyman; A Leo Iniguez; Judith Janette; Morten Jensen; Masaomi Kato; W James Kent; Ellen Kephart; Vishal Khivansara; Ekta Khurana; John K Kim; Paulina Kolasinska-Zwierz; Eric C Lai; Isabel Latorre; Amber Leahey; Suzanna Lewis; Paul Lloyd; Lucas Lochovsky; Rebecca F Lowdon; Yaniv Lubling; Rachel Lyne; Michael MacCoss; Sebastian D Mackowiak; Marco Mangone; Sheldon McKay; Desirea Mecenas; Gennifer Merrihew; David M Miller; Andrew Muroyama; John I Murray; Siew-Loon Ooi; Hoang Pham; Taryn Phippen; Elicia A Preston; Nikolaus Rajewsky; Gunnar Rätsch; Heidi Rosenbaum; Joel Rozowsky; Kim Rutherford; Peter Ruzanov; Mihail Sarov; Rajkumar Sasidharan; Andrea Sboner; Paul Scheid; Eran Segal; Hyunjin Shin; Chong Shou; Frank J Slack; Cindie Slightam; Richard Smith; William C Spencer; E O Stinson; Scott Taing; Teruaki Takasaki; Dionne Vafeados; Ksenia Voronina; Guilin Wang; Nicole L Washington; Christina M Whittle; Beijing Wu; Koon-Kiu Yan; Georg Zeller; Zheng Zha; Mei Zhong; Xingliang Zhou; Julie Ahringer; Susan Strome; Kristin C Gunsalus; Gos Micklem; X Shirley Liu; Valerie Reinke; Stuart K Kim; LaDeana W Hillier; Steven Henikoff; Fabio Piano; Michael Snyder; Lincoln Stein; Jason D Lieb; Robert H Waterston
Journal:  Science       Date:  2010-12-22       Impact factor: 47.728

4.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

5.  ARACHNE: a whole-genome shotgun assembler.

Authors:  Serafim Batzoglou; David B Jaffe; Ken Stanley; Jonathan Butler; Sante Gnerre; Evan Mauceli; Bonnie Berger; Jill P Mesirov; Eric S Lander
Journal:  Genome Res       Date:  2002-01       Impact factor: 9.043

6.  Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins.

Authors:  Eric T Wang; Neal A L Cody; Sonali Jog; Michela Biancolella; Thomas T Wang; Daniel J Treacy; Shujun Luo; Gary P Schroth; David E Housman; Sita Reddy; Eric Lécuyer; Christopher B Burge
Journal:  Cell       Date:  2012-08-17       Impact factor: 41.582

7.  Reactome: a database of reactions, pathways and biological processes.

Authors:  David Croft; Gavin O'Kelly; Guanming Wu; Robin Haw; Marc Gillespie; Lisa Matthews; Michael Caudy; Phani Garapati; Gopal Gopinath; Bijay Jassal; Steven Jupe; Irina Kalatskaya; Shahana Mahajan; Bruce May; Nelson Ndegwa; Esther Schmidt; Veronica Shamovsky; Christina Yung; Ewan Birney; Henning Hermjakob; Peter D'Eustachio; Lincoln Stein
Journal:  Nucleic Acids Res       Date:  2010-11-09       Impact factor: 16.971

Review 8.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

9.  Architecture of the human regulatory network derived from ENCODE data.

Authors:  Mark B Gerstein; Anshul Kundaje; Manoj Hariharan; Stephen G Landt; Koon-Kiu Yan; Chao Cheng; Xinmeng Jasmine Mu; Ekta Khurana; Joel Rozowsky; Roger Alexander; Renqiang Min; Pedro Alves; Alexej Abyzov; Nick Addleman; Nitin Bhardwaj; Alan P Boyle; Philip Cayting; Alexandra Charos; David Z Chen; Yong Cheng; Declan Clarke; Catharine Eastman; Ghia Euskirchen; Seth Frietze; Yao Fu; Jason Gertz; Fabian Grubert; Arif Harmanci; Preti Jain; Maya Kasowski; Phil Lacroute; Jing Jane Leng; Jin Lian; Hannah Monahan; Henriette O'Geen; Zhengqing Ouyang; E Christopher Partridge; Dorrelyn Patacsil; Florencia Pauli; Debasish Raha; Lucia Ramirez; Timothy E Reddy; Brian Reed; Minyi Shi; Teri Slifer; Jing Wang; Linfeng Wu; Xinqiong Yang; Kevin Y Yip; Gili Zilberman-Schapira; Serafim Batzoglou; Arend Sidow; Peggy J Farnham; Richard M Myers; Sherman M Weissman; Michael Snyder
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

10.  Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks.

Authors:  Tom Michoel; Riet De Smet; Anagha Joshi; Yves Van de Peer; Kathleen Marchal
Journal:  BMC Syst Biol       Date:  2009-05-07
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  92 in total

1.  PheNetic: network-based interpretation of molecular profiling data.

Authors:  Dries De Maeyer; Bram Weytjens; Joris Renkens; Luc De Raedt; Kathleen Marchal
Journal:  Nucleic Acids Res       Date:  2015-04-15       Impact factor: 16.971

2.  Compressive mapping for next-generation sequencing.

Authors:  Deniz Yorukoglu; Yun William Yu; Jian Peng; Bonnie Berger
Journal:  Nat Biotechnol       Date:  2016-04       Impact factor: 54.908

3.  Application guide for omics approaches to cell signaling.

Authors:  Zhong Yao; Julia Petschnigg; Robin Ketteler; Igor Stagljar
Journal:  Nat Chem Biol       Date:  2015-05-15       Impact factor: 15.040

4.  Quality score compression improves genotyping accuracy.

Authors:  Y William Yu; Deniz Yorukoglu; Jian Peng; Bonnie Berger
Journal:  Nat Biotechnol       Date:  2015-03       Impact factor: 54.908

5.  Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.

Authors:  Elizabeth Brunk; Roger L Chang; Jing Xia; Hooman Hefzi; James T Yurkovich; Donghyuk Kim; Evan Buckmiller; Harris H Wang; Byung-Kwan Cho; Chen Yang; Bernhard O Palsson; George M Church; Nathan E Lewis
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-09       Impact factor: 11.205

6.  Right ventricular long noncoding RNA expression in human heart failure.

Authors:  Thomas G Di Salvo; Yan Guo; Yan Ru Su; Travis Clark; Evan Brittain; Tarek Absi; Simon Maltais; Anna Hemnes
Journal:  Pulm Circ       Date:  2015-03       Impact factor: 3.017

7.  A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803.

Authors:  Timo R Maarleveld; Joost Boele; Frank J Bruggeman; Bas Teusink
Journal:  Plant Physiol       Date:  2014-01-08       Impact factor: 8.340

Review 8.  Collection, integration and analysis of cancer genomic profiles: from data to insight.

Authors:  Jianjiong Gao; Giovanni Ciriello; Chris Sander; Nikolaus Schultz
Journal:  Curr Opin Genet Dev       Date:  2014-02-27       Impact factor: 5.578

Review 9.  Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics.

Authors:  Eleni Stylianou
Journal:  Mol Diagn Ther       Date:  2018-02       Impact factor: 4.074

Review 10.  WONOEP appraisal: new genetic approaches to study epilepsy.

Authors:  Elsa Rossignol; Katja Kobow; Michele Simonato; Jeffrey A Loeb; Thierry Grisar; Krista L Gilby; Jonathan Vinet; Shilpa D Kadam; Albert J Becker
Journal:  Epilepsia       Date:  2014-06-25       Impact factor: 5.864

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