Literature DB >> 27390891

Computational challenges in modeling gene regulatory events.

Abhijeet Pataskar1, Vijay K Tiwari1.   

Abstract

Cellular transcriptional programs driven by genetic and epigenetic mechanisms could be better understood by integrating "omics" data and subsequently modeling the gene-regulatory events. Toward this end, computational biology should keep pace with evolving experimental procedures and data availability. This article gives an exemplified account of the current computational challenges in molecular biology.

Keywords:  epigenetic mechanisms; gene regulation; systems biology; transcription; transcription factors

Mesh：

Year:  2016        PMID： 27390891      PMCID： PMC5066510          DOI： 10.1080/21541264.2016.1204491

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


  44 in total

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Authors:  R David Hawkins; Gary C Hon; Bing Ren
Journal:  Nat Rev Genet       Date:  2010-07       Impact factor: 53.242

2.  GeneProf: analysis of high-throughput sequencing experiments.

Authors:  Florian Halbritter; Harsh J Vaidya; Simon R Tomlinson
Journal:  Nat Methods       Date:  2011-12-28       Impact factor: 28.547

Review 3.  Single-cell epigenomics: techniques and emerging applications.

Authors:  Omer Schwartzman; Amos Tanay
Journal:  Nat Rev Genet       Date:  2015-10-13       Impact factor: 53.242

Review 4.  The model organism as a system: integrating 'omics' data sets.

Authors:  Andrew R Joyce; Bernhard Ø Palsson
Journal:  Nat Rev Mol Cell Biol       Date:  2006-03       Impact factor: 94.444

5.  Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.

Authors:  Sean Whalen; Rebecca M Truty; Katherine S Pollard
Journal:  Nat Genet       Date:  2016-04-04       Impact factor: 38.330

Review 6.  Dynamic regulation of transcriptional states by chromatin and transcription factors.

Authors:  Ty C Voss; Gordon L Hager
Journal:  Nat Rev Genet       Date:  2013-12-17       Impact factor: 53.242

7.  Single-cell ATAC-seq: strength in numbers.

Authors:  Sebastian Pott; Jason D Lieb
Journal:  Genome Biol       Date:  2015-08-21       Impact factor: 13.583

8.  Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.

Authors:  Richard I Sherwood; Tatsunori Hashimoto; Charles W O'Donnell; Sophia Lewis; Amira A Barkal; John Peter van Hoff; Vivek Karun; Tommi Jaakkola; David K Gifford
Journal:  Nat Biotechnol       Date:  2014-01-19       Impact factor: 54.908

Review 9.  Data integration in the era of omics: current and future challenges.

Authors:  David Gomez-Cabrero; Imad Abugessaisa; Dieter Maier; Andrew Teschendorff; Matthias Merkenschlager; Andreas Gisel; Esteban Ballestar; Erik Bongcam-Rudloff; Ana Conesa; Jesper Tegnér
Journal:  BMC Syst Biol       Date:  2014-03-13

Review 10.  Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.

Authors:  Lijing Yao; Benjamin P Berman; Peggy J Farnham
Journal:  Crit Rev Biochem Mol Biol       Date:  2015-10-08       Impact factor: 8.250
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  2 in total

1.  Multiomics Reveals Ectopic ATP Synthase Blockade Induces Cancer Cell Death via a lncRNA-mediated Phospho-signaling Network.

Authors:  Yi-Wen Chang; Chia-Lang Hsu; Cheng-Wei Tang; Xiang-Jun Chen; Hsuan-Cheng Huang; Hsueh-Fen Juan
Journal:  Mol Cell Proteomics       Date:  2020-08-11       Impact factor: 5.911

Review 2.  Application of Precision Medicine in Neurodegenerative Diseases.

Authors:  Claudia Strafella; Valerio Caputo; Maria R Galota; Stefania Zampatti; Gianluca Marella; Silvestro Mauriello; Raffaella Cascella; Emiliano Giardina
Journal:  Front Neurol       Date:  2018-08-23       Impact factor: 4.003
  2 in total

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