Sarath Chandra Janga

Sarath Chandra Janga

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Sarath Chandra Janga

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Human protein-RNA interaction network is highly stable across mammals.

BMC Genomics 2019 Dec 30;20(Suppl 12):1004. Epub 2019 Dec 30.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, 46202, USA.

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http://dx.doi.org/10.1186/s12864-019-6330-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936122PMC
December 2019

SliceIt: A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome.

Methods 2019 Sep 5. Epub 2019 Sep 5.

Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, United States; Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.09.004DOI Listing
September 2019

Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins.

Genes (Basel) 2019 08 6;10(8). Epub 2019 Aug 6.

Department of BioHealth Informatics, School of Informatics and Computing, IUPUI, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.3390/genes10080593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722645PMC
August 2019

A conserved enhancer regulates Il9 expression in multiple lineages.

Nat Commun 2018 11 15;9(1):4803. Epub 2018 Nov 15.

Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.

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http://dx.doi.org/10.1038/s41467-018-07202-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237898PMC
November 2018

Epitranscriptomic Code and Its Alterations in Human Disease.

Trends Mol Med 2018 10 14;24(10):886-903. Epub 2018 Aug 14.

Department of BioHealth Informatics, School of Informatics and Computing, Walker Plaza Building, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Suite 319, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, 975 West Walnut Street, Indianapolis, IN 46202, USA; Centre for Computational Biology and Bioinformatics, 5021 Health Information and Translational Sciences, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN 46202, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molmed.2018.07.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168408PMC
October 2018

Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues.

Exp Eye Res 2018 03 11;168:57-68. Epub 2018 Jan 11.

Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN, 46202, United States. Electronic address:

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http://dx.doi.org/10.1016/j.exer.2018.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826895PMC
March 2018

Mutational landscape of RNA-binding proteins in human cancers.

RNA Biol 2018 01 14;15(1):115-129. Epub 2017 Nov 14.

a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA.

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http://dx.doi.org/10.1080/15476286.2017.1391436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786023PMC
January 2018

Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations.

Sci Rep 2017 09 14;7(1):11572. Epub 2017 Sep 14.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana, 46202, USA.

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http://dx.doi.org/10.1038/s41598-017-10615-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599659PMC
September 2017

Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach.

PLoS One 2016 28;11(7):e0160228. Epub 2016 Jul 28.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana, 46202, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160228PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965051PMC
August 2017

Community-acquired rhinovirus infection is associated with changes in the airway microbiome.

J Allergy Clin Immunol 2017 07 19;140(1):312-315.e8. Epub 2017 Mar 19.

Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis; Department of Medicine, University of Wisconsin-Madison, Madison, Wis.

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http://dx.doi.org/10.1016/j.jaci.2017.01.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496777PMC
July 2017

RNA Editing in Pathogenesis of Cancer.

Cancer Res 2017 07 30;77(14):3733-3739. Epub 2017 Jun 30.

School of Informatics and Computing, Indiana University Purdue University, Indianapolis, Indiana.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0520DOI Listing
July 2017

Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles.

RNA 2017 06 23;23(6):836-846. Epub 2017 Mar 23.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202, USA.

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http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.059089.11
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http://dx.doi.org/10.1261/rna.059089.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5435856PMC
June 2017

Paracrine IL-2 Is Required for Optimal Type 2 Effector Cytokine Production.

J Immunol 2017 06 3;198(11):4352-4359. Epub 2017 May 3.

Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202;

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http://dx.doi.org/10.4049/jimmunol.1601792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470780PMC
June 2017

Differential Expression of miRNAs in Nontumor Liver Tissue of Patients With Hepatocellular Cancer Caused by Nonalcoholic Steatohepatitis Cirrhosis.

Clin Gastroenterol Hepatol 2017 03 22;15(3):465-467. Epub 2016 Oct 22.

Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana. Electronic address:

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http://dx.doi.org/10.1016/j.cgh.2016.10.017DOI Listing
March 2017

Comparative and temporal transcriptome analysis of peste des petits ruminants virus infected goat peripheral blood mononuclear cells.

Virus Res 2017 02 23;229:28-40. Epub 2016 Dec 23.

School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN, 46202, United States. Electronic address:

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http://dx.doi.org/10.1016/j.virusres.2016.12.014DOI Listing
February 2017

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex.

J Mol Biol 2017 01 12;429(2):324-344. Epub 2016 Dec 12.

Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.12.008DOI Listing
January 2017

OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes.

Biomed Res Int 2015 12;2015:318217. Epub 2015 Oct 12.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis (IUPUI), 719 Indiana Avenue, Suite 319, Walker Plaza Building, Indianapolis, IN 46202, USA ; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, USA ; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, USA.

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http://www.hindawi.com/journals/bmri/2015/318217/
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http://dx.doi.org/10.1155/2015/318217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4620388PMC
September 2016

Building integrated ontological knowledge structures with efficient approximation algorithms.

Biomed Res Int 2015 13;2015:501528. Epub 2015 Oct 13.

Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1155/2015/501528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4621328PMC
August 2016

ExSurv: A Web Resource for Prognostic Analyses of Exons Across Human Cancers Using Clinical Transcriptomes.

Cancer Inform 2016 7;15(Suppl 2):17-24. Epub 2016 Aug 7.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, USA.; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), Indianapolis, IN, USA.; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, Indianapolis, IN, USA.

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http://journals.sagepub.com/doi/10.4137/CIN.S39367
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http://dx.doi.org/10.4137/CIN.S39367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976794PMC
August 2016

Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches.

BMC Genomics 2016 08 22;17 Suppl 7:507. Epub 2016 Aug 22.

Department of Bio Health Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IA, 46202, USA.

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http://dx.doi.org/10.1186/s12864-016-2895-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001211PMC
August 2016

RNA-binding proteins in eye development and disease: implication of conserved RNA granule components.

Wiley Interdiscip Rev RNA 2016 07 1;7(4):527-57. Epub 2016 May 1.

Department of Biological Sciences, University of Delaware, Newark, DE, USA.

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http://dx.doi.org/10.1002/wrna.1355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909581PMC
July 2016

Differential miRNA Expression in Cells and Matrix Vesicles in Vascular Smooth Muscle Cells from Rats with Kidney Disease.

PLoS One 2015 26;10(6):e0131589. Epub 2015 Jun 26.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, Indiana, United States of America; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), Indianapolis, Indiana, United States of America; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, Indianapolis, Indiana, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131589PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482652PMC
May 2016

Knowledge Discovery Using Big Data in Biomedical Systems.

IEEE/ACM Trans Comput Biol Bioinform 2015 Jul-Aug;12(4):726-8

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http://dx.doi.org/10.1109/tcbb.2015.2454551DOI Listing
May 2016

Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks.

Sci Rep 2016 05 10;6:25711. Epub 2016 May 10.

Department of Bio Health Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202, USA.

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http://www.nature.com/articles/srep25711
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http://dx.doi.org/10.1038/srep25711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861959PMC
May 2016

Database of RNA binding protein expression and disease dynamics (READ DB).

Database (Oxford) 2015 25;2015:bav072. Epub 2015 Jul 25.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN, 46202, USA, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA, and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN, 46202, USA

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http://dx.doi.org/10.1093/database/bav072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515031PMC
March 2016

The human RBPome: from genes and proteins to human disease.

J Proteomics 2015 Sep 14;127(Pt A):61-70. Epub 2015 May 14.

Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, United States. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S18743919150023
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http://dx.doi.org/10.1016/j.jprot.2015.04.031DOI Listing
September 2015

Expression levels of SF3B3 correlate with prognosis and endocrine resistance in estrogen receptor-positive breast cancer.

Mod Pathol 2015 May 28;28(5):677-85. Epub 2014 Nov 28.

1] Department of Pathology and Laboratory Medicine, Indianapolis, IN, USA [2] Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA [3] Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA.

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http://dx.doi.org/10.1038/modpathol.2014.146DOI Listing
May 2015

Role of lncRNAs in health and disease-size and shape matter.

Brief Funct Genomics 2015 Mar 11;14(2):115-29. Epub 2014 Sep 11.

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http://dx.doi.org/10.1093/bfgp/elu034DOI Listing
March 2015

Uncovering RNA binding proteins associated with age and gender during liver maturation.

Sci Rep 2015 Mar 31;5:9512. Epub 2015 Mar 31.

1] Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202 [2] Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, Indiana, 46202 [3] Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, Indiana, 46202.

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http://dx.doi.org/10.1038/srep09512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379467PMC
March 2015

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance.

ISME J 2014 Dec 18;8(12):2431-44. Epub 2014 Jul 18.

1] The Institute for Genomic Biology, University of Illinois, Urbana, IL, USA [2] Department of Anthropology, University of Illinois, Urbana, IL, USA.

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http://dx.doi.org/10.1038/ismej.2014.90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260710PMC
December 2014

An intricate network of conserved DNA upstream motifs and associated transcription factors regulate the expression of uromodulin gene.

J Urol 2014 Sep 1;192(3):981-9. Epub 2014 Mar 1.

Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, Indiana; Department of Medical and Molecular Genetics, School of Medicine, Indiana University and Roudebush Veterans Affairs Medical Center, Indianapolis, Indiana; Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University and Roudebush Veterans Affairs Medical Center, Indianapolis, Indiana. Electronic address:

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http://dx.doi.org/10.1016/j.juro.2014.02.095DOI Listing
September 2014

Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome.

Proteins 2014 Apr 22;82(4):640-7. Epub 2013 Nov 22.

School of Informatics and Computing, Indiana University Purdue University, Indianapolis, Indiana, 46202; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, 46202.

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http://dx.doi.org/10.1002/prot.24441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949140PMC
April 2014

Whole-genome sequence of sungri/96 vaccine strain of peste des petits ruminants virus.

Genome Announc 2014 Feb 13;2(1). Epub 2014 Feb 13.

Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.

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http://dx.doi.org/10.1128/genomeA.00056-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924372PMC
February 2014

Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli.

Mol Biosyst 2012 Nov 10;8(11):3028-35. Epub 2012 Sep 10.

Institute of Mathematical and Computer Sciences, University of São Paulo, 13560-970, São Carlos, SP, Brazil.

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http://xlink.rsc.org/?DOI=c2mb25279a
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http://dx.doi.org/10.1039/c2mb25279aDOI Listing
November 2012

From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks.

Brief Funct Genomics 2012 Nov 3;11(6):505-21. Epub 2012 Nov 3.

School of Informatics, Indiana University Purdue University, Indianapolis, Indiana, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 719 Indiana Ave Ste 319, Walker Plaza Building, IN 46202, USA.

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https://academic.oup.com/bfg/article-lookup/doi/10.1093/bfgp
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http://dx.doi.org/10.1093/bfgp/els046DOI Listing
November 2012

MicroRNAs as post-transcriptional machines and their interplay with cellular networks.

Adv Exp Med Biol 2011 ;722:59-74

University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://link.springer.com/10.1007/978-1-4614-0332-6_4
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http://dx.doi.org/10.1007/978-1-4614-0332-6_4DOI Listing
October 2011

Interplay between posttranscriptional and posttranslational interactions of RNA-binding proteins.

J Mol Biol 2011 Jun 9;409(3):466-79. Epub 2011 Apr 9.

Biozentrum, University of Basel, Klingelbergstrasse, Switzerland.

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http://dx.doi.org/10.1016/j.jmb.2011.03.064DOI Listing
June 2011

Transcriptional profiling of fetal hypothalamic TRH neurons.

BMC Genomics 2011 May 10;12:222. Epub 2011 May 10.

Departamento de Genética y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos.

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http://dx.doi.org/10.1186/1471-2164-12-222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3126781PMC
May 2011

Genome-wide analysis of mRNA decay patterns during early Drosophila development.

Genome Biol 2010 21;11(9):R93. Epub 2010 Sep 21.

Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.

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http://dx.doi.org/10.1186/gb-2010-11-9-r93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965385PMC
February 2011

Comparative analysis of gene expression and regulation of replicative aging associated genes in S. cerevisiae.

Mol Biosyst 2011 Feb 1;7(2):403-10. Epub 2010 Nov 1.

Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S A S Nagar, Punjab 160062, India.

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http://dx.doi.org/10.1039/c0mb00161aDOI Listing
February 2011

Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach.

Nucleic Acids Res 2010 Nov 14;38(20):6841-56. Epub 2010 Jul 14.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkq612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978377PMC
November 2010

A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes.

PLoS One 2010 Nov 11;5(11):e15499. Epub 2010 Nov 11.

Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.

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http://www.iupui.edu/~jangalab/Scherrer-PLoS-One-2010.pdf
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http://dx.plos.org/10.1371/journal.pone.0015499
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015499PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988813PMC
November 2010

Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.

Mol Biol Evol 2010 Jun 1;27(6):1449-59. Epub 2010 Feb 1.

Departamento de Ingeniería Celular y Biocatálisis, IBT-UNAM, AP 565-A, Cuernavaca, Morelos, México.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msq033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872624PMC
June 2010

Structure and organization of drug-target networks: insights from genomic approaches for drug discovery.

Mol Biosyst 2009 Dec 4;5(12):1536-48. Epub 2009 Sep 4.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK.

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http://xlink.rsc.org/?DOI=b908147j
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http://dx.doi.org/10.1039/B908147jDOI Listing
December 2009

Scaling relationship in the gene content of transcriptional machinery in bacteria.

Mol Biosyst 2009 Dec 17;5(12):1494-501. Epub 2009 Jul 17.

Departamento de Ingeniería Celular y Biocatálisis, IBT-UNAM. AP. 565-A, Cuernava-ca, Morelos, 62210, México.

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http://xlink.rsc.org/?DOI=b907384a
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http://dx.doi.org/10.1039/b907384aDOI Listing
December 2009

Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks.

Proc Natl Acad Sci U S A 2009 Dec 16;106(48):20300-5. Epub 2009 Nov 16.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0906940106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777960PMC
December 2009

Interfacing systems biology and synthetic biology.

Genome Biol 2009 26;10(6):309. Epub 2009 Jun 26.

Centre for Integrated Systems Biology of Ageing and Nutrition (CISBAN) and School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2009-10-6-309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718492PMC
September 2009

Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families.

Comput Biol Chem 2009 Aug 26;33(4):261-8. Epub 2009 Jun 26.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S147692710900050
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http://dx.doi.org/10.1016/j.compbiolchem.2009.06.004DOI Listing
August 2009

Transcriptional regulation shapes the organization of genes on bacterial chromosomes.

Nucleic Acids Res 2009 Jun 16;37(11):3680-8. Epub 2009 Apr 16.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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http://dx.doi.org/10.1093/nar/gkp231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699516PMC
June 2009

Network-based approaches for linking metabolism with environment.

Genome Biol 2008 24;9(11):239. Epub 2008 Nov 24.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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February 2009

Transcript stability in the protein interaction network of Escherichia coli.

Mol Biosyst 2009 Feb 9;5(2):154-62. Epub 2008 Dec 9.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK CB2 0QH.

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February 2009

Eukaryotic gene regulation in three dimensions and its impact on genome evolution.

Curr Opin Genet Dev 2008 Dec 27;18(6):571-82. Epub 2008 Nov 27.

MRC Laboratory of Molecular Biology, Cambridge, UK.

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December 2008

Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes.

Proc Natl Acad Sci U S A 2008 Oct 7;105(41):15761-6. Epub 2008 Oct 7.

Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 0QH, United Kingdom.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562535PMC
October 2008

Functional organisation of Escherichia coli transcriptional regulatory network.

J Mol Biol 2008 Aug 29;381(1):238-47. Epub 2008 May 29.

Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Campus Guanajuato, Irapuato 36500, México.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726282PMC
August 2008

Ten simple rules for organizing a scientific meeting.

PLoS Comput Biol 2008 Jun 27;4(6):e1000080. Epub 2008 Jun 27.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367436PMC
June 2008

Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles.

Proteins 2008 Feb;70(2):344-52

Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON N2L 3C5, Canada.

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February 2008

Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli.

Nucleic Acids Res 2007 12;35(20):6963-72. Epub 2007 Oct 12.

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62100, México.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2175315PMC
December 2007

Structure and evolution of gene regulatory networks in microbial genomes.

Res Microbiol 2007 Dec 15;158(10):787-94. Epub 2007 Oct 15.

Program of Computational Genomics, CCG-UNAM, Apdo Postal 565-A, Cuernavaca, Morelos, 62100 Mexico.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696542PMC
December 2007

Conservation of transcriptional sensing systems in prokaryotes: a perspective from Escherichia coli.

FEBS Lett 2007 Jul 2;581(18):3499-506. Epub 2007 Jul 2.

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62100, Mexico.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238691PMC
July 2007

Internal versus external effector and transcription factor gene pairs differ in their relative chromosomal position in Escherichia coli.

J Mol Biol 2007 Apr 12;368(1):263-72. Epub 2007 Jan 12.

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62100, México.

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April 2007

The distinctive signatures of promoter regions and operon junctions across prokaryotes.

Nucleic Acids Res 2006 12;34(14):3980-7. Epub 2006 Aug 12.

Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5.

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http://dx.doi.org/10.1093/nar/gkl563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557821PMC
September 2006

Bacterial regulatory networks are extremely flexible in evolution.

Nucleic Acids Res 2006 13;34(12):3434-45. Epub 2006 Jul 13.

Programa de Genomica Computacional, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Apdo. Postal 565-A, Avenue Universidad, Cuernavaca, Morelos, 62100 Mexico, Mexico. [corrected]

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July 2006

Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach.

BMC Genomics 2006 Jun 13;7:147. Epub 2006 Jun 13.

Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62100, México.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524751PMC
June 2006

Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli.

Trends Microbiol 2006 Jan 28;14(1):22-7. Epub 2005 Nov 28.

Programa de Genómica Computacional, Centro de Ciencias Genómicas, UNAM, Cuernavaca, Morelos 62100, México.

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January 2006

The network of transcriptional interactions imposes linear constrains in the genome.

OMICS 2005 ;9(2):139-45

Program of Computational Genomics, Centro de Ciencias Genómicas (CCG)-UNAM, Morelos, Mexico.

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September 2005

Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons.

Nucleic Acids Res 2005 2;33(8):2521-30. Epub 2005 May 2.

Program of Computational Genomics, CCG-UNAM Apdo Postal 565-A, Cuernavaca, Morelos, 62100 Mexico.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088069PMC
May 2005

Conservation of adjacency as evidence of paralogous operons.

Nucleic Acids Res 2004 11;32(18):5392-7. Epub 2004 Oct 11.

Program of Computational Genomics, CIFN-UNAM, Apdo Postal 565-A, Cuernavaca, Morelos, 62100 Mexico.

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October 2004