Publications

Comparative Analysis of Alternative Splicing Profiles in Th Cell Subsets Reveals Extensive Cell Type-Specific Effects Modulated by a Network of Transcription Factors and RNA-Binding Proteins.
Mir Q, Lakshmipati DK, Ulrich BJ, Kaplan MH, Janga SC. (2021 Sep 28)
Immunohorizons. pii: immunohorizons.2100060.doi: 10.4049/immunohorizons.2100060

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Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components.
Srivastava M, Hall D, Omoru OB, Gill HM, Smith S, Janga SC. (2021 Aug 24)
Microorganisms. pii: microorganisms9091794.doi: 10.3390/microorganisms9091794

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Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets.
Koonchanok R, Daulatabad SV, Mir Q, Reda K, Janga SC. (2021 Jul 7)
BMC Genomics. pii: 10.1186/s12864-021-07791-z.doi: 10.1186/s12864-021-07791-z

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Lantern: an integrative repository of functional annotations for lncRNAs in the human genome.
Daulatabad SV, Srivastava R, Janga SC. (2021 May 26)
BMC Bioinformatics. pii: 10.1186/s12859-021-04207-3.doi: 10.1186/s12859-021-04207-3

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Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq.
Srivastava M, Srivastava R, Janga SC. (2021 Jan 13)
Sci Rep. pii: 10.1038/s41598-020-80846-5.doi: 10.1038/s41598-020-80846-5

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The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway.
Hao Q, Zong X, Sun Q, Lin YC, Song YJ, Hashemikhabir S, Hsu RY, Kamran M, Chaudhary R, Tripathi V, Singh DK, Chakraborty A, Li XL, Kim YJ, Orjalo AV, Polycarpou-Schwarz M, Moriarity BS, Jenkins LM, Johansson HE, Zhu YJ, Diederichs S, Bagchi A, Kim TH, Janga SC, Lal A, Prasanth SG, Prasanth KV. (2020 Oct 27)
Elife. pii: 55102.doi: 10.7554/eLife.55102

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Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans.
Srivastava R, Daulatabad SV, Srivastava M, Janga SC. (2020 Sep 25)
Int J Mol Sci. pii: ijms21197090.doi: 10.3390/ijms21197090

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STAT5 promotes accessibility and is required for BATF-mediated plasticity at the Il9 locus.
Fu Y, Wang J, Panangipalli G, Ulrich BJ, Koh B, Xu C, Kharwadkar R, Chu X, Wang Y, Gao H, Wu W, Sun J, Tepper RS, Zhou B, Janga SC, Yang K, Kaplan MH. (2020 Sep 28)
Nat Commun. pii: 10.1038/s41467-020-18648-6.doi: 10.1038/s41467-020-18648-6

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A long non-coding RNA (Lrap) modulates brain gene expression and levels of alcohol consumption in rats.
Saba LM, Hoffman PL, Homanics GE, Mahaffey S, Daulatabad SV, Janga SC, Tabakoff B. (2021 Feb)
Genes Brain Behav.doi: 10.1111/gbb.12698

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Granzyme A-producing T helper cells are critical for acute graft-versus-host disease.
Park S, Griesenauer B, Jiang H, Adom D, Mehrpouya-Bahrami P, Chakravorty S, Kazemian M, Imam T, Srivastava R, Hayes TA, Pardo J, Janga SC, Paczesny S, Kaplan MH, Olson MR. (2020 Sep 17)
JCI Insight. pii: 124465.doi: 10.1172/jci.insight.124465

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Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans.
Srivastava R, Daulatabad SV, Srivastava M, Janga SC. (2020 Sep 22)
bioRxiv.doi: 10.1101/2020.07.06.190348

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New Twists in Detecting mRNA Modification Dynamics.
Anreiter I, Mir Q, Simpson JT, Janga SC, Soller M. (2021 Jan)
Trends Biotechnol. pii: S0167-7799(20)30166-9.doi: 10.1016/j.tibtech.2020.06.002

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Targeting Bim via a lncRNA Morrbid Regulates the Survival of Preleukemic and Leukemic Cells.
Cai Z, Aguilera F, Ramdas B, Daulatabad SV, Srivastava R, Kotzin JJ, Carroll M, Wertheim G, Williams A, Janga SC, Zhang C, Henao-Mejia J, Kapur R. (2020 Jun 23)
Cell Rep. pii: S2211-1247(20)30797-X.doi: 10.1016/j.celrep.2020.107816

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Bcl6 and Blimp1 reciprocally regulate ST2+ Treg-cell development in the context of allergic airway inflammation.
Koh B, Ulrich BJ, Nelson AS, Panangipalli G, Kharwadkar R, Wu W, Xie MM, Fu Y, Turner MJ, Paczesny S, Janga SC, Dent AL, Kaplan MH. (2020 Nov)
J Allergy Clin Immunol. pii: S0091-6749(20)30340-7.doi: 10.1016/j.jaci.2020.03.002

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Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects.
Sarmah S, Srivastava R, McClintick JN, Janga SC, Edenberg HJ, Marrs JA. (2020 Mar 3)
Sci Rep. pii: 10.1038/s41598-020-59043-x.doi: 10.1038/s41598-020-59043-x

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A Circular RNA from the MDM2 Locus Controls Cell Cycle Progression by Suppressing p53 Levels.
Chaudhary R, Muys BR, Grammatikakis I, De S, Abdelmohsen K, Li XL, Zhu Y, Daulatabad SV, Tsitsipatis D, Meltzer PS, Gorospe M, Janga SC, Lal A. (2020 Apr 13)
Mol Cell Biol. pii: MCB.00473-19.doi: 10.1128/MCB.00473-19

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Human protein-RNA interaction network is highly stable across mammals.
Ramakrishnan A, Janga SC. (2019 Dec 30)
BMC Genomics. pii: 10.1186/s12864-019-6330-9.doi: 10.1186/s12864-019-6330-9

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SliceIt: A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome.
Vemuri S, Srivastava R, Mir Q, Hashemikhabir S, Dong XC, Janga SC. (2020 Jun 1)
Methods. pii: S1046-2023(19)30111-2.doi: 10.1016/j.ymeth.2019.09.004

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Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins.
Porto FW, Daulatabad SV, Janga SC. (2019 Aug 6)
Genes (Basel). pii: genes10080593.doi: 10.3390/genes10080593

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Odyssey: a semi-automated pipeline for phasing, imputation, and analysis of genome-wide genetic data.
Eller RJ, Janga SC, Walsh S. (2019 Jun 28)
BMC Bioinformatics. pii: 10.1186/s12859-019-2964-5.doi: 10.1186/s12859-019-2964-5

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Early transcriptome profile of goat peripheral blood mononuclear cells (PBMCs) infected with peste des petits ruminant’s vaccine virus (Sungri/96) revealed induction of antiviral response in an interferon independent manner.
Manjunath S, Saxena S, Mishra B, Santra L, Sahu AR, Wani SA, Tiwari AK, Mishra BP, Singh RK, Janga SC, Kumar GR. (2019 Jun)
Res Vet Sci. pii: S0034-5288(18)30351-5.doi: 10.1016/j.rvsc.2019.03.014

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Splicing factor ESRP1 controls ER-positive breast cancer by altering metabolic pathways.
Gökmen-Polar Y, Neelamraju Y, Goswami CP, Gu Y, Gu X, Nallamothu G, Vieth E, Janga SC, Ryan M, Badve SS. (2019 Feb)
EMBO Rep. pii: embr.201846078.doi: 10.15252/embr.201846078

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Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
Brown P, RELISH Consortium ., Zhou Y. (2019 Jan 1)
Database (Oxford). pii: 5608006.doi: 10.1093/database/baz085

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A conserved enhancer regulates Il9 expression in multiple lineages.
Koh B, Abdul Qayum A, Srivastava R, Fu Y, Ulrich BJ, Janga SC, Kaplan MH. (2018 Nov 15)
Nat Commun. pii: 10.1038/s41467-018-07202-0.doi: 10.1038/s41467-018-07202-0

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Epitranscriptomic Code and Its Alterations in Human Disease.
Kadumuri RV, Janga SC. (2018 Oct)
Trends Mol Med. pii: S1471-4914(18)30149-7.doi: 10.1016/j.molmed.2018.07.010

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Loss of epigenetic regulator TET2 and oncogenic KIT regulate myeloid cell transformation via PI3K pathway.
Palam LR, Mali RS, Ramdas B, Srivatsan SN, Visconte V, Tiu RV, Vanhaesebroeck B, Roers A, Gerbaulet A, Xu M, Janga SC, Takemoto CM, Paczesny S, Kapur R. (2018 Feb 22)
JCI Insight. pii: 94679.doi: 10.1172/jci.insight.94679

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Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues.
Budak G, Dash S, Srivastava R, Lachke SA, Janga SC. (2018 Mar)
Exp Eye Res. pii: S0014-4835(16)30560-7.doi: 10.1016/j.exer.2018.01.009

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Mutational landscape of RNA-binding proteins in human cancers.
Neelamraju Y, Gonzalez-Perez A, Bhat-Nakshatri P, Nakshatri H, Janga SC. (2018 Jan 2)
RNA Biol.doi: 10.1080/15476286.2017.1391436

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Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations.
Srivastava R, Budak G, Dash S, Lachke SA, Janga SC. (2017 Sep 14)
Sci Rep. pii: 10.1038/s41598-017-10615-4.doi: 10.1038/s41598-017-10615-4

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RNA Editing in Pathogenesis of Cancer.
Baysal BE, Sharma S, Hashemikhabir S, Janga SC. (2017 Jul 15)
Cancer Res. pii: 0008-5472.CAN-17-0520.doi: 10.1158/0008-5472.CAN-17-0520

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PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes.
Singh DK, Gholamalamdari O, Jadaliha M, Ling Li X, Lin YC, Zhang Y, Guang S, Hashemikhabir S, Tiwari S, Zhu YJ, Khan A, Thomas A, Chakraborty A, Macias V, Balla AK, Bhargava R, Janga SC, Ma J, Prasanth SG, Lal A, Prasanth KV. (2017 Oct 1)
Carcinogenesis. pii: 3869807.doi: 10.1093/carcin/bgx062

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Paracrine IL-2 Is Required for Optimal Type 2 Effector Cytokine Production.
Olson MR, Ulrich BJ, Hummel SA, Khan I, Meuris B, Cherukuri Y, Dent AL, Janga SC, Kaplan MH. (2017 Jun 1)
J Immunol. pii: jimmunol.1601792.doi: 10.4049/jimmunol.1601792

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Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles.
Budak G, Srivastava R, Janga SC. (2017 Jun)
RNA. pii: rna.059089.116.doi: 10.1261/rna.059089.116

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Community-acquired rhinovirus infection is associated with changes in the airway microbiome.
Kloepfer KM, Sarsani VK, Poroyko V, Lee WM, Pappas TE, Kang T, Grindle KA, Bochkov YA, Janga SC, Lemanske RF Jr, Gern JE. (2017 Jul)
J Allergy Clin Immunol. pii: S0091-6749(17)30411-6.doi: 10.1016/j.jaci.2017.01.038

No abstract found.

Comparative and temporal transcriptome analysis of peste des petits ruminants virus infected goat peripheral blood mononuclear cells.
Manjunath S, Mishra BP, Mishra B, Sahoo AP, Tiwari AK, Rajak KK, Muthuchelvan D, Saxena S, Santra L, Sahu AR, Wani SA, Singh RP, Singh YP, Pandey A, Kanchan S, Singh RK, Kumar GR, Janga SC. (2017 Feb 2)
Virus Res. pii: S0168-1702(16)30549-4.doi: 10.1016/j.virusres.2016.12.014

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The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex.
Wong KS, Bhandari V, Janga SC, Houry WA. (2017 Jan 20)
J Mol Biol. pii: S0022-2836(16)30537-X.doi: 10.1016/j.jmb.2016.12.008

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Differential Expression of miRNAs in Nontumor Liver Tissue of Patients With Hepatocellular Cancer Caused by Nonalcoholic Steatohepatitis Cirrhosis.
Liang T, Chalasani NP, Williams KE, Sarasani V, Janga SC, Vuppalanchi R. (2017 Mar)
Clin Gastroenterol Hepatol. pii: S1542-3565(16)30981-8.doi: 10.1016/j.cgh.2016.10.017

No abstract found.

Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches.
Cherukuri Y, Janga SC. (2016 Aug 22)
BMC Genomics. pii: 10.1186/s12864-016-2895-8.doi: 10.1186/s12864-016-2895-8

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ExSurv: A Web Resource for Prognostic Analyses of Exons Across Human Cancers Using Clinical Transcriptomes.
Hashemikhabir S, Budak G, Janga SC. (2016)
Cancer Inform. pii: cin-suppl.2-2016-017.doi: 10.4137/CIN.S39367

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Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach.
Srivastava R, Zhang Y, Xiong X, Zhang X, Pan X, Dong XC, Liangpunsakul S, Janga SC. (2016)
PLoS One. pii: PONE-D-16-00328.doi: 10.1371/journal.pone.0160228

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Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks.
Nishtala S, Neelamraju Y, Janga SC. (2016 May 10)
Sci Rep. pii: srep25711.doi: 10.1038/srep25711

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RNA-binding proteins in eye development and disease: implication of conserved RNA granule components.
Dash S, Siddam AD, Barnum CE, Janga SC, Lachke SA. (2016 Jul)
Wiley Interdiscip Rev RNA.doi: 10.1002/wrna.1355

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Knowledge Discovery Using Big Data in Biomedical Systems.
Janga SC, Zhu D, Chen JY, Zaki MJ. (2015 Jul-Aug)
IEEE/ACM Trans Comput Biol Bioinform.doi: 10.1109/tcbb.2015.2454551

No abstract found.

Building integrated ontological knowledge structures with efficient approximation algorithms.
Xiang Y, Janga SC. (2015)
Biomed Res Int.doi: 10.1155/2015/501528

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OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes.
Chetal K, Janga SC. (2015)
Biomed Res Int.doi: 10.1155/2015/318217

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A Framework for Identifying Genotypic Information from Clinical Records: Exploiting Integrated Ontology Structures to Transfer Annotations between ICD Codes and Gene Ontologies.
Hashemikhabir S, Xia R, Xiang Y, Janga SC. (2018 Jul-Aug)
IEEE/ACM Trans Comput Biol Bioinform.doi: 10.1109/TCBB.2015.2480056

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Database of RNA binding protein expression and disease dynamics (READ DB).
Hashemikhabir S, Neelamraju Y, Janga SC. (2015)
Database (Oxford). pii: bav072.doi: 10.1093/database/bav072

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Differential miRNA Expression in Cells and Matrix Vesicles in Vascular Smooth Muscle Cells from Rats with Kidney Disease.
Chaturvedi P, Chen NX, O’Neill K, McClintick JN, Moe SM, Janga SC. (2015)
PLoS One. pii: PONE-D-15-06910.doi: 10.1371/journal.pone.0131589

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The human RBPome: from genes and proteins to human disease.
Neelamraju Y, Hashemikhabir S, Janga SC. (2015 Sep 8)
J Proteomics. pii: S1874-3919(15)00230-4.doi: 10.1016/j.jprot.2015.04.031

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Genomic analysis of host – Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways.
Manjunath S, Kumar GR, Mishra BP, Mishra B, Sahoo AP, Joshi CG, Tiwari AK, Rajak KK, Janga SC. (2015 Feb 24)
Vet Res. pii: s13567-015-0153-8.doi: 10.1186/s13567-015-0153-8

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Uncovering RNA binding proteins associated with age and gender during liver maturation.
Chaturvedi P, Neelamraju Y, Arif W, Kalsotra A, Janga SC. (2015 Mar 31)
Sci Rep. pii: srep09512.doi: 10.1038/srep09512

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Prognostic impact of HOTAIR expression is restricted to ER-negative breast cancers.
Gökmen-Polar Y, Vladislav IT, Neelamraju Y, Janga SC, Badve S. (2015 Mar 5)
Sci Rep. pii: srep08765.doi: 10.1038/srep08765

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Expression levels of SF3B3 correlate with prognosis and endocrine resistance in estrogen receptor-positive breast cancer.
Gökmen-Polar Y, Neelamraju Y, Goswami CP, Gu X, Nallamothu G, Janga SC, Badve S. (2015 May)
Mod Pathol. pii: modpathol2014146.doi: 10.1038/modpathol.2014.146

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Role of lncRNAs in health and disease-size and shape matter.
Mohanty V, Gökmen-Polar Y, Badve S, Janga SC. (2015 Mar)
Brief Funct Genomics. pii: elu034.doi: 10.1093/bfgp/elu034

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Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance.
Yildirim S, Yeoman CJ, Janga SC, Thomas SM, Ho M, Leigh SR, Primate Microbiome Consortium., White BA, Wilson BA, Stumpf RM. (2014 Dec)
ISME J. pii: ismej201490.doi: 10.1038/ismej.2014.90

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An intricate network of conserved DNA upstream motifs and associated transcription factors regulate the expression of uromodulin gene.
Srivastava R, Micanovic R, El-Achkar TM, Janga SC. (2014 Sep)
J Urol. pii: S0022-5347(14)00353-X.doi: 10.1016/j.juro.2014.02.095

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Whole-genome sequence of sungri/96 vaccine strain of peste des petits ruminants virus.
Siddappa M, Gandham RK, Sarsani V, Mishra BP, Mishra B, Joshi CG, Sahoo AP, Tiwari AK, Janga SC. (2014 Feb 13)
Genome Announc. pii: 2/1/e00056-14.doi: 10.1128/genomeA.00056-14

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Dissecting the expression landscape of RNA-binding proteins in human cancers.
Kechavarzi B, Janga SC. (2014 Jan 10)
Genome Biol. pii: gb-2014-15-1-r14.doi: 10.1186/gb-2014-15-1-r14

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Diversity and abundance of phosphonate biosynthetic genes in nature.
Yu X, Doroghazi JR, Janga SC, Zhang JK, Circello B, Griffin BM, Labeda DP, Metcalf WW. (2013 Dec 17)
Proc Natl Acad Sci U S A. pii: 1315107110.doi: 10.1073/pnas.1315107110

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Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome.
Zhao H, Yang Y, Janga SC, Kao CC, Zhou Y. (2014 Apr)
Proteins.doi: 10.1002/prot.24441

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Relationship between differential hepatic microRNA expression and decreased hepatic cytochrome P450 3A activity in cirrhosis.
Vuppalanchi R, Liang T, Goswami CP, Nalamasu R, Li L, Jones D, Wei R, Liu W, Sarasani V, Janga SC, Chalasani N. (2013)
PLoS One. pii: PONE-D-13-19922.doi: 10.1371/journal.pone.0074471

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From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks.
Janga SC. (2012 Nov)
Brief Funct Genomics. pii: els046.doi: 10.1093/bfgp/els046

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The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis.
Vo DT, Subramaniam D, Remke M, Burton TL, Uren PJ, Gelfond JA, de Sousa Abreu R, Burns SC, Qiao M, Suresh U, Korshunov A, Dubuc AM, Northcott PA, Smith AD, Pfister SM, Taylor MD, Janga SC, Anant S, Vogel C, Penalva LO. (2012 Nov)
Am J Pathol. pii: S0002-9440(12)00601-3.doi: 10.1016/j.ajpath.2012.07.031

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Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli.
Antiqueira L, Janga SC, Costa Lda F. (2012 Nov)
Mol Biosyst.doi: 10.1039/c2mb25279a

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Synthesis of methylphosphonic acid by marine microbes: a source for methane in the aerobic ocean.
Metcalf WW, Griffin BM, Cicchillo RM, Gao J, Janga SC, Cooke HA, Circello BT, Evans BS, Martens-Habbena W, Stahl DA, van der Donk WA. (2012 Aug 31)
Science. pii: 337/6098/1104.doi: 10.1126/science.1219875

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DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.
Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA. (2012 Jul 27)
Mol Cell. pii: S1097-2765(12)00553-9.doi: 10.1016/j.molcel.2012.06.028

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Construction, structure and dynamics of post-transcriptional regulatory network directed by RNA-binding proteins.
Janga SC, Mittal N. (2011)
Adv Exp Med Biol.doi: 10.1007/978-1-4614-0332-6_7

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MicroRNAs as post-transcriptional machines and their interplay with cellular networks.
Janga SC, Vallabhaneni S. (2011)
Adv Exp Med Biol.doi: 10.1007/978-1-4614-0332-6_4

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Structural coupling between RNA polymerase composition and DNA supercoiling in coordinating transcription: a global role for the omega subunit?
Geertz M, Travers A, Mehandziska S, Sobetzko P, Chandra-Janga S, Shimamoto N, Muskhelishvili G. (2011)
mBio. pii: mBio.00034-11.doi: 10.1128/mBio.00034-11

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Transcriptional profiling of fetal hypothalamic TRH neurons.
Guerra-Crespo M, Pérez-Monter C, Janga SC, Castillo-Ramírez S, Gutiérrez-Rios RM, Joseph-Bravo P, Pérez-Martínez L, Charli JL. (2011 May 10)
BMC Genomics. pii: 1471-2164-12-222.doi: 10.1186/1471-2164-12-222

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Interplay between posttranscriptional and posttranslational interactions of RNA-binding proteins.
Mittal N, Scherrer T, Gerber AP, Janga SC. (2011 Jun 10)
J Mol Biol. pii: S0022-2836(11)00353-6.doi: 10.1016/j.jmb.2011.03.064

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A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes.
Scherrer T, Mittal N, Janga SC, Gerber AP. (2010 Nov 11)
PLoS One.doi: 10.1371/journal.pone.0015499

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Comparative analysis of gene expression and regulation of replicative aging associated genes in S. cerevisiae.
Dhami SP, Mittal N, Janga SC, Roy N. (2011 Feb)
Mol Biosyst.doi: 10.1039/c0mb00161a

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Genome-wide analysis of mRNA decay patterns during early Drosophila development.
Thomsen S, Anders S, Janga SC, Huber W, Alonso CR. (2010)
Genome Biol. pii: gb-2010-11-9-r93.doi: 10.1186/gb-2010-11-9-r93

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Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach.
Janga SC, Contreras-Moreira B. (2010 Nov)
Nucleic Acids Res. pii: gkq612.doi: 10.1093/nar/gkq612

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Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.
Pérez-Rueda E, Janga SC. (2010 Jun)
Mol Biol Evol. pii: msq033.doi: 10.1093/molbev/msq033

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Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks.
Mittal N, Roy N, Babu MM, Janga SC. (2009 Dec 1)
Proc Natl Acad Sci U S A. pii: 0906940106.doi: 10.1073/pnas.0906940106

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Scaling relationship in the gene content of transcriptional machinery in bacteria.
Pérez-Rueda E, Janga SC, Martínez-Antonio A. (2009 Dec)
Mol Biosyst.doi: 10.1039/b907384a

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Structure and organization of drug-target networks: insights from genomic approaches for drug discovery.
Janga SC, Tzakos A. (2009 Dec)
Mol Biosyst.doi: 10.1039/B908147j

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Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families.
Janga SC, Pérez-Rueda E. (2009 Aug)
Comput Biol Chem. pii: S1476-9271(09)00050-4.doi: 10.1016/j.compbiolchem.2009.06.004

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Interfacing systems biology and synthetic biology.
Lister A, Charoensawan V, De S, James K, Janga SC, Huppert J. (2009)
Genome Biol. pii: gb-2009-10-6-309.doi: 10.1186/gb-2009-10-6-309

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Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.
Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A. (2009 Apr 28)
PLoS Biol. pii: 08-PLBI-RA-4517.doi: 10.1371/journal.pbio.1000096

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Transcriptional regulation shapes the organization of genes on bacterial chromosomes.
Janga SC, Salgado H, Martínez-Antonio A. (2009 Jun)
Nucleic Acids Res. pii: gkp231.doi: 10.1093/nar/gkp231

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Transcript stability in the protein interaction network of Escherichia coli.
Janga SC, Babu MM. (2009 Feb)
Mol Biosyst.doi: 10.1039/b816845h

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Network-based approaches for linking metabolism with environment.
Janga SC, Babu MM. (2008)
Genome Biol. pii: gb-2008-9-11-239.doi: 10.1186/gb-2008-9-11-239

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Eukaryotic gene regulation in three dimensions and its impact on genome evolution.
Babu MM, Janga SC, de Santiago I, Pombo A. (2008 Dec)
Curr Opin Genet Dev. pii: S0959-437X(08)00147-0.doi: 10.1016/j.gde.2008.10.002

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Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes.
Janga SC, Collado-Vides J, Babu MM. (2008 Oct 14)
Proc Natl Acad Sci U S A. pii: 0806317105.doi: 10.1073/pnas.0806317105

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Functional organisation of Escherichia coli transcriptional regulatory network.
Martínez-Antonio A, Janga SC, Thieffry D. (2008 Aug 1)
J Mol Biol. pii: S0022-2836(08)00632-3.doi: 10.1016/j.jmb.2008.05.054

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Ten simple rules for organizing a scientific meeting.
Corpas M, Gehlenborg N, Janga SC, Bourne PE. (2008 Jun 27)
PLoS Comput Biol.doi: 10.1371/journal.pcbi.1000080

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Structure and evolution of gene regulatory networks in microbial genomes.
Janga SC, Collado-Vides J. (2007 Dec)
Res Microbiol. pii: S0923-2508(07)00176-3.doi: 10.1016/j.resmic.2007.09.001

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Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli.
Janga SC, Salgado H, Martínez-Antonio A, Collado-Vides J. (2007)
Nucleic Acids Res. pii: gkm743.doi: 10.1093/nar/gkm743

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Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles.
Moreno-Hagelsieb G, Janga SC. (2008 Feb 1)
Proteins.doi: 10.1002/prot.21564

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Conservation of transcriptional sensing systems in prokaryotes: a perspective from Escherichia coli.
Salgado H, Martínez-Antonio A, Janga SC. (2007 Jul 24)
FEBS Lett. pii: S0014-5793(07)00718-1.doi: 10.1016/j.febslet.2007.06.059

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Internal versus external effector and transcription factor gene pairs differ in their relative chromosomal position in Escherichia coli.
Janga SC, Salgado H, Collado-Vides J, Martínez-Antonio A. (2007 Apr 20)
J Mol Biol. pii: S0022-2836(07)00046-0.doi: 10.1016/j.jmb.2007.01.019

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The distinctive signatures of promoter regions and operon junctions across prokaryotes.
Janga SC, Lamboy WF, Huerta AM, Moreno-Hagelsieb G. (2006)
Nucleic Acids Res. pii: gkl563.doi: 10.1093/nar/gkl563

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Bacterial regulatory networks are extremely flexible in evolution.
Lozada-Chávez I, Janga SC, Collado-Vides J. (2006)
Nucleic Acids Res. pii: 34/12/3434.doi: 10.1093/nar/gkl423

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Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes–a genomic approach.
Moreno-Campuzano S, Janga SC, Pérez-Rueda E. (2006 Jun 13)
BMC Genomics. pii: 1471-2164-7-147.doi: 10.1186/1471-2164-7-147

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The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons.
González V, Santamaría RI, Bustos P, Hernández-González I, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramírez MA, Jiménez-Jacinto V, Collado-Vides J, Dávila G. (2006 Mar 7)
Proc Natl Acad Sci U S A. pii: 0508502103.doi: 10.1073/pnas.0508502103

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Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli.
Martínez-Antonio A, Janga SC, Salgado H, Collado-Vides J. (2006 Jan)
Trends Microbiol. pii: S0966-842X(05)00305-7.doi: 10.1016/j.tim.2005.11.002

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The network of transcriptional interactions imposes linear constrains in the genome.
Menchaca-Mendez R, Janga SC, Collado-Vides J. (2005 Summer)
OMICS.doi: 10.1089/omi.2005.9.139

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Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons.
Janga SC, Collado-Vides J, Moreno-Hagelsieb G. (2005)
Nucleic Acids Res. pii: 33/8/2521.doi: 10.1093/nar/gki545

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Conservation of adjacency as evidence of paralogous operons.
Janga SC, Moreno-Hagelsieb G. (2004)
Nucleic Acids Res. pii: 32/18/5392.doi: 10.1093/nar/gkh882

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