User Publications

Microarray characterization of gene expression changes in blood during acute ethanol exposure.

Kupfer DM, White VL, Strayer DL, Crouch DJ, Burian D.
BMC Med Genomics. 2013 Jul.


Gene expression analysis in response to low and high temperature and oxidative stresses in rice: Combination of stresses evokes different transcriptional changes as against stresses applied individually.

Mittal D, Madhyastha DA, Grover A.
Plant Sci. 2012 Dec.


Molecular profiling of synovial joints: Use of microarray analysis to identify factors that direct the development of the knee and elbow.

Pazin DE, Gamer LW, Cox KA, Rosen V.
Dev Dyn. 2012 Nov.


Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.

Kulis M, Heath S, Bibikova M, Queirós AC, Navarro A, Clot G, Martínez-Trillos A, Castellano G, Brun-Heath I, Pinyol M, Barberán-Soler S, Papasaikas P, Jares P, Beà S, Rico D, Ecker S, Rubio M, Royo R, Ho V, Klotzle B, Hernández L, Conde L, López-Guerra M, Colomer D, Villamor N, Aymerich M, Rozman M, Bayes M, Gut M, Gelpí JL, Orozco M, Fan JB, Quesada V, Puente XS, Pisano DG, Valencia A, López-Guillermo A, Gut I, López-Otín C, Campo E, Martín-Subero JI.
Nat Genet. 2012 Oct 14.


A metabolic prosurvival role for PML in breast cancer.

Carracedo A, Weiss D, Leliaert AK, Bhasin M, de Boer VC, Laurent G, Adams AC, Sundvall M, Song SJ, Ito K, Finley LS, Egia A, Libermann T, Gerhart-Hines Z, Puigserver P, Haigis MC, Maratos-Flier E, Richardson AL, Schafer ZT, Pandolfi PP.
J Clin Invest. 2012 Sep 4.


Computational predictions of common transcription factor binding sites on the genes of proline metabolism in plants.

Kiran U, Abdin MZ.
Bioinformation. 2012 Sep.


Paneth Cells in Intestinal Homeostasis and Tissue Injury

Sabrina Roth, Patrick Franken, Andrea Sacchetti, Andreas Kremer, Kurt Anderson, Owen Sansom, Riccardo Fodde
PlosOne. 2012 June


Gene Set Enrichment Analysis Identifies LIF as a Negative Regulator of Human Th2 Cell Differentiation

Ubaid Ullah, Parul Tripathi, Riitta Lahesmaa, and Kanury V. S. Raoa
Sci Rep. 2012; 2: 464.


Transcriptional regulation of gene expression during osmotic stress responses by the mammalian target of rapamycin.

Ortells MC, Morancho B, Drews-Elger K, Viollet B, Laderoute KR, López-Rodríguez C, Aramburu J.
Nucleic Acids Res. 2012 May 1;40(10):4368-84. Epub 2012 Jan 28.


Transcriptome analysis using next generation sequencing reveals molecular signatures of diabetic retinopathy and efficacy of candidate drugs.

Kandpal RP, Rajasimha HK, Brooks MJ, Nellissery J, Wan J, Qian J, Kern TS, Swaroop A.
Mol Vis. 2012;18:1123-46. Epub 2012 May 2.


Differential expression of the putative Kex2 processed and secreted aspartic proteinase gene family of Cryphonectria parasitica.

Jacob-Wilk D, Moretti M, Turina M, Kazmierczak P, Van Alfen NK.
Fungal Biol. 2012 Mar;116(3):363-78. Epub 2012 Jan 6.


In Silico Analysis of Combinatorial microRNA Activity Reveals Target Genes and Pathways Associated with Breast Cancer Metastasis.

Dombkowski AA, Sultana Z, Craig DB, Jamil H.
Cancer Inform. 2011 Feb 17;10:13-29

Interview with Dr. Dombkowski and how he utilized ExPlain to identify central nodes downstream of numerous microRNA target genes.


A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms.

Plank M, Wuttke D, van Dam S, Clarke SA, de Magalhães JP.
Mol Biosyst. 2012 Feb 10.


Proteomic Analysis (GeLC-MS/MS) of ePFT-Collected Pancreatic Fluid in Chronic Pancreatitis.

Paulo JA, Kadiyala V, Lee LS, Banks PA, Conwell DL, Steen H.
J Proteome Res. 2012 Feb 7.


Sclerostin expression is induced by BMPs in human Saos-2 osteosarcoma cells but not via direct effects on the sclerostin gene promoter or ECR5 element.

Yu L, der Valk M, Cao J, Han CY, Juan T, Bass MB, Deshpande C, Damore MA, Stanton R, Babij P.
Bone. 2011 Dec;49(6):1131-40. Epub 2011 Aug 26


Estrogen upregulates L-type Ca2+ channels via Estrogen-Receptor-α by a regional genomic mechanism in female rabbit hearts.

Yang X, Chen G, Papp R, Defranco DB, Zeng F, Salama G.
J Physiol. 2011 Nov 28.


Development and evaluation of a genomic signature for the prediction and mechanistic assessment of nongenotoxic hepatocarcinogens in the rat.

Fielden MR, Adai A, Dunn RT 2nd, Olaharski A, Searfoss G, Sina J, Aubrecht J, Boitier E, Nioi P, Auerbach S, Jacobson-Kram D, Raghavan N, Yang Y, Kincaid A, Sherlock J, Chen SJ, Car B
Predictive Safety Testing Consortium, Carcinogenicity Working Group. Toxicol Sci. 2011 Nov;124(1):54-74. Epub 2011 Aug 2.


Left ventricular remodeling in swine after myocardial infarction: a transcriptional genomics approach.

Kuster DW, Merkus D, Kremer A, van Ijcken WF, de Beer VJ, Verhoeven AJ, Duncker DJ.
Basic Res Cardiol. 2011 Nov;106(6):1269-81. Epub 2011 Nov 5.


Identification of hypoxia-induced genes in human SGBS adipocytes by microarray analysis.

Geiger K, Leiherer A, Muendlein A, Stark N, Geller-Rhomberg S, Saely CH, Wabitsch M, Fraunberger P, Drexel H.
PLoS One. 2011;6(10):e26465. Epub 2011 Oct 19.


Estrogen-regulated genes in rat testes and their relationship to recovery of spermatogenesis after irradiation.

Zhou W, Bolden-Tiller OU, Shao SH, Weng CC, Shetty G, Abuelhija M, Pakarinen P, Huhtaniemi I, Momin AA, Wang J, Stivers DN, Liu Z, Meistrich ML. Biol Reprod. 2011 Oct. 85(4):8232-33. Epub 2011 Jun 8.


Specific regulatory motifs predict glucocorticoid responsiveness of hippocampal gene expression.

Datson NA, Polman JA, de Jonge RT, van Boheemen PT, van Maanen EM, Welten J, McEwen BS, Meiland HC, Meijer OC.
Endocrinology. 2011 Oct 152(10):3749-57. Epub 2011 Aug 16.


Express path analysis identifies tyrosine kinase Src centric network regulating divergent host responses to mycobacterium tuberculosis function.

Karim AF, Chandra P, Chopra A, Siddiqui Z, Bhaskar A, Singh A, Kumar D.
J Biol Chem. Epub 2011 Sep 27.


Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states.

Paulo JA, Urrutia R, Banks PA, Conwell DL, Steen H.
J Proteome Res. 2011 Aug 13 10(10):4835-44.


Mir193b-365 is essential for brown fat differentiation.

Sun L, Xie H, Mori MA, Alexander R, Yuan B, Hattangadi SM, Liu Q, Kahn CR, Lodish HF.
Nat Cell Biol. 2011 Jul 10 13(8):958-65.


Conceptual thinking for in silico prioritization of candidate disease genes.

Tiffin N. Methods
Mol Biol. 2011 760:175-87.


Drug target identification from protein dynamics using quantitative pathway analysis

Good DM, Zubarev RA.
J Proteome Res. 2011 May 6 10(5):2679-83. Epub 2011 Apr 21.


Early transcriptional regulation by C-peptide in freshly isolated rat proximal tubular cells.

Lindahl E, Nordquist L, Müller P, El Agha E, Friederich M, Dahlman-Wright K, Palm F, Jörnvall H.
Diabetes Metab Res Rev. 2011 May 26. doi: 10.1002/dmrr.1220. [Epub ahead of print]


Unique cellular and mitochondrial defects mediate FK506-induced islet β-cell dysfunction.

Rostambeigi N, Lanza IR, Dzeja PP, Deeds MC, Irving BA, Reddi HV, Madde P, Zhang S, Asmann YW, Anderson JM, Schimke JM, Nair KS, Eberhardt NL, Kudva YC.
Transplantation. 2011 Mar 27 91(6):615-23.


A20 modulates lipid metabolism and energy production to promote liver regeneration.

Damrauer SM, Studer P, da Silva CG, Longo CR, Ramsey HE, Csizmadia E, Shrikhande GV, Scali ST, Liberman TA, Bhasin MK, Ferran C. PLoS One. 2011 Mar 17 6(3):e17715.


C/EBPβ regulates dexamethasone-induced muscle cell atrophy and expression of atrogin-1 and MURF1.

Gonnella P, Alamdari N, Tizio S, Aversa Z, Petkova V, Hasselgren PO.
J Cell Biochem. 2011 Mar 4. doi: 10.1002/jcb.23093.


Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch.

Román AC, González-Rico FJ, Moltó E, Hernando H, Neto A, Vicente-Garcia C, Ballestar E, Gómez-Skarmeta JL, Vavrova-Anderson J, White RJ, Montoliu L, Fernández-Salguero PM.
Genome Res. 2011 Mar;21(3):422-32. Epub 2011 Feb 3.


Proteomic pathway analysis reveals inflammation increases myeloid-derived suppressor cell resistance to apoptosis.

Chornoguz O, Grmai L, Sinha P, Artemenko KA, Zubarev RA, Ostrand-Rosenberg S.
Mol Cell Proteomics. 2011 Mar 10(3):M110.002980. Epub 2010 Dec 29.


Rare structural variation of synapse and neurotransmission genes in autism.

Gai X, Xie HM, Perin JC, Takahashi N, Murphy K, Wenocur AS, D’arcy M, O’Hara RJ, Goldmuntz E, Grice DE, Shaikh TH, Hakonarson H, Buxbaum JD, Elia J, White PS.
Mol Psychiatry. 2011 Mar 1.


Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch.

Roman AC, Gonzalez-Rico FJ, Molto E, Hernando H, Neto A, Vicente-Garcia C, Ballestar E, Gomez-Skarmeta JL, Vavrova-Anderson J, White RJ, Montoliu L, Fernandez-Salguero PM.
Genome Res. 2011 Mar 21(3):422-32. Epub 2011 Feb 3.


Prodynorphin mutations cause the neurodegenerative disorder spinocerebellar ataxia type 23.

Bakalkin G, Watanabe H, Jezierska J, Depoorter C, Verschuuren-Bemelmans C, Bazov I, Artemenko KA, Yakovleva T, Dooijes D, Vand de Warrenburg BP, Zubarev RA, Kremer B, Knapp PE, Hauser KF, Wijmenga C, Nyberg F, Sinke RJ, Verbeek DS.
Am J Hum Genet. 2010 Nov 12 87(5):593-603. Epub 2010 Oct 28.


Rare structural vaiants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes.

Elia J, Gai X, Xie HM, Perin JC, Geiger E, Glessner JT, D’arcy M, deBerardinis R, Frankelton E, Kim C, Lantieri F, Muganga BM, Wang L, Takeda T, Rappaport EF, Grant SF, Berrettini W, Devoto M, Shaikh TH, Hakonarson H, White PS.
Mol Psychiatry. 2010 June 15(6):637-46. Epub 2009 Jun 23.


Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates.

Sobolev B, Filimonov D, Lagunin A, Zakharov A, Koborova O, Kel A, Poroikov V.
BMC Bioinformatics. 2010 Jun 10 11:313.
*Department of Bioinformatics, Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 119121, Pgogdinskaya str, 10, Moscow, Russia.


Bioinformatic identification and characterization of human endothelial cell-restricted genes.

Bhasin M, Yuan L, Keskin DB, Otu HH, Libermann TA, Oettgen P.
BMC Genomics. 2010 May 28 11:342.


Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes.

Qattan AT, Mulvey C, Crawford M, Natale DA, Godovac-Zimmermann J.
J Proteome Res. 2010 Jan 9(1):495-508.


In silico dynamic molecular interaction networks for the  discovery of new therapeutic targets.
Vujasinovic T, Zampera AS, Jackers P, Sanoudou D, Depaulis A.
Curr Pharm Des. 2010 16(20):2241-51.


Apoptotic, regenerative, and immune-related signaling in human islets from type 2 diabetes individuals.

Nyblom HK, Bugliani M, Fung E, Boggi U, Zubarev R, Marchetti P, Bergsten P.
J Proteome Res. 2009 Dec 8(12):5650-6.


Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism.

Yoshikawa N, Nagasaki M, Sano M, Tokudome S, Ueno K, Shimizu N, Imoto S, Miyano S, Suematsu M, Fukuda K, Morimoto C, Tanaka H. Am J Physiol Endocrinol Metab. 2009 Jun;296(6):E1363-73. Epub 2009 Mar 17


Proteomics and pathway analysis identifies JNK signaling as critical for high linear energy transfer radiation-induced apoptosis in non-small lung cancer cells.

Stahl S, Fung E, Adams C, Lengqvist J, Mork B, Stenerlow B, Lewensohn R, Lehtio J, Zubarev R, Viktorsson K.
Mol Cell Proteomics. 2009 May 8(5):1117-29. Epub 2009 Jan 23.


Systems-level analysis of cell-specific AQP2 gene expression in renal collecting duct.

Yu MJ, Miller RL, Uawithya P, Rinschen MM, Khositseth S, Braucht DW, Chou CL, Pisitkun T, Nelson RD, Knepper MA.
Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2441-6. Epub 2009 Feb 3


Comparative analysis of neurological disorders focuses genome-wide search for autism genes.

Wall DP, Esteban FJ, Deluca TF, Huyck M, Monaghan T, Velez de Mendizabal N, Goñí J, Kohane IS.
Genomics. 2009 Feb 93(2):120-9. Epub 2008 Nov 12


Novel sphingolipid derivatives promote keratinocyte differentiation.

Paragh G, Schling P, Ugocsai P, Kel AE, Liebisch G, Heimerl S, Moehle C, Schiemann Y, Wegmann M, Farwick M, Wikonkál NM, Mandl J, Langmann T, Schmitz G.
Exp Dermatol. 2008 Dec 17(12):1004-16.


A computational analysis of protein-protein interaction networks in neurodegenerative diseases.

Goni J, Esteban FJ, de Mendizabal NV, Sepulcre J, Ardanza-Trevijano S, Agirrezabal I, Villoslada P.
BMC Syst Biol. 2008 Jun 20 2:52.


Identification of dominant signaling pathways from proteomics expression data.
Zubarev RA*, Nielsen ML*, Fung EM*, Savitski MM*, Kel-Margoulis O, Wingender E, Kel A.
J Proteomics. 2008 Apr 30;71(1):89-96. Epub 2008 Jan 17
*Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, SE-75 124 Uppsala, Sweden.

BIOBASE Publications

Genome-Wide Transcriptional Profiles during Temperature and Oxidative Stress Reveal Coordinated Expression Patterns and Overlapping Regulons in Rice

Dheeraj Mittal, Dinesh A. Madhyastha, Anil Grover
PLoS One. 2012;7(7):e40899. Epub  2012 Jul 16.


Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer.

Stegmaier P, Voss N, Meier T, Kel A, Wingender E, Borlak J.
PLoS One. 2011 Mar 28 6(3):e17738.


Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.

Ghedira K, Hornischer K, Konovalova T, Jenhani AZ, Benkahla A, Kel A.
Infect Genet Evol. 2010 Nov 18. [Epub ahead of print].


ExPlain™ WAX: causal analysis of gene batteries and identification of key nodes in signal transduction networks.

Becker S, Homeyer N, Konovalova T, Stegmaier P, Lewicki-Potapov B, Voss N, Kel A.
Appl. Comput. Math. V.9 Special Issue 2010 pp.34-49.


ExPlain: finding upstream drug targets in disease gene regulatory networks.

Kel A, Voss N, Valeev T, Stegmaier P, Kel-Margoulis O, Wingender E.
SAR QSAR Environ Res. 2008;19(5-6):481-94.


Beyond microarrays: Find key transcription factors controlling signal transduction pathways.

Kel, A., Voss, N., Jauregui, R., Kel-Margoulis, O. and Wingender, E.
BMC Bioinformatics, 7(Suppl. 2), S13 (2006).


Composite Module Analyst: A fitness-based tool for identification of transcription factor binding site combinations.

Kel, A., Konovalova, T., Valeev, T., Cheremushkin, E., Kel-Margoulis, O., Wingender, E.
Bioinformatics 2006 May 15;22(10):1190-7. Epub 2006 Feb 10.


Composite Module Analyst: A Fitness-Based Tool for Prediction of Transcription Regulation

Kel, A., Konovalova, T., Valeev, T., Cheremushkin, E., Kel-Margoulis, O., Wingender, E.
Proceedings of German Conference on Bioinformatics 2005 GCB 2005 October 5-7, 2005, Hamburg, Germany. Lecture Notes in Informatics (LNI) – Proceedings Series of the Gesellschaft für Informatik (GI) Volume P-71 (Andrew Torda, Stefan Kurtz, Matthias Rarey eds.), 63-76 (2005).