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Items: 19

1.

PAI-1 augments mucosal damage in colitis.

Kaiko GE, Chen F, Lai CW, Chiang IL, Perrigoue J, Stojmirović A, Li K, Muegge BD, Jain U, VanDussen KL, Goggins BJ, Keely S, Weaver J, Foster PS, Lawrence DA, Liu TC, Stappenbeck TS.

Sci Transl Med. 2019 Mar 6;11(482). pii: eaat0852. doi: 10.1126/scitranslmed.aat0852.

PMID:
30842312
2.

Abnormal Small Intestinal Epithelial Microvilli in Patients With Crohn's Disease.

VanDussen KL, Stojmirović A, Li K, Liu TC, Kimes PK, Muegge BD, Simpson KF, Ciorba MA, Perrigoue JG, Friedman JR, Towne JE, Head RD, Stappenbeck TS.

Gastroenterology. 2018 Sep;155(3):815-828. doi: 10.1053/j.gastro.2018.05.028. Epub 2018 May 18.

3.

A functional genomics predictive network model identifies regulators of inflammatory bowel disease.

Peters LA, Perrigoue J, Mortha A, Iuga A, Song WM, Neiman EM, Llewellyn SR, Di Narzo A, Kidd BA, Telesco SE, Zhao Y, Stojmirovic A, Sendecki J, Shameer K, Miotto R, Losic B, Shah H, Lee E, Wang M, Faith JJ, Kasarskis A, Brodmerkel C, Curran M, Das A, Friedman JR, Fukui Y, Humphrey MB, Iritani BM, Sibinga N, Tarrant TK, Argmann C, Hao K, Roussos P, Zhu J, Zhang B, Dobrin R, Mayer LF, Schadt EE.

Nat Genet. 2017 Oct;49(10):1437-1449. doi: 10.1038/ng.3947. Epub 2017 Sep 11.

4.

Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci.

Di Narzo AF, Peters LA, Argmann C, Stojmirovic A, Perrigoue J, Li K, Telesco S, Kidd B, Walker J, Dudley J, Cho J, Schadt EE, Kasarskis A, Curran M, Dobrin R, Hao K.

Clin Transl Gastroenterol. 2016 Jun 23;7(6):e177. doi: 10.1038/ctg.2016.34.

5.

NDEx, the Network Data Exchange.

Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobrin R, Braxenthaler M, Kuentzer J, Demchak B, Ideker T.

Cell Syst. 2015 Oct 28;1(4):302-305.

6.

Topology-function conservation in protein-protein interaction networks.

Davis D, Yaveroğlu ÖN, Malod-Dognin N, Stojmirovic A, Pržulj N.

Bioinformatics. 2015 May 15;31(10):1632-9. doi: 10.1093/bioinformatics/btv026. Epub 2015 Jan 20.

7.

Log-odds sequence logos.

Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF.

Bioinformatics. 2015 Feb 1;31(3):324-31. doi: 10.1093/bioinformatics/btu634. Epub 2014 Oct 6.

8.

Building a hierarchical organization of protein complexes out of protein association data.

Stojmirović A, Yu YK.

PLoS One. 2014 Jun 30;9(6):e100098. doi: 10.1371/journal.pone.0100098. eCollection 2014.

9.

Revealing the hidden language of complex networks.

Yaveroğlu ÖN, Malod-Dognin N, Davis D, Levnajic Z, Janjic V, Karapandza R, Stojmirovic A, Pržulj N.

Sci Rep. 2014 Apr 1;4:4547. doi: 10.1038/srep04547.

10.

PFMFind: a system for discovery of peptide homology and function.

Stojmirović A, Andreae P, Boland M, Jordan TW, Pestov VG.

Similarity Search Appl. 2013;8199`:319-324.

11.

CytoITMprobe: a network information flow plugin for Cytoscape.

Stojmirović A, Bliskovsky A, Yu YK.

BMC Res Notes. 2012 May 15;5:237. doi: 10.1186/1756-0500-5-237.

12.

Information flow in interaction networks II: channels, path lengths, and potentials.

Stojmirović A, Yu YK.

J Comput Biol. 2012 Apr;19(4):379-403. doi: 10.1089/cmb.2010.0228. Epub 2012 Mar 12.

13.

CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores.

Stojmirovic A, Bliskovsky A, Yu YK.

Bioinformatics. 2012 Mar 15;28(6):893-4. doi: 10.1093/bioinformatics/bts041. Epub 2012 Feb 15.

14.

ppiTrim: constructing non-redundant and up-to-date interactomes.

Stojmirović A, Yu YK.

Database (Oxford). 2011 Aug 27;2011:bar036. doi: 10.1093/database/bar036. Print 2011.

15.

Robust and accurate data enrichment statistics via distribution function of sum of weights.

Stojmirović A, Yu YK.

Bioinformatics. 2010 Nov 1;26(21):2752-9. doi: 10.1093/bioinformatics/btq511. Epub 2010 Sep 8.

16.

ITM Probe: analyzing information flow in protein networks.

Stojmirović A, Yu YK.

Bioinformatics. 2009 Sep 15;25(18):2447-9. doi: 10.1093/bioinformatics/btp398. Epub 2009 Jun 27.

17.

Geometric aspects of biological sequence comparison.

Stojmirović A, Yu YK.

J Comput Biol. 2009 Apr;16(4):579-610. doi: 10.1089/cmb.2008.0100.

18.

The effectiveness of position- and composition-specific gap costs for protein similarity searches.

Stojmirović A, Gertz EM, Altschul SF, Yu YK.

Bioinformatics. 2008 Jul 1;24(13):i15-23. doi: 10.1093/bioinformatics/btn171.

19.

Information flow in interaction networks.

Stojmirović A, Yu YK.

J Comput Biol. 2007 Oct;14(8):1115-43.

PMID:
17985991

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