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Items: 1 to 20 of 32


BAFF (B cell activating factor) transcript level in peripheral blood of patients with SLE is associated with same-day disease activity as well as global activity over the next year.

Zollars E, Bienkowska J, Czerkowicz J, Allaire N, Ranger AM, Magder L, Petri M.

Lupus Sci Med. 2015 Jun 18;2(1):e000063. doi: 10.1136/lupus-2014-000063. eCollection 2015.


Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.

Simmons S, Peng J, Bienkowska J, Berger B.

J Comput Biol. 2015 Aug;22(8):715-28. doi: 10.1089/cmb.2015.0085. Epub 2015 Jun 22.


Lymphotoxin-LIGHT pathway regulates the interferon signature in rheumatoid arthritis.

Bienkowska J, Allaire N, Thai A, Goyal J, Plavina T, Nirula A, Weaver M, Newman C, Petri M, Beckman E, Browning JL.

PLoS One. 2014 Nov 18;9(11):e112545. doi: 10.1371/journal.pone.0112545. eCollection 2014.


ProbeSelect: selecting differentially expressed probes in transcriptional profile data.

Hosur R, Szak S, Thai A, Allaire N, Bienkowska J.

Bioinformatics. 2014 Feb 15;30(4):574-5. doi: 10.1093/bioinformatics/btt720. Epub 2013 Dec 13.


A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

Hosur R, Peng J, Vinayagam A, Stelzl U, Xu J, Perrimon N, Bienkowska J, Berger B.

Genome Biol. 2012 Aug 31;13(8):R76. doi: 10.1186/gb-2012-13-8-r76.


Lymphotoxin-beta receptor blockade reduces CXCL13 in lacrimal glands and improves corneal integrity in the NOD model of Sjögren's syndrome.

Fava RA, Kennedy SM, Wood SG, Bolstad AI, Bienkowska J, Papandile A, Kelly JA, Mavragani CP, Gatumu M, Skarstein K, Browning JL.

Arthritis Res Ther. 2011;13(6):R182. doi: 10.1186/ar3507. Epub 2011 Nov 1.


Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis.

Xing H, McDonagh PD, Bienkowska J, Cashorali T, Runge K, Miller RE, Decaprio D, Church B, Roubenoff R, Khalil IG, Carulli J.

PLoS Comput Biol. 2011 Mar;7(3):e1001105. doi: 10.1371/journal.pcbi.1001105. Epub 2011 Mar 10.


iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions.

Hosur R, Xu J, Bienkowska J, Berger B.

J Mol Biol. 2011 Feb 4;405(5):1295-310. doi: 10.1016/j.jmb.2010.11.025. Epub 2010 Dec 3.


Convergent Random Forest predictor: methodology for predicting drug response from genome-scale data applied to anti-TNF response.

Bienkowska JR, Dalgin GS, Batliwalla F, Allaire N, Roubenoff R, Gregersen PK, Carulli JP.

Genomics. 2009 Dec;94(6):423-32. doi: 10.1016/j.ygeno.2009.08.008. Epub 2009 Aug 20.


Serious diabetes-specific emotional problems in patients with type 2 diabetes who have different levels of comorbid depression: a Polish study from the European Depression in Diabetes (EDID) Research Consortium.

Kokoszka A, Pouwer F, Jodko A, Radzio R, Mućko P, Bieńkowska J, Kuligowska E, Smoczyńska O, Skłodowska Z.

Eur Psychiatry. 2009 Oct;24(7):425-30. doi: 10.1016/j.eurpsy.2009.04.002. Epub 2009 Jun 21.


Optimal contact map alignment of protein-protein interfaces.

Pulim V, Berger B, Bienkowska J.

Bioinformatics. 2008 Oct 15;24(20):2324-8. doi: 10.1093/bioinformatics/btn432. Epub 2008 Aug 18.


Experimental comparison and cross-validation of Affymetrix HT plate and cartridge array gene expression platforms.

Allaire NE, Rieder LE, Bienkowska J, Carulli JP.

Genomics. 2008 Nov;92(5):359-65. doi: 10.1016/j.ygeno.2008.06.010. Epub 2008 Sep 17.


Comparative expression analysis of four breast cancer subtypes versus matched normal tissue from the same patients.

Martini PG, Taylor DM, Bienkowska J, Jackson J, McAllister G, Keilhack H, Campbell RK.

J Steroid Biochem Mol Biol. 2008 Apr;109(3-5):207-11. doi: 10.1016/j.jsbmb.2008.03.020. Epub 2008 Mar 14.


LTHREADER: prediction of extracellular ligand-receptor interactions in cytokines using localized threading.

Pulim V, Bienkowska J, Berger B.

Protein Sci. 2008 Feb;17(2):279-92. Epub 2007 Dec 20.


LTHREADER: prediction of ligand-receptor interactions using localized threading.

Pulim V, Bienkowska J, Berger B.

Pac Symp Biocomput. 2007:64-75.


Estrogen receptors alpha and beta mediate distinct pathways of vascular gene expression, including genes involved in mitochondrial electron transport and generation of reactive oxygen species.

O'Lone R, Knorr K, Jaffe IZ, Schaffer ME, Martini PG, Karas RH, Bienkowska J, Mendelsohn ME, Hansen U.

Mol Endocrinol. 2007 Jun;21(6):1281-96. Epub 2007 Mar 20.


Computational characterization of proteins.

Bienkowska J.

Expert Rev Proteomics. 2005 Jan;2(1):129-38. Review.


A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells?

Bienkowska JR, Hartman H, Smith TF.

Protein Eng. 2003 Dec;16(12):897-904.

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