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Jadwiga Bienkowska

TitleAdjunct Professor
InstitutionUniversity of California San Diego
DepartmentMedicine
Address9500 Gilman Drive #0835
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Simmons S, Peng J, Bienkowska J, Berger B. Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. J Comput Biol. 2015 Aug; 22(8):715-28. PMID: 26098139; PMCID: PMC4523039.
    2. Zollars E, Bienkowska J, Czerkowicz J, Allaire N, Ranger AM, Magder L, Petri M. 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. Lupus Sci Med. 2015; 2(1):e000063. PMID: 26113988; PMCID: PMC4477150.
    3. Bienkowska J, Allaire N, Thai A, Goyal J, Plavina T, Nirula A, Weaver M, Newman C, Petri M, Beckman E, Browning JL. Lymphotoxin-LIGHT pathway regulates the interferon signature in rheumatoid arthritis. PLoS One. 2014; 9(11):e112545. PMID: 25405351; PMCID: PMC4236099.
    4. Hosur R, Szak S, Thai A, Allaire N, Bienkowska J. ProbeSelect: selecting differentially expressed probes in transcriptional profile data. Bioinformatics. 2014 Feb 15; 30(4):574-5. PMID: 24336808; PMCID: PMC3928527.
    5. Allaire NE, Bushnell SE, Bienkowska J, Brock G, Carulli J. Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects. BMC Res Notes. 2013 Jan 05; 6:8. PMID: 23289891; PMCID: PMC3560109.
    6. Hosur R, Peng J, Vinayagam A, Stelzl U, Xu J, Perrimon N, Bienkowska J, Berger B. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biol. 2012 Aug 31; 13(8):R76. PMID: 22937800; PMCID: PMC4053744.
    7. Fava RA, Kennedy SM, Wood SG, Bolstad AI, Bienkowska J, Papandile A, Kelly JA, Mavragani CP, Gatumu M, Skarstein K, Browning JL. Lymphotoxin-beta receptor blockade reduces CXCL13 in lacrimal glands and improves corneal integrity in the NOD model of Sjögren's syndrome. Arthritis Res Ther. 2011; 13(6):R182. PMID: 22044682; PMCID: PMC3334628.
    8. Xing H, McDonagh PD, Bienkowska J, Cashorali T, Runge K, Miller RE, Decaprio D, Church B, Roubenoff R, Khalil IG, Carulli J. Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis. PLoS Comput Biol. 2011 Mar; 7(3):e1001105. PMID: 21423713; PMCID: PMC3053315.
    9. Hosur R, Xu J, Bienkowska J, Berger B. iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. J Mol Biol. 2011 Feb 04; 405(5):1295-310. PMID: 21130772; PMCID: PMC3028939.
    10. Bienkowska J, Dalgin GS, Batliwalla F, Allaire N, Roubenoff R, Gregersen PK, Carulli JP. Convergent Random Forest predictor: methodology for predicting drug response from genome-scale data applied to anti-TNF response. Genomics. 2009 Dec; 94(6):423-32. PMID: 19699293; PMCID: PMC4476397.
    11. Allaire NE, Rieder LE, Bienkowska J, Carulli JP. Experimental comparison and cross-validation of Affymetrix HT plate and cartridge array gene expression platforms. Genomics. 2008 Nov; 92(5):359-65. PMID: 18672051.
      View in: PubMed
    12. Pulim V, Berger B, Bienkowska J. Optimal contact map alignment of protein-protein interfaces. Bioinformatics. 2008 Oct 15; 24(20):2324-8. PMID: 18710876; PMCID: PMC2562013.
    13. Martini PG, Taylor DM, Bienkowska J, Jackson J, McAllister G, Keilhack H, Campbell RK. Comparative expression analysis of four breast cancer subtypes versus matched normal tissue from the same patients. J Steroid Biochem Mol Biol. 2008 Apr; 109(3-5):207-11. PMID: 18424034.
      View in: PubMed
    14. Pulim V, Bienkowska J, Berger B. LTHREADER: prediction of extracellular ligand-receptor interactions in cytokines using localized threading. Protein Sci. 2008 Feb; 17(2):279-92. PMID: 18096641; PMCID: PMC2222721.
    15. O'Lone R, Knorr K, Jaffe IZ, Schaffer ME, Martini PG, Karas RH, Bienkowska J, Mendelsohn ME, Hansen U. 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. Mol Endocrinol. 2007 Jun; 21(6):1281-96. PMID: 17374850.
      View in: PubMed
    16. Pulim V, Bienkowska J, Berger B. LTHREADER: prediction of ligand-receptor interactions using localized threading. Pac Symp Biocomput. 2007; 64-75. PMID: 17992745.
      View in: PubMed
    17. Bienkowska J. Computational characterization of proteins. Expert Rev Proteomics. 2005 Jan; 2(1):129-38. PMID: 15966858.
      View in: PubMed
    18. Hayete B, Bienkowska J. Gotrees: predicting go associations from protein domain composition using decision trees. Pac Symp Biocomput. 2005; 127-38. PMID: 15759620.
      View in: PubMed
    19. Bienkowska J, Hartman H, Smith TF. A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells? Protein Eng. 2003 Dec; 16(12):897-904. PMID: 14983069.
      View in: PubMed
    20. Bienkowska J. Using fold recognition to search for useful proteins: Bayesian approach to fold recognition. Brief Bioinform. 2002 Mar; 3(1):45-58. PMID: 12002223.
      View in: PubMed
    21. Bienkowska J, Yu L, Zarakhovich S, Rogers RG, Smith TF. Protein fold recognition by total alignment probability. Proteins. 2000 Aug 15; 40(3):451-62. PMID: 10861936.
      View in: PubMed
    22. Bienkowska J, Rogers RG, Smith TF. Eliminating superfluous neighbor pairs while threading fold models. Pac Symp Biocomput. 2000; 107-18. PMID: 10902161.
      View in: PubMed
    23. Bienkowska J, Rogers RG, Smith TF. Filtered neighbors threading. Proteins. 1999 Nov 15; 37(3):346-59. PMID: 10591096.
      View in: PubMed
    24. Bienkowska J, Rogers RG, Smith TF. Performance of threading scoring functions designed using new optimization method. J Comput Biol. 1999 Fall-Winter; 6(3-4):299-311. PMID: 10582568.
      View in: PubMed
    25. Das S, Yu L, Gaitatzes C, Rogers R, Freeman J, Bienkowska J, Adams RM, Smith TF, Lindelien J. Biology's new Rosetta stone. Nature. 1997 Jan 02; 385(6611):29-30. PMID: 8985242.
      View in: PubMed
    26. Smith TF, Lo Conte L, Bienkowska J, Gaitatzes C, Rogers RG, Lathrop R. Current limitations to protein threading approaches. J Comput Biol. 1997; 4(3):217-25. PMID: 9278056.
      View in: PubMed