Program in Bioinformatics & Proteomics/Genomics

Recent Publications

Publications Co-Authored by BPG Faculty/Staff/Students (past four years)

Kuhlman DR, Khuder SA, Lane RD. Factors influencing the diameter of human anterior and posterior intercostal arteries.  Clinical Anatomy. 219-26. March 2015 (In process)

Patki M, Salaar MD, Trumbly R, Ratnam M. Differential effects of estrogen-dependent transactivation vs. transrepression by the estrogen receptor on invasiveness of HER2 overexpressing breast cancer cells. Biochemistry Biophysics Res Commun. 404-411. January 2015 

Fedorov A, BPG Students. Inference of distant genetic relations in humans using "1000 Genomes".  Genome Biology and Evolution. 481-92. January 2015

Mopidevi B, Kaw MK, Puri N, Ponnala M, Jain S, Rana A, Keetha NR, Khuder SA, Fiering SN, Kumar A. Viable transcriptional regulation of the human aldosterone synthase gene causes salt-dependent high blood pressure in transgenic mice. Circ Cardiovascular Genet.  December 2014

Khuder SA, Al-Hashimi I, Mutgi AB, Altorok N. Identification of potential genomic biomarkers for Sjogren's syndrome using data pooling of gene expression microarrays.  Rheumatology Int.  October 2014

Khan AR, Binabdulhak AA, Alastal Y, Khan S, Faricy-Beredo BM, Luni FK, Lee WM, Khuder S, Tinkel J. Cardioprotectivve role of ischemic post-conditioning in acute myocardial infarction: a systematic review and meta-analysis. American Heart Journal. 512-521. October 2014 

Khan AR, Khan S, Sheikh MA, Khuder S, Grubb B, Moukarbel GV. Catheter ablation and antiarrhythmic drug thereapy as first or second-line therapy in the management of atrial fibrillation: systematic review and meta-analysis. Circ Arrhythm Electrophysiology. 853-60. October 2014

Akkuratov EE, Walters L, Saha-Mandal A, Khandekar S, Crawford E, Zirbel CL, Leisner S, Prakash A, Fedorova L, Fedorov A. Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence. Gene: 6548 (1): 81-90. September 2014

Stechschulte LA, Hinds TD Jr, Khuder SS, Shou W, Najjar SM, Sanchez ER. FKBP51 controls cellular adipogenesis through p38 kinase-mediated phosphorylation of GRz and PPARy. Mol Endocrinol. 1265-75. August 2014

Lecha-Czernik B, Stechschulte LA.  Bone and fat: a relationship of different shades.  Arch Biochemistry Biophysics. 00212-4. June 2014

Kolli V, Stechschulte LA, Dowling AR, Rahman S, Czernik PJ, Lecka-Czernik B. Partial agonist, telmisartan, maintains PPARy serine 112 phosphorylation, and does not affect osteoblast differentiation and bone mass. PLoS One.  May 2014

Qiu S, McSweeny A, Choulet S, Saha-Mandal A, Fedorova L, Fedorov A. Genome evolution by matrix algorithms: cellular automata approach to population genetics.  Genome Biology Evolution: 988-99.  April 2014

Liu Y, Olenrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X. Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Research; 4859-67.  April 2014

Wijayasinghe YS, Blumenthal RM, Viola RE. Producing proficient methyl donors from alternative substrates of S-adenosylmethionine synthetase. Biochemistry: 1521-6.  March 2014 

Yeo J, Crawford EL, Blomquist TM, Stanoszek LM, Dannemiller RE, Zyrek J, De Las Casas LE, Khuder SA, Willey JC. A multiplex two-color real-time PCR method for quality-controlled molecular diagnostic testing of FFPE samples. PLoS One. February 2014

Kim JH, Meyers MS, Khuder SS, Abdallah SL, Muturi HT, Russo L, Tate CR, Havener AL, Najjar SM, Leloup C, Mauvais-Jarvin F. Tissue-selective estrogen complexes with bazedoxifene prevent metabolic dysfunction in female mice. Molecular Metabolism 177-90. January 2014

Mantripragada VP, Lecka-Czernik B, Ebraheim NA, Jayasuriya AC. An overview of recent advances in designing orthopedic and craniofacial implants.  Journal of Biomedical Material Research. 3349-64. November 2013

Saha-Mandal A, Cheng Xi, Qiu Shuhao, Serpen J, Fedorova L, Fedorov A. What do 1000 genomes tell us about biased gene conversion hypothesis? Submitted September 2013.

Baylan N, Bhat S, Ditto M, Lawrence JG, Lecka-Czernik B, Yildirim-Ayan E. Polycaproiactone nanofiber interspersed collagen type-1 scaffold for bone regeneration: a unique injectable osteogenic scaffold. Biomedical Material. 045011. August 2013

Rahman S, Lu Y, Czernik PJ, Rosen CJ, Enerback S, Lecka-Czernik B. Inducible brown adipose tissue, or beige fat, is anabolic for the skeleton. Endocrinology 2687-701. August 2013

Qiu S, McSweeny A, Choulet S, Saha-Mandal A, Fedorova L, Fedorov A. Matrix Algorithms for genome evolution (MAGE).   Submitted July 2013

Nabiyouni M, Prakash A, Fedorov A. Vertebrate condon bias suggest a highly GD-rich ancestral genome. Gene; 519(1): 113-119. April 2013.

Williams K, Savageau MA, Blumenthal RM. A bistable hysteretic switch in an activator-repressor regulated restriction-modification system.  Nucleic Acid Res. 41: 6045-6057.  PMC3695507 Featured article. July 2013

Liang J, Blumenthal RM. Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins. BMC Evolution Biology, 13:218.  October 2013

Liu Y, Zhang X, Blumenthal RM, Cheng X.  A common mode of recongnition for methylated CpG.  Trends Biochemical Science 38: 177-183. July 2013

Patki M, Chari V, Sivakumaran S, Gonit M, Trumbly R, Ratnam M. The ETS domain transcription factor ELK1 directs a critical component of growth signaling by the androgen receptor in prostate cancer cells. Journal of Biology & Chemistry. 11047-65. April 2013

Geng S, Matsushima H, Okamoto T, Yao Y, Lu R, Page K, Blumenthal RM, Ward NL, Miyazaki T, Takashima A. Emergence, origin and function of neutrophil-dendritic cell hybrids in experimantally induced inflammatory lesions in mice. Blood 121: 1690-1700.  March  2013

Taleb M, Khuder S, Tinkel J, Khouri SJ.  The diagnostic accuracy of Doppler Echocardiography in assessment of pulmonary artery systolic pressure: A meta-analysis.  Echocardiography, Dec. 10, 2012.

Sofi AA, Silverman AL, Khuder S, Garborg K, Westerink MJ, Nawras A. Relationship of symptom duration and  fecal bacteriotherapy in clostridium difficile infection-polled data analysis and a systematic review. Scand J. Gastroenterol, Nov. 19, 2012.

Koffman B, Khuder S, Mutgi S, Crooks R, Herial N. Impact of oral health in patients with multiple sclerosis and epilepsy; a survey in a neurology clinic. Spec Care Dentist, 32(4): 150-4. July-August 2012.

Rega PP, Roberts SM, Khuder S, Boardley D, Brickman K, Regent C.  The delivery of a health promotion intervention by a public health promotion specialist improves patient satisfaction in the emergency department.  Acad Emerg Med 3:313-7, Mar. 19, 2012.

Khaskhely N, Mosadowski J, Thompson RS, Khuder S, Smithson SL, Westerink MA.  Phenotypic analysis of pneumococcal polysacchaide-specific B cells
J Immunol. Mar 1, 2012

Shepard S, McSweeny A, Serpen G, Fedorov A. Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models. Nucleic Acids Research doi: 10.1093/nar/gks154, 2012.

Nabiyouni M, Prakash A., Fedorov A. Peculiarities in vertebrate codon bias suggest a highly GC-rich ancestral genome. Submitted, December 2011.

Rogers SO.  2012 Integrated Molecular Evolution (textbook). CRC Press, Boca Raton, FL. (Released, July 2011; 2012 copyright date).
McCullough A.C., Seifried M, Zhao X, Haase J, Kabat WJ, Yogev R, Blumenthal RM, and Mukundan D. Higher incidence of perineal community acquired MRSA infections among toddlers. BMC Pediatrics, 11:96, October 2011  

Hart BR, Mishra PK, Lintner RE, Hinerman JM, Herr AB, and Blumenthal RM. Recognition of DNA by the Helix-Turn-Helix global regulatory protein Lrp is modulated by the amino terminus. J. Bacteriol.;193:3794-3803, August 2011.

He J, Shepard S.S., Fedorov A., Leisner S. Identification of candidate genes regulated through argonaute4-dependent RNA-dependent DNA methylation in Arabidopsis. Under revision for Gene.

Shepard S, McSweeny A, Serpen G, Fedorov A. Binary-absrtacted Markov models and their application to sequence classification. Under minor review in Nucleic Acids Research, 2011

Yu B, Fey P, Kestin-Pilcher KE, Fedorov A, Prakash A, Chisholm RL, Wu JY. Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae. Protein Cell. May;2(5):395-409, 2011.

Prakash A, Bechtel J, Fedorov A. Genomic MRI – a public resource for studying sequence patterns within genomic DNA. J Vis Exp. 9;(51). pii: 2663, 2011.

Rearick D, Prakash A, McSweeny A, Shepard S.S, Fedorova L, Fedorov A. Critical association of ncRNA with introns. Nucleic Acids Research, 39(6):2357-66, 2011.

Fedorova L. and Fedorov A. Mid-range Inhomogeneity of Eukaryotic Genomes. The Scientific World Journal: Genes & Genomics. 11:842-854, 2011.

Fedorov A, Fedorova L. An Intricate Mosaic of Genomic Patterns at Mid-range Scale. Chapter for a book “Advances in Genome Sequence Analysis and Pattern Discovery. Science, Engineering, and Biology Informatics, Vol. 7; Eds: L. Elnitski, H. Piontkivska, and L.R.Welch. World Scientific Publishing Co. Pte. Ltd. Singapore, 2011.

Harris LB, Rogers SO. Evolution of small putative group I introns in the SSU rRNA gene locus of Phialophora species. BMC Res. Notes 4:258-262, 2011.

Shang W, Svergun DI, Borbulevych OY, Ivanow I, Aleem AM, Jankun J, Kühn H, Skrzypczak-Jankun E. Probing dimerization and structural flexibility of mammalian lipoxygenases by small-angle X-ray scattering. J. Mol. Biol. 409: (4), 654-668, 2011

Jankun J, Skotnicka M, Lysiak-Szydlowska W, Al-Senaidy A, Skrzypczak-Jankun E. Diverse inhibition of plasminogen activator inhibitor type 1 by theaflavins of black tea. International Journal of Molecular Medicine, 27: 525-529, 2011.

Jankun J, Skrzypczak-Jankun E. Val17Ile Single Nucleotide Polymorphisms Similarly as Ala15Thr Could be Related to the Lower Secretory Dynamics of PAI-1 Secretion - Theoretical Evidence. Current Molecular Medicine, 11:(6), 512-516, 2011.

Jankun J. Protein-based nanotechnology: antibody conjugated with photosensitizer in targeted anticancer photoimmunotherapy. International Journal of Oncology, 39: (4), 949-953, 2011.

Skotnicka M, Chorostowska-Wynimko J, Jankun J, Skrzypczak-Jankun E. The black tea bioactivity: an overview. Eastern European Journal of Immunology, 36:4, 2011.

Szefel J, Piotrowska M, Kruszewski WJ, Skrzypczak-Jankun E. Jankun J, Lysiak-Szydlowska W. The Eicosanoids in prevention and management of diseases. Current Molecular Medicine, 11:1, 13-25, 2011.

Abu Almakaren A, Petrov A, Stombaugh J, Zirbel C, Leontis N. Geometric Classification and Comprehensive Survey of Base Triples in RNA Structures.  Nucleic Acids Research. Publication date (web): November 3, 2011.

Zgarbova M,  Jurecka P, Banas P, Otyepka M, Sponer JE, Leontis NB, Zirbel CL, Sponer J.  Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base – phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. J. Phys. Chem. A. DOI: 10.1021/jp204820b. Publication date (web): September 12, 2011.

Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan C, Halvorsen M, Knight R, Leontis N, Mathews DH,  Ritz J, Stombaugh J, Weeks K, Zirbel C, Laederach A. Sharing and archiving nucleic acid structure mapping data. RNA 17:1204-1212, 2011.

Petrov A, Zirbel C, Leontis N.  WebFR3D - a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Research. doi:10.1093/nar/gkr249, 2011.

Hoehndorf R, Batchelor C, Bittner T, Dumontier M, Eilbeck K, Knight R, Mungall CJ, Richardson JS, Stombaugh J, Westhof E, Zirbel CL, Leontis NB. The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data. Applied Ontology. 6(1) 53-89, 2011.


Publications Co-Authored by BPG Faculty/Staff/Students (2009 and 2010)

Cheng X, Blumenthal RM. Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochemistry 2010 Apr 13: 49(14): 2999-3008.

Zhang J, Gonit M, D’Alincourt Salazar M, Shatnawi A, Shemshedini L, Trumbly R, Ratnam M.C/EBPalpha redirects androgen receptor signaling through a unique bimodal interaction.  Oncogene 2010, 29:723-38.

Tang H, Park S, Sun SC, Trumbly R, Ren G, Tsung E, Yeung KC. RKIP inhibits NF-kappaB in cancer cells by regulating upstream signaling components of the IkappaB kinase complex. FEBS Lett. 2010, 584:662-8.

Mikho-Szkudlarek M, and Chin KV. Inhibition of adipogenesis by prieurianin mediated by the transcriptional repressor Zfp68. submitted, 2010.

Shao Q, and Chin KV. Corn products consumption and the rising trends in obesity. submitted, 2010.

Saladi SV, Keenen B, Marathe HG, Qi H, Chin KV, de la Serna IL. Modulation of extracellular matrix/adhesion molecule expression by BRG1 is associated with increased melanoma invasiveness. submitted, 2010.

Qasem A, Saunders RA, Szkudlarek M, Chin AJB, Bosio R, Wu Q, Fujii K, Shapiro J, Beauchemin N, Najjar S, and Chin KV. Dual mechanistic anorexigenic and anti-adipogenic therapeutic for the treatment of obesity. submitted, 2010.

Saunders RA, Fuji K, Alabanza L, Ravatn R, Kita T, Kudoh K, and Chin KV. Induction of the Phospholipid Transfer Protein Gene Expression by Topoisomerase I Inhibitors. Biochem. Pharm., in press, 2010.

Nestor Kalinoski AL, Ramdath RS, Langenderfer KM, Sikanderkhel S, DeRaedt S, Welch M, Park J, Pringle T, Joe B, Cicila GT, Allison DC.  Neointimal hyperplasia and vasoreactivity are controlled by genetic elements on rat chromosome 3. Hypertension 2010, 55(2):555-56

Mruk I, Blumenthal RM. Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system. Nucleic Acids Res.2009, 37: 983-998.

Blumenthal RM, Cheng XStructural and biochemical advances in mammalian DNA methylation. In: Epigenomics (Ferguson-Smith, A.C., Greally, J.M., and Martienssen, R.A., eds.). 2009, New York: Springer. pp. 85-100; 438 pp. 

Cicila, GT, Morgan EE, Lee SJ, Farms P, Yerga-Woolwine S, Toland EJ, Ramdath RS, Gopalakrishnan K, Bohman K, Nestor-Kalinoski A, Khuder SA, Joe B. Identification of epistatic genetic determinants of blood pressure and mortality in a rat model of salt-sensitive hypertension. Hypertension 2009, 53(4):725-732.

Szkudlarek M, Bosio R, Kudoh Alabanza L, and Chin K-VInteraction of the regulatory subunit of the cAMP-Dependent Protein Kinase with PATZ1 (ZNF278). Biochem. Biophy. Res. Commun., 2010, 391:1318-1323.

Yang W-L, Ravatn R, Kudoh Alabanza L, and Chin K-V. Interaction of the regulatory subunit of the cAMP-Dependent Protein Kinase with PATZ1 (ZNF278). Biochem. Biophy. Res. Commun., 2010, 391:1318-1323.

Jankun J, Aleem A, Selman SH, Basrur V, Skrzypczak-Jankun E. VLHL plasminogen activator inhibitor spontaneously reactivates from the latent to active form. International Journal of Molecular Medicine, 2009, 23(1), 57-63, (on the cover).

Jankun J, Skrzypczak-Jankun E. Yin and Yang of the plasminogen activator inhibitor. Pol Archives of Internal Medicine, 2009, 119(6):410-417.

Jankun J, Aleem AM, Struniawski R, Lysiak-Szydlowska W, Selman SH, Skrzypczak-Jankun E. Accelerated Thrombus Lysis in the blood of plasminogen activator inhibitor deficient mice is inhibited by PAI-1 with a very long half-life. Pharmacological Reports, 2009, 61(4): 673-80.

Ansari M, Aleem AM, Wells L, Jankun J, Walther M. Kühn H, Reinartz J, Skrzypczak-Jankun E. Human platelet 12-lipoxygenase: Naturally occurring Q261/R261 variants and N544L mutant show altered activity but unaffected substrate binding and membrane association behavior. International Journal of Molecular Medicine, 2009, 24(6):759-64.

Jankun J, Selman SH, Keck RW, Lysiak-Szydłowska W, Skrzypczak-Jankun E. Very long half-life plasminogen activator inhibitor Type 1 reduces bleeding in a mouse model. British Journal Urology Int., 2009, Nov 13. [Epub ahead of print]

Ilikchyan, IN, McKay RML, Zehr JP, Dyhrman ST, Bullerjahn GS.  Detection and expression of the phosphonate transporter gene phnD in marine and freshwater picocyanobacteria.  Environ. Microbiol. 2009, 11:1314-132.

Sharma AK, Sommerfeld K, Bullerjahn GS, Matteson A, Wilhelm SW, Jezbera J, Brandt U, Doolittle WF, Hahn MW.  Widespread distribution of actinorhodopsin genes in freshwater habitats and among diverse actinobacterial lineages.  ISME J. 2009, 3: 726-737.

D'Elia T, Veerapaneni R, Theraisnathan V, Rogers SO.  Isolation of fungi from Lake Vostok accretion ice. Mycologia 1 2009, 01:751-763.

Hassler CS, Havens SM, Bullerjahn GS, McKay RML, Twiss MR.  An evaluation of iron bioavailability and speciation in western Lake Superior with the use of combined physical, chemical, and biological assessment. Limnol. Oceanogr. 2009, 54: 987-1001.

Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB. Classification and energetics of the base-phosphate interactions in RNA.  Nucleic Acids Res. 2009 Aug;37(15):4898-918. Epub 2009, Jun 14.

Stombaugh J, Zirbel CL, Westhof E, Leontis NB. Frequency and isostericity of RNA base pairsNucleic Acids Res. 2009, Apr;37(7):2294-312. Epub 2009, Feb 24.




Last Updated: 6/26/15