The University of Toledo

Recent Publications

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

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.

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, 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. TheScientificWorld 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.

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.

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 X. Structural 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-V.  Interaction 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 pairs. Nucleic Acids Res. 2009, Apr;37(7):2294-312. Epub 2009, Feb 24.