Featured Past Publications & Posters

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Publications

D Vasudevan, JR Hickok, RC Bovee, V Pham, LL Mantell, N Bahroos, P Kanabar, XJ Cao, M Maienschein-Cline, BA Garcia, DD Thomas. Nitric Oxide Regulates Gene Expression in Cancers by Controlling Histone Posttranslational Modifications. Cancer Res, 75, 5299-5308, 2015.

M Mandal, KM Hamel, M Maienschein-Cline, A Tanaka, G Teng, JH Tuteja, JJ Bunker, N Bahroos, JJ Eppig, DG Schatz, MR Clark. Histone reader BRWD1 targets and restricts recombination to the Igk locus. Nat Immunol, 16, 1094-1103, 2015.

AH Hutchison*, M Maienschein-Cline*, AH Chiang*, SMA Tabei, H Gudjonson, N Bahroos, R Allada, AR Dinner. Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data. PLOS Comp Biol, 11, e1004094, 2015. *co-authors contributed equally

LM Tai, S Ghura, KP Koster, V Liakaite, M Maienschein-Cline, P Kabanar, N Collins, M Ben-Aissa, Z Lei, N Bahroos, S Green, B Hendrickson, LJ Eldik, MJ LaDu. APOE-modulated Aβ-induced neuroinflammation in Alzheimer’s disease: current landscape, novel data and future perspective. J Neurochem, 133, 465-488, 2015.

AJ Kinloch, A Chang, K Ko, C Dunand, S Henderson, M Maienschein-Cline, N Kaverina, B Rovin, FM Salgado, D Wolfgeher, V Liarski, J Haddon, PJ Utz, PC Wilson, and MR Clark. Vimentin is a dominant target of in situ humoral immunity in human lupus tubulointerstitial nephritis. Arthritis Rheumatol, 66, 3359-3370, 2014.

V Gardeux, I Achour, J Li, M Maienschein-Cline, H Li, L Pesce, G Parinandi, N Bahroos, R Winn, I Foster, JGN Garcia, and YA Lussier. “N-of-1-pathways” unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine. J Am Med Inform Assoc, 21, 1015-1025, 2014.

M Maienschein-Cline, Z Lei, V Gardeux, T Abbasi, RF Machado, V Gordeuk, AA Desai, S Saraf, N Bahroos, and Y Lussier. ARTS: Automated Randomization of Multiple Traits for Study Design. Bioinformatics, 20, 1637-1639, 2014.

YA Lussier, H Li, and M Maienschein-Cline. Conquering computational challenges of omics data and post-ENCODE paradigms. Genome Biol, 14, 310, 2013.

Lei Z, Kanabar P, Maienschein-Cline M, Karpenko O, Chukhman M, Johnson R, Bahroos N. Identification of three common molecular subtypes between gastric cancer and pancreatic cancer, Great Lakes Bioinformatics Conference 2014, Cincinnati Children's Hospital, University of Cincinnati, May 16-18, 2014

Lei Z, Kanabar P, Maienschein-Cline M, Karpenko O, Chukhman M, Bahroos N. A pathway based genomic classifier for prediction of gastric cancer subtypes, Great Lakes Bioinformatics Conference 2015, Purdue University, May 18-20, 2015

KJ Popovich, E Snitkin E, SJ Green, A Aroutcheva, MK Hayden, B Hota, RA Weinstein. Genomic Epidemiology of USA300 Methicillin-Resistant Staphylococcus aureus in an Urban Community. Clin Infect Dis. 2016 Jan 1;62(1):37-44. doi: 10.1093/cid/civ794. Epub 2015 Sep 7.


Posters

Detection and interpretation of extrachromosomal microDNAs from next-generation sequencing data. M Maienschein-Cline, Z Lei, P Kanabar, H Hu, G Chlipala, M Chukhman, N Bahroos, S Green, and C Zhang. 2015 ISCB Rocky Mountain Bioinformatics Conference, Aspen, CO.

Creating a library of genome-wide chromatin state patterns during B lymphopoiesis. M Maienschein- Cline, Z Lei, P Kanabar, H Hu, G Chlipala, M Chukhman, N Bahroos, M Mandal, and M Clark. 2015 RECOMB/ISCB Conference on Regulatory and Systems Genomics, Philadelphia, PA.

Isolation of double-stranded RNA for detection of viruses in infected host cells. M Maienschein-Cline, Z Lei, P Kanabar, M Chukhman, N Bahroos, and H Lipton. 2015 University of Illinois Department of Medicine Scholarly Activities Day, Chicago, IL.

Isolation of double-stranded RNA for detection of viruses in infected host cells. M Maienschein- Cline, Z Lei, P Kanabar, M Chukhman, N Bahroos, and H Lipton. 2015 GLBIO Conference, Purdue University, West Lafayette, IN.

Detection of short extrachromosomal circular DNA from short-read DNA sequencing. M Maienschein- Cline, Z Lei, P Kanabar, O Karpenko, M Chukhman, R Johnson, N Bahroos, S Green, and C Zhang. 2014 GLBIO Conference, Cincinnati Children’s Hospital, Cincinnati, OH.

Lei Z, Kanabar P, Maienschein-Cline M, Karpenko O, Chukhman M, Johnson R, Bahroos N. Identification of three common molecular subtypes between gastric cancer and pancreatic cancer, Great Lakes Bioinformatics Conference 2014, Cincinnati Children's Hospital, University of Cincinnati, May 16-18, 2014

Lei Z, Kanabar P, Maienschein-Cline M, Karpenko O, Chukhman M, Bahroos N. A pathway based genomic classifier for prediction of gastric cancer subtypes, Great Lakes Bioinformatics Conference 2015, Purdue University, May 18-20, 2015


Talks

Obtaining high-quality, genome-wide genotypes from archival FFPE tissue samples. 2016 AMIA Joint Summits on Translational Science, San Francisco, CA.

Detection and interpretation of extrachromosomal microDNAs from next-generation sequencing data. 2015 ISCB Rocky Mountain Bioinformatics Conference, Aspen, CO.

Creatng a library of genome-wide chromatin state patterns during B lymphopoiesis. 2015 RECOMB/ISCB Conference on Regulatory and Systems Genomics, Philadelphia, PA.

Automated Batch Randomization for Better Study Design. 2014 AMIA Joint Summits on Translational Science, San Francisco, CA.