KBRIN Bioinformatics Journal Club

Spring 2017 Schedule

NOTE: All meetings are held at 12:00pm unless otherwise noted


Jan 11CTR 124Julia Chariker, Ph.D., Research Scientist, Psychological and Brain Sciences and KBRIN Networks and Data Visualization SpecialistTopic: "New scoring system to identify RNA G-quadruplex folding." Read article

Jan 18CTR 124Cassandra Scalf, Doctoral student, Western Kentucky UniversityTopic: "Transcriptomic Response to Immune Challenge in Zebra Finch (Taeniopygia guttata) using RNA-seq."

Jan 25CTR 124Xiaohong Li, KBRIN Biostatistician, Small Genomes, Variants and SNP Analyses SpecialistTopic: Gut microbiome alterations in patients with stage 4 hepatitis C. Access article

Feb 1CTR 124Cynthia Gomes, Ph.D. Postdoc, UofL Dept. of Anatomical Sciences and NeurobiologyTopic: Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Access Article

Feb 8CTR 124Kalina Andreeva, PhD, UofL Postdoctoral Scholar, Dept. of Anatomical Sciences and NeurobiologyTopic: Oncogenic Role of Fusion-circRNAs Derived from Cancer-Associated Chromosomal Translocations. Access Article

Feb 15CTR 124Shizuka Uchida, Associate Professor, School of Medicine; Investigator, Cardiovascular Innovative Institute’s Division of Regenerative MedicineTopic: Long Non-Coding RNAs and Circular RNAs. Learn more about Dr. Uchida's research

Feb 22CTR 124Andrey Smelter, PhD student in Bioinformatics Topic: Simulation-based comprehensive benchmarking of RNA-seq aligners. Access Paper

Mar 1CTR 124Michal Hetman, Professor of Neurological Surgery; Endowed Chair in Molecular Signaling at the Kentucky Spinal Cord Injury Research CenterTopic: "Is there a role for ribosomal stress in neuropathogenesis of Zika virus infection?"

Mar 8CTR 124Tyler Weirick, a doctoral candidate at the Institute for Cardiovascular Regeneration, Goethe University and a senior research technologist at the UofL Cardiovascular Innovation InstituteTopic: "Towards distributed automated science through solving scientific reproducibility problems."

Mar 22CTR 124Christine Dolin, graduate student, Department of Pharmacology and Toxicology at UofLTopic: "A systems-based approach to discover alcohol-induced mechanisms in the liver, lung, and kidney."

Mar 29CTR 124Samantha Carlisle, graduate student, Department of Pharmacology and Toxicology at UofLTopic: "A Multi-omic Approach to Elucidating the Role of Arylamine N-acetyltransferase 1 (NAT1) in Breast Cancer Cell Metabolism"

Apr 5CTR 124Jun Yan, PhD, Professor of Medicine and Endowed Chair in Translational Research in the James Graham Brown Cancer CenterTopic: "Regulation of Immunosuppressive Macrophages by Transcription Factor c-Maf"

Apr 12CTR 123Hong Gao, PhD, Research Associate in the Genomics Core at U of L Topic: "The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies." Access Paper

Apr 19CTR 124David Tieri, PhD, postdoctoral associate in the KBRIN Bioinformatics CoreNational Cancer Institute's Genomic Data Commons (GDC) Read background info: Nature article or the UChicagoNEWS article



Sep 7CTR 124Eric Rouchka, UofL Doctoral Student in BioinformaticsTopic: "Sense-antisense gene-pairs in breast cancer and associated pathological pathways." Read article

Sep 14CTR 124Julia CharikerTopic: Cytoscape: PhosphoPath

Sep 21CTR 124Juw Won ParkTopic: "rMAPS: RNA map analysis and plotting server for alternative exon regulation." Article

Sep 28
12:30 pm
CTR 124Mohammed Sayed, Doctoral Student, CECS, UofLTopic: "microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network." Oncogene (2016). Read Paper

Oct 5CTR 124Ataur Katebi, PhDTitle: Conformational Variability of Proteins and Chromatin View Abstract


12:30 pm Oct 19CTR 123Mohamed Chaabane"RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application." View Article

Oct 26TBDRakesh Kaundal, Ph.D.Title: Systems biology approach to study gut microbiota-host interaction

Nov 2CTR 124Xiaoxi Dong, PhDCentralizing Bioinformatics via High-Performance Computing: Opportunities and Challenges in the -Omics era. Read abstract

Nov 9CTR 124Patrick Trainor"Revealing disease-associated pathways by network integration of untargeted metabolomics." View Article

Nov 16CTR 123Aanchal MalhotraRegulation of circRNA biogenesis. Article


Nov 30CTR 123John Caskey, Division of Biotechnology and Molecular Medicine and the Center for Computation & Technology at Louisiana State UniversityTBD


Jan 13CTR 124Ben Harrison, PhD,UofL Dept. of Anatomical Sciences and Neurobiology"Tunable protein synthesis by transcript isoforms in human cells” Access Article

Jan 20CTR 124Sen Yao,UofL Doctoral Student in Bioinformatics“Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis,” Access paper on KBRIN site

Jan 27CTR 124Andrey Smelter, UofL Doctoral Student in Bioinformatics“Experimental protein structure verification by scoring with a single, unassigned NMR spectrum,” Access paper on KBRIN site

Feb 3CTR 124Ernur Saka, UofL Doctoral Student, Dept. of Computer Engineering and Computer Science“FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data,” Access paper

Feb 10CTR 124Hui Zhang, PhD, UofL Asst Professor, Dept. of Computer Engineering & Computer Science"Visual Informatics and Data-intensive Computing for Scientific Investigation."Access paper

Feb 17CTR 124Kalina Andreeva, PhD, UofL Postdoctoral Scholar, Dept. of Anatomical Sciences and NeurobiologyNeural circular RNAs are derived from synaptic genes and regulated by development and plasticity Access paper

Feb 24CTR 124Robert Flight, PhD, Senior Bioinformatics Research Associate, University of Kentucky"Cancer Classification and Power Analysis From Metabolomics"

Mar 2CTR 124Sen Yao,UofL Doctoral Student in Bioinformatics“Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis,” Access paper on KBRIN site

Mar 9CTR 124TBA"High-throughput Sequencing Analysis at the KBRIN Bioinformatics Core”


Mar 23CTR 124Mohammed Sayed, Doctoral Student in Computer Science (Location: Rouchka Lab on Belknap)“Discover hidden splicing variations by mapping personal transcriptomes to personal genomes.” Access Paper

Mar 30CTR 124Xiao Li, KBRIN Bioinformatics Core"Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data" Access Paper

Apr 6CTR 124Julia Chariker, KBRIN Bioinformatics Core "Spark: A navigational paradigm for genomic data exploration."

Apr 13CTR 124Ali Magableh"Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer Cells," Access Paper

Apr 20CTR 124Maha Soliman, KBRIN Bioinformatics Core

Apr 27CTR 124Michael Merchant, Associate Professor, Division of Nephrology & Hypertension"The evolving revolution in proteomic dataset search strategies. Where will they lead us?" Dr. Merchant will use research data to illustrate how approaches to data set analysis continually improve and how this has a significant impact on proteomic research.

May 4CTR 124Patrick Trainor,


Sept 9CTR 124Eric Rouchka

Sept 16 CTR 124 Julia Chariker

Sept 23CTR 124 Ben Harrison

Sept 30CTR 124Xiao Li

Sept 23CTR 124 Ben Harrison

Oct 7, 12pmCTR 124Juw Won Park"Complementary sequence-mediated exon circularization” Read Paper

Oct 13-14CTR 124Genome Browser Workshop

Oct 21CECS Dept.Eric Rouchka"Bioinformatics Challenges, Competitions and Hackathons.” On Belknap campus today in the Bioinformatics Lab, Duthie 238 or Join Via Browser

Oct 28Research!Louisville

Nov 4, 12pmCTR 124Patrick Trainor"Computational and statistical analysis of metabolomics data"
Access Article

Nov 11Cancelled due to IDeA Conference

Nov 18CTR 124 Kalpi deSilva"A comparative encyclopedia of DNA elements in the mouse genome"
Access Article

Nov 25Thanksgiving

Dec 2CTR 124 Sudhir Srivastava