Journal Club

Fall 2019 Schedule

NOTE: All meetings are held from 2:45 am to 3:45 pm in the KBRIN Conference Room unless otherwise noted


DATELOCATIONPRESENTER TOPIC

Wed., Feb. 26
at 2:45 pm
KY INBRE Conference Room, 522 E. Gray St.All participate Topic: "Spatial mapping of cell types by integration of transcriptomics data" You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

Wed., Feb. 5
at 2:45 pmKY INBRE
 Conference Room, 522 E. Gray St.All participate Topic: "Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes " You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

ARCHIVE

DATELOCATIONPRESENTERTOPIC

Wed., Nov 20
at 12:15 pm
KBRIN Conference Room, 522 E. Gray St.All participate Topic: "An accurate and robust imputation method scImpute for single-cell RNA-seq data" You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

Wed., Nov 13
at 12:15 pm
KBRIN Conference Room, 522 E. Gray St.All participate Topic: "Bias, robustness and scalability in single-cell differential expression analysis" You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

Wed., Oct. 23
at 12:15 pm
KBRIN Conference Room, 522 E. Gray St.All participate Topic: "Single-cell epigenomics: Recording the past and predicting the future" You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

Wed., Oct. 16
at 1:30 pmm
KBRIN Conference Room, 522 E. Gray St.All participate Topic: "Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM" You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

Wed., Oct. 9
at 12:15 pm
KBRIN Conference Room, 522 E. Gray St.All participate Topic: "Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs" You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

Wed., Sept. 25
at 12:15 pm
KBRIN Conference Room, 522 E. Gray St.All participate Topic: "Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression" You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

<p >Wed., Sept. 18
at 12:15 pm
KBRIN Conference Room, 522 E. Gray St.All participate Topic: "Supervised classification enables rapid annotation of cell atlases" You can access the article here. Send your questions to Julia Chariker at: julia.chariker@louisville.edu

DATELOCATIONPRESENTERTOPIC

Wed., Apr 17
at 11:30 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Jae Hwang, Postdoctoral Assoc, CECS, UofL Topic: "Accurate classification of BRCA1 variants with saturation genome editing." You can access the article here. Send your discussion questions to Jae Hwang at: jae.hwang@louisville.edu

Wed., Apr 3
at 11:30 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Mohammed Sayed, Doctoral Student, CECS, UofL Topic: "Gain-of-function mutation of microRNA-140 in human skeletal dysplasia." You can access the article here. Send your discussion questions to Mohammed Sayed at: mohammed.sayed@louisville.edu

Wed., Mar 27
at 11:30 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Martin Heil, Bioinformatics Research Developer at the UofL Bioinformatics Lab Topic: "Predicting Cancer Drug Response using a Recommender System." You can access the article here. Send your discussion questions to Martin Heil at: xiaohong.li@louisville.edu

Wed., Mar 20
at 11:30 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Xiao Li, RNA and DNA Sequencing Analysis Specialist, KBRIN Core Staff Topic: "Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data." You can access the article here. Send your discussion questions to Xiao Li at: xiaohong.li@louisville.edu

Wed., Mar 6
at 11:30 am
Belknap Campus in Duthie Center, Room 238Group leader: David Tieri, Anatomical Sciences and Neurobiology and KBRIN Core Staff Topic: "Practical guidelines for B-cell receptor repertoire sequencing analysis." You can access the article here. Send your discussion questions to David Tieri at: david.tieri@louisville.edu

Wed., Feb 20
at 11:30 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Grant Park, Student Assistant Speed-Computer Engineering Computer Science Topic: "Transfer learning for biomedical named entity recognition with neural networks." You can access the article here. Send your discussion questions to Grant Park at: grant.park@louisville.edu

Wed., Feb 13
at 11:30 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Jonah Daneshmand, Graduate Fellow, SIGS Program in Bioinformatics Topic: Shared and Species-Specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species." You can access the article here. Send your discussion questions to Kalpi De Silva at: kandaudamalinika.desilva@louisville.edu

Wed., Jan 30
at 11:30 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Jonah Daneshmand, Graduate Fellow, SIGS Program in Bioinformatics Topic: Widespread RNA editing dysregulation in brains from autistic individuals." You can access the article here. Send your discussion questions to Jonah Daneshmand at: jonah.daneshmand@louisville.edu

Wed., Jan 23
at 11:30 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Julia Chariker, Postdoctoral Scholar, Department of Neuroscience Training, KBRIN Bioinformatics Core Topic: APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data." You can access the article here. Send your discussion questions to Julia Chariker at: julia.chariker@louisville.edu

Wed., Jan 16,
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Aryan Neupane, Doctoral Student, Interdisciplinary Ph.D. Program in Bioinformatics, UofLTopic: "Isoform-level gene expression patterns in single-cell RNA-sequencing data" You can access the article here. Send your discussion questions to Aryan Neupane at: goonerrn@gmail.com

Wednesday, Nov 28
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Jae Hwang, Doctoral Associate, Computer Engineering and Computer Science, UofLTopic: "Circular RNA expression in human hematopoietic cells is widespread and cell-type specific." You can access the article here. Send your discussion questions to Jae Hwang at: jae.hwang@louisville.edu

Wednesday, Nov 14
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Aryan Neupane, Doctoral Student, Interdisciplinary Ph.D. Program in Bioinformatics, UofLTopic: "Isoform-level gene expression patterns in single-cell RNA-sequencing data." You can access the article here. Send your discussion questions to Aryan Neupane at: goonerrn@gmail.com

Wednesday, Nov 7
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Juw Won Park, PhD RNA Sequencing Analysis, KBRINTopic: "RNA velocity of single cells" You can access the article here. You may find the associated commentary useful in thinking about the paper: Technique to measure the expression dynamics of each gene in a single cell. Send your discussion questions to Juw Won Park : mohammed.sayed@louisville.edu

Wednesday, Oct. 31st
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Mohammed Sayed, Doctoral Student, CECS, UofLTopic: "Expanding the horizons of microRNA bioinformatics." You can access the article here. Send your discussion questions to Marty Heil: mohammed.sayed@louisville.edu

Wednesday, Oct. 24th
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Marty Heil, Speed Computer Engineering & Computer ScienceTopic: "PennDiff: detecting differential alternative splicing and transcription by RNA sequencing." You can access the article here. Send your discussion questions to Marty Heil: martin.heil@louisville.edu

Wednesday, Oct. 17th
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Xiao Li, PhD, KBRIN Core RNA and DNA Sequencing Analysis SpecialistTopic: "Pooling across cells to normalize single-cell RNA sequencing data with many zero counts." You can access the article here. Send your discussion questions to Xiao Li: xiaohong.li@louisville.edu

Wednesday, Oct. 3rd
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: David Tieri, PhD, Anatomical Sciences and Neurobiology and KBRIN Core StaffTopic: "Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires." You can access the article here. Send your discussion questions to David Tieri: david.tieri@louisville.edu

Wednesday, Sept. 26th
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Aanchal Malhotra, Ph.D. Student, Program in Interdisciplinary Studies: Specialization in Bioinformatics Topic: "TRCirc: a resource for transcriptional regulation information of circRNAs." You can access the article here. Send your discussion questions to Aanchal Malhotra: aanchal.malhotra@louisville.edu

Sept. 19th
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Grant Park, Student Asst in Speed-Computer Engineering & Computer Science Topic: "STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts." You can access the article here. Send your discussion questions to grant.park@louisville.edu

Sept. 12th
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Julia Chariker Postdoctoral Scholar, Department of Neuroscience Training, KBRIN Bioinformatics Core Topic: "Dynamic Axonal Translation in Developing and Mature Visual Circuits." You can access the article here. Send your discussion questions to julia.chariker@louisville.edu

Sept. 5th
at 11:15 am
KBRIN Conference Room, 522 E. Gray St.Group leader: Eric Rouchka Associate Professor, Computer Engineering & Computer ScienceTopic: "AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes". You can access the article here.

DATELOCATIONPRESENTERTOPIC

March 29th CTR Room 123Patrick Trainor,, a doctoral Doctoral Student in BioinformaticsTopic: High Performance R: Parallel computing, seamless C++ integration, optimizing linear algebra routines, and deep learning in the R language. Feel free to bring lunch to the meeting.

ABSTRACT: <span >In this talk, an overview of methods for employing the R language for select high performance computing applications will be presented. First, we will introduce straightforward and approachable ways to multi-thread specific processes in R and for making efficient use of the multiple cores / threads that are present on personal computers. Next we will discuss the Rcpp API for orchestrating the compilation, linkage, and calling of compiled C++ code within R functions, R scripts, and interactive R sessions. Beyond accessing the C++ standard library, we will touch on templated C++ linear algebra libraries such as Armadillo and Eigen. As most statistical and machine learning applications require “under the hood” linear algebra routines, we will discuss how to optimize these routines in R and C++ utilizing the OpenBLAS and Intel MKL libraries. We will conclude with a short introduction to R the APIs for TensorFlow and Keras that facilitate deep learning in R. This talk is oriented towards attendees gaining conceptual understandings of the techniques and how they may be applied in biomedical research.

March 22th CTR Room 123Samantha Carlisle, a doctoral candidate and Graduate Research Fellow in Pharmacology and ToxicologyTopic: Deciphering the Role of Human Arylamine N-acetyltransferase 1 in Breast Cancer Cell Metabolism Using a Systems Biology Approach. Feel free to bring lunch to the meeting.

March 8thCTR Room 123Everyone discussesTopic: "Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair." Access article.

FEB 22 CTR Room 123Everyone discussesTopic: "Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development" Access article.

FEB 15 Duthie Center conference room (DC 225), Belknap Campus (Parking info)Everyone discussesTopic: "Efficient backsplicing produces translatable circular mRNAs." Access article. Lunch is not provided. Please feel free to bring your own lunch.

FEB 8Duthie Center conference room (DC 225), Belknap Campus (Parking info)Aanchal Malhotra Topic: "Circular RNAs: emerging cancer biomarkers and targets" Access article. Lunch is not provided. Please feel free to bring your own lunch.

FEB 1CTR 123Mohammed Sayed Topic: "Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function" Read article describing scientific relevance

JAN 25CTR 123Patrick Trainor, Cardiovascular Innovation Institute Topic: "Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets" Read article

JAN 18CTR 123Yi Zhang, doctoral student in the UK Department of Computer Science Topic: "Discerning novel splice junctions derived from RNA-seq alignment through deep learning"

JAN 11CTR 123Tyler Weirick, Cardiovascular Innovation Institute Topic: "Blockchain Project " Read article describing scientific relevance

DATELOCATIONPRESENTERTOPIC

Nov 29CTR 123Keun Seok Seo, an Assistant Professor in the College of Veterinary Medicine, Mississippi State UniversityTopic: "Mechanism of immunosuppression by staphylococcal superantigen." Read article

Nov 16CTR 102Aryan Neupane, graduate student, Department of Bioinformatics & BiostatisticsTopic: "Near-optimal probabilistic Rna-seq quantification." Read article

Nov 9CTR 123Sam Das, Research Scholar, Department of Bioinformatics & BiostatisticsTopic: "Statistical Approaches for Gene Selection, Hub Gene Identification and Module Interaction in Gene Co-Expression Network Analysis: An Application to Aluminum Stress in Soybean (Glycine max L.)" Read article 1 and Read article 2 and Read article 3

Nov 4CTR 123Eric Rouchka, D.Sc., Director of KBRIN Bioinformatics CoreTopic: "Design and Analysis of Single-Cell Sequencing Experiments" Read article 1 and Read article 2 and Read article 3

Oct 19CTR 123Robert Skolik, PhD,, Doctoral Student,Department of Biology at UofL

Oct 12CTR 123Xiao Li, M.S., Small Genomes, Variants and SNP Analyses SpecialistTopic: "Comparative Analysis of Single-Cell RNA Sequencing Methods" Read article

Oct 5CTR 123David Tieri, PhD,, Research Scientist, Psychological and Brain Sciences and KBRIN Topic: "Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer." Read article

Sept 28CTR 123Kalina Andreeva, Ph.D., Research Scientist, Psychological and Brain Sciences Topic: "Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis." Read article

Sept 21CTR 123Julia Chariker, Ph.D., Research Scientist, Psychological and Brain Sciences and KBRIN Networks and Data Visualization SpecialistTopic: "Analysis methods for studying the 3D architecture of the genome." Read article

DATELOCATIONPRESENTERTOPIC

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

DATELOCATIONPRESENTERTOPIC

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

Oct 12RESEARCH LOUISVILLE

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 23THANKSGIVING

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

DATELOCATIONPRESENTERTOPIC

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 16SPRING BREAK

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,

DATELOCATIONPRESENTERTOPIC

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