Past Seminars

Bioinformatics Seminar Series

Hosted by: Department of Computer and Information Sciences
Department of Electrical and Computer Engineering
Center for Bioinformatics and Computational Biology

Fall 2020

Prediction Model for COVID-19 Patient Visits in the Ambulatory Setting Riza Li Graduate Student University of Delaware	September 14, 2020 3:30 PM
Molecular insights into wooden breast in broiler chickens suggest similar pathomechanism to diabetes mellitus Juniper Lake Graduate Student University of Delaware Utilizing the genotypic features of phage replication modules to make sense of viral dark matter Zach Schreiber Graduate Student University of Delaware	September 21, 2020 3:30 PM
RNASeq in Sey Mice suggests key Pathways in Aniridic Cataract Adam Pater-Faranda Graduate Student University of Delaware Predictive Modeling of Opioid Epidemic in United States Sachin Gavali Graduate Student University of Delaware	September 28, 2020 3:30 PM
Capturing mutations and their impact in Alzheimer's disease via text mining methods Xihan Qin Graduate Student University of Delaware Whole-genome metagenomic analysis of the gut microbiome in horse keepers Jose Daniel Chazi Capelo Graduate Student University of Delaware	October 5, 2020 3:30 PM
A Brief Introduction to Viral Bioinformatics and its Applications from Lab to Field Studies Sarah Schwenk Graduate Student Scripps Institution of Oceanography, UC San Diego	October 15, 2020 12:30 PM
Genetic studies of developmental stuttering: From linkage analysis to next-generation sequence Ho Ming Chow Assistant Professor, Communication Sciences & Disorders University of Delaware Carlos Frigerio Domingues Research Assistant, Communication Sciences & Disorders University of Delaware	October 19, 2020 3:30 PM
Tumor evolution at multiple dimensions Subhajyoti De Associate Professor, Center for Systems and Computational Biology Department of Pathology & Laboratory Medicine Rutgers Cancer Institute of New Jersey, Rutgers University	October 26, 2020 3:30 PM
HIV latency, the major hurdle in HIV eradication; and the impact of cocaine on HIV gene expression and replication Mudit Tyagi Associate Professor Thomas Jefferson University	November 2, 2020 3:30 PM
Combinatorial Optimization for Computational Vaccine Design Oliver Kohlbacher Professor, Applied Bioinformatics University of Tuebingen and the Max Planck Institute, Germany	November 12, 2020 2:30 PM
Signaling Dynamics Directs Collective Cell Behavior: From Tissue Culture to Mouse Models Sergi Regot Assistant Professor, Department of Molecular Biology and Genetics Johns Hopkins University	November 16, 2020 3:30 PM
Thanksgiving Break	November 23, 2020
Quantifying and Characterizing Cancer Cell Death Kinetics Scott Dixon Assistant Professor, Biology Stanford University	November 30, 2020 3:30 PM
Patterns of Metabolic Reprogramming in the Post-hatch Broiler Chick as Characterized by Integrated Correlation Analysis of High-Throughput Data Heidi Van Every Graduate Student University of Delaware Optogenetics Stimulation In Non-Invasive Skeletal Muscle Activation: Biomarker Identification Via Key Gene Expressions In Calcium Signaling Pathway Iman Bhattacharya Graduate Student University of Delaware	December 7, 2020 3:30 PM

Spring 2020

InteinFinder: automated intein detection from large protein datasets Ryan Moore Graduate Student University of Delaware Use of high-throughput data to characterize post hatch hepatic development in the modern broiler chicken Heidi Van Every Graduate Student University of Delaware	February 10, 2020 3:30 PM
The role of chromatin reorganization and alternative splicing events in head and neck cancer development Daria Gaykalova Assistant Professor Johns Hopkins University	February 17, 2020 3:30 PM
An Introduction to Extraction and Analysis of EHR-derived Phenotypes Rebecca Hubbard Associate Professor University of Pennsylvania	February 24, 2020 3:30 PM
Design Principles of Dynamic Gene Control Bomyi Lim Assistant Professor University of Pennsylvania	March 2, 2020 3:30 PM
Perspectives gained when transitioning from hypothesis-driven to discovery-driven research Jacob Dums Post-Doctoral Researcher University of Delaware	March 9, 2020 3:30 PM
The role of ADAM9 in colorectal cancer Congyu Lu Graduate Student University of Delaware An online microbial data management system to uncover the horse gut microbiome Daniel Jose Capelo Graduate Student University of Delaware	March 30, 2020 3:30 PM
A comparison of the chicken intestinal microbiome associated with age-, breed- and immune-related differences Chi Zhang Graduate Student University of Delaware Predictive modeling of substance use treatment completion in pregnant opioid users Matthew Walt Graduate Student University of Delaware	April 6, 2020 3:30 PM
Transcriptional response of actinobacteria in light/dark cycling Priscilla Hempel Graduate Student University of Delaware Understanding Plant Stress Responses: Using Systems Biology Approaches and Text Mining Methods Rita Hayford Graduate Student University of Delaware	April 13, 2020 3:30 PM
Association between socioeconomic status and comorbid conditions in a population of diabetes patients Riza Li Graduate Student University of Delaware Metabolic pathway membership inference by machine learning method Imam Cartealy Graduate Student University of Delaware	April 20, 2020 3:30 PM
Bioinformatics Student Career Panel BiSA Career Panel University of Delaware	April 27, 2020 3:30 PM
Investigation of small microRNAs in Tdrd7-/- Mammalian Lens Salma Al Saai Graduate Student University of Delaware iTextMine framework for Alzheimer's and other neurodegenerative diseases Xihan Qin Graduate Student University of Delaware	May 4, 2020 3:30 PM
Uncovering Viral Dark Matter Zach Schreiber Graduate Student University of Delaware Transcriptomic insight into the mechanisms of Aniridic Cataract Adam Pater-Faranda Graduate Student University of Delaware	May 11, 2020 3:30 PM
Systems biology reveals mechanism of BMP signaling gradient formation Mary Mullins Professor and Vice Chair of the Department of Cell and Developmental Biology University of Pennsylvania Perelman School of Medicine	May 18, 2020 3:30 PM

Fall 2019

Applications of ultra-wideband radio frequency identification device (uwb rfid) technologies to the continuous assessment of health behaviors and related health outcomes Mary Elizabeth (Libbey) Bowen Associate Professor University of Delaware	September 9, 2019 3:30 PM
Predictive Modeling of Long-Term Type 2 Diabetes Complications Using Patient Data in Electronic Health Records Riza Li Graduate Student University of Delaware BiomeSeq: A Tool for the Characterization of Animal Microbiomes from Metagenomic Data Kelly Mulholland Graduate Student University of Delaware	September 16, 2019 3:30 PM
Epigenetic Mechanisms of Cellular Heterogeneity in Gene Expression Keji Zhao Senior Investigator, Systems Biology Center, National Heart, Lung and Blood Institute National Institutes of Health (NIH)	September 23, 2019 3:30 PM
Translating DATA into Insight to Guide Drug Discovery & Development Gunaretnam Rajagopal VP, Global Head, Computational Sciences, Discovery Sciences Janssen, Pharmaceutical Companies of Johnson and Johnson	September 30, 2019 3:30 PM
Utilizing fluctuations in a transcription factor to create cell size patterns Adrienne Roeder Associate Professor Cornell University	October 7, 2019 3:30 PM
Improve large-scale automatic information extraction for biomedical knowledge discovery and curation Jia Ren Graduate Student University of Delaware Using an integrated bioinformatics approach to understand the role of intrinsically disordered regions in cancer associated proteins Rita Hayford Graduate Student University of Delaware	October 14, 2019 3:30 PM
Mining the "Data Landfill": Linking Multisource Administrative Data to Study the Health of Women and their Children Deborah Ehrenthal Associate Professor University of Wisconsin	October 21, 2019 3:30 PM
iPTMnet: A Case Study Towards FAIR Data Principles Sachin Gavali Graduate Student University of Delaware Increased expression of lipid metabolism genes in early stages of wooden breast links myopathy of broilers to metabolic syndrome in humans Juniper Lake Graduate Student University of Delaware	October 28, 2019 3:30 PM
A Scalable Web Portal for Large Biological Ontology Zida Fan Graduate Student University of Delaware	October 28, 2019 3:30 PM
Evolution and gene expression with single cell resolution David Gresham Associate Professor New York University	November 4, 2019 3:30 PM
*SPECIAL SEMINAR: John R. Mather Visiting Scholars Lecture* Genes, Patents, and Race: The History of Science as a Bridge between Disciplines Myles Jackson (click to register) Professor, History of Science Institute for Advanced Study	November 7, 2019 7:00 PM
A framework for the analysis of heritable information Anthony Jose Associate Professor University of Maryland	November 11, 2019 3:30 PM
Probing single alleles and mRNAs in live cells Bin Wu Assistant Professor Johns Hopkins University	November 18, 2019 3:30 PM
Computational approaches enabling non-standard amino acid biosynthesis and application Aditya Kunjapur Assistant Professor University of Delaware	December 2, 2019 3:30 PM

Spring 2019

Gene expression variability, form single cells to populations Teresa Przytycka Senior Investigator, Computational Biology Branch National Institute of Health	February 11, 2019 3:30 PM
Biotechnology Career Panel and Networking Dinner Invitation BISA Career Panel Workshop University of Delaware	February 18, 2019 3:30 PM
Collective chemotaxis: signaling and mechanics Brian Camley Assistant Professor in the Department of Physics and Astronomy Johns Hopkins University	February 25, 2019 3:30 PM
Protein archeology: How proteins emerged and evolve? Nir Ben Tal Professor Tel Aviv University	March 7, 2019 3:00 PM
Unsupervised, semi-supervised and supervised learning methods for large-scale biological data analysis: An integrative approach Karthik Devarajan Associate Research Professor, Population Science Fox Chase Cancer Center	March 11, 2019 3:30 PM
Genome-wide association study and blood metabolite profiling of wooden breast disease Juniper Lake Graduate Student University of Delaware Development of a novel tool for genome assembly quality evaluation and its application to establish a reference assembly for cho cells Madolyn Macdonald Graduate Student University of Delaware	March 18, 2019 3:30 PM
Informatics and collaboration, a millenial's perspective Matthew Ralston Research Scientist Bristol-Myers Squibb	March 25, 2019 3:30 PM
Global regulation mediated by intron retention in immune system Weiqun Peng Professor, Physics and Adjunct Professor, Anatomy and Cell Biology George Washington University	April 8, 2019 3:30 PM
Understanding cell signal perception via high-throughput optogenetics Lukasz Bugaj *SEMINAR IS CANCELLED* Assistant Professor, Bioengineering University of Pennsylvania	April 15, 2019 3:30 PM
Fidelity during Protein Synthesis: from Population to Single cells Jiqiang Ling Assistant Professor, Department of Cell Biology & Molecular Genetics University of Maryland	April 22, 2019 3:30 PM
miRador: A Novel Plant miRNA Prediction Tool Reza Hammond Graduate Student University of Delaware Genomic and transcriptomic analysis of heterotrophic actinobacteria with light-enhanced growth Priscilla Hempel Graduate Student University of Delaware	April 29, 2019 3:30 PM
Genes prediction in metabolic pathway by using go term semantic similarity Imam Cartealy Graduate Student University of Delaware	April 29, 2019 3:30 PM
Genetic Variations in Human Papillomavirus Affecting Carcinogenicity & Diversity of the Global HPV Infections & Diseases Sam Biswas Professor, Medical & Molecular Sciences University of Delaware	May 6, 2019 3:30 PM
A Computational Approach to Characterizing the Avian Respiratory Microbiome Kelly Mulholland Graduate Student University of Delaware The Data Analysis and prediction of Maize Brace Root Traits by Statistical Methods and Data Mining Wenbo Zhao Graduate Student University of Delaware	May 13, 2019 3:30 PM
TransAtlasDB: An integrated database connecting expression data, metadata and variants Modupe Adetunji Graduate Student University of Delaware The HeNN App for Addressing Substance Use Disorders Haibi Hu Graduate Student University of Delaware	May 20, 2019 3:30 PM

Fall 2018

This Looks Weird!: Size Homeostasis during Anomalous Bacterial Growth Javier Buceta Associate Professor Bioengineering Lehigh University	September 10, 2018 3:30 PM
Healthy lAIfe, AI for healthier lives Rahmat Beheshti Assistant Professor Computer & Information Sciences University of Delaware	September 17, 2018 3:30 PM
Molecular dynamics simulations of large macromolecular complexes Juan Perilla Assistant Professor Chemistry & Biochemistry University of Delaware	September 24, 2018 3:30 PM
Pushing Science Frontiers through Computational and Data-enabled Research Rudolf Eigenmann Professor of Electrical and Computer Engineering University of Delaware	October 1, 2018 3:30 PM
Integration of Heterogeneous Data for Protein Ontology Database Using Semantic Web Technology Xiang Li M.S. Bioinformatics Student University of Delaware	October 8, 2018 3:30 PM
Supporting patient centered care through big data analytics Qing Zeng Director; Biomedical Informatics Center, Professor; Clinical Research and Leadership George Washington University	October 15, 2018 3:30 PM
Systems-level investigation of multi-species bacterial interactions Anupama Khare Head, Systems Biology Unit NIH Stadtman Investigator National Cancer Institute, NIH	October 22, 2018 3:30 PM
Introduction to Biomedical and Health Informatics Vaibhav Goyal Neonatology Pediatrics Christiana Care Health Systems	October 29, 2018 3:30 PM
The dynamic microbiome of bone marrow transplantation patients Joao Xavier Associate Faculty, Computational & Systems Biology Memorial Sloan Kettering Cancer Center	November 5, 2018 3:30 PM
Optogenetics for intracellular codebreaking: how ERK dynamics control gene expression and cell fate Jared Toettcher Assistant Professor of Molecular Biology Princeton University	November 12, 2018 3:30 PM
Immersive Technologies and Interactive Games: Applications in Education and Healthcare Systems Leila Roghayeh Barmaki Assistant Professor, Computer & Information Sciences University of Delaware	November 26, 2018 3:30 PM
Methods and Applications of Long-read Sequencing in Medical Genomics Kai Wang Associate Professor of Pathology and Laboratory Medicine University of Pennsylvania	December 3, 2018 3:30 PM

Spring 2018

Single molecule imaging of gene fusion transcripts and RNA Trafficking Mona Batish Assistant Professor, Department of Medical Laboratory Sciences University of Delaware	February 5, 2018 3:30 PM
Gene Mutations & Cancer - The Rest of the Story Bruce Boman Director, Cancer Genetics and Stem Cell Biology, Center for Translational Cancer Research, Helen F. Graham Cancer Center and Research Institute, Associate Professor of Biological Sciences Christiana Care Health Systems, University of Delaware	February 12, 2018 3:30 PM
Identifying Key Gene Sets in Metastatic Dormancy; Ontology enrichment in publically available Human Breast Cancer data Adam Pater-Feranda Graduate Student University of Delaware Probing breast cancer cell activation in response to microenvironment cues in well-defined synthetic extracellular matrices for insights into late recurrence April M. Kloxin Assistant Professor, Chemical & Biomolecular Engineering University of Delaware	February 26, 2018 3:30 PM
The development and function of aerial roots in plants Erin Sparks Assistant Professor, Plant and Soil Sciences University of Delaware	March 5, 2018 3:30 PM
PerplExosomes: Elucidating the Complexity of Muscle Derived Extracellular Vesicles Matthew Hudson Assistant Professor, Kinesiology & Applied Physiology University of Delaware	March 12, 2018 3:30 PM
The Promise of Precision Medicine in Pediatric Oncology: New Challenges and Hope Anders Kolb Director, Blood & Bone Marrow Transplant Nemours, A.I. DuPont Hospital for Children	March 19, 2018 3:30 PM
Biomarker analysis in cancer immunotherapy Timothy Burn Vice President of Bioinformatics and Molecular Diagnostics, Translational Sciences Incyte Corp	April 2, 2018 3:30 PM
Age-Associated Differentially Methylated Regions in the Human Genome and Maternal Age at Birth Adam Davey Professor, Department of Behavioral Health and Nutrition University of Delaware	April 9, 2018 3:30 PM
MOLECULAR MECHANISM UNDERLYING ALS-LINKED FUS MUTATION Sua Myong Associate Professor, Biophysics Department Johns Hopkins University	April 16, 2018 3:30 PM
A Computational Approach to Characterizing Viral Communities of the Microbiome Kelly Mulholland Graduate Student University of Delaware	April 23, 2018 3:30 PM
The Ins and Outs of Bacterial Signaling Vijay Parashar Assistant Professor, Medical Laboratory Sciences University of Delaware	April 30, 2018 3:30 PM
Chondro-protective Mechanism of Statin Mengxi Lv Graduate Student University of Delaware	May 7, 2018 3:30 PM

Fall 2017

Visualization of transcription dynamics in living Drosophila embryos Mike Levine Professor and Director of the Lewis-Sigler Institute for Integrative Genomics, Professor of Molecular Biology Princeton University	September 11, 2017 3:30 PM
The Future of Data-Powered Health Patricia Flatley Brennan Director National Library of Medicine	September 20, 2017 4:00 PM
iTextMine: Integrated Text Mining System for Large-Scale Knowledge Extraction from Literature Jia Ren PhD Student Bioinformatics and Systems Biology	September 25, 2017 3:30 PM
Precision Medicine meets imprecise medicine Michael Liebman Managing Director, IPQ Analytics, LLC Adjunct Professor, First Hospital of Wenzhou Medical University Drexel College of Medicine	October 2, 2017 3:30 PM
Parallel Processing of the Genomes, by the Genomes and for the Genomes Erez Lieberman Aiden Assistant Professor of Molecular and Human Genetics, Assistant Professor of Computer Science Baylor College of Medicine & Rice University	October 17, 2017 10:15 AM
Wilmington's Elevated Rates of Urban Firearm Violence and Opportunities for Prevention (A Predictability Model) Rita M. Landgraf Professor of Practice and Distinguished Health & Social Services Administrator in Residence Director-UD Partnership for Healthy Communities University of Delaware	October 23, 2017 3:30 PM
Mathematical and computational modeling of the tear film Tobin Driscoll Professor of Mathematical Sciences Joint Faculty in Biomedical Engineering Director, Center for Applications of Mathematics in Medicine University of Delaware	October 30, 2017 3:30 PM
Turing Large Healthcare Data into Clinical Intelligence Outcomes Research of Revascularization Strategies Zugui Zhang Senior Biostatistician Value Institute Christiana Care Health Systems	November 6, 2017 3:30 PM
Rare cell variability in cancer therapy resistance Arjun Raj Associate Professor Bioengineering University of Pennsylvania	November 13, 2017 3:30 PM
Thanksgiving Break	November 20, 2017
Summer experience at Cold Spring Harbor Laboratory Saleh Tamim PhD Student, Engineering, Bioinformatics and Systems Biology at Center for Bioinformatics and Computational Biology University of Delaware Design of a prokaryote-specific peptide array for analysis of bacterial kinomes Giovanni Pagano Masters Student, Computational and Systems Biology University of Delaware	November 27, 2017 3:30 PM
Liver Disease through Glycoscience Glasses Radoslav Goldman Professor, Department of Oncology Georgetown University	December 4, 2017 3:30 PM

Spring 2017

Multi-Scale Simulation of Breast Tissue David Pokrajac Professor and Associate Dean for Research & Analytics Delaware State University	February 6, 2017 3:30 PM
Utilizing Next Generation Sequencing to Generate Bacterial Genomic Sequences for Evolutionary Analysis Derrick Scott Assistant Professor of Bioinformatics Delaware State University	February 13, 2017 3:30 PM
Student Meeting; closed seminar Karen Hoober Assistant Director, Graduate Education & Outreach, Center for Bioinformatics & Computational Biology University of Delaware	February 20, 2017 3:30 PM
Non-Bisulfite Epigenetic Profiling of DNA Methylation Enables Patient Stratification Biomarker Discovery Adam Marsh Associate Professor, School of Marine Science and Policy University of Delaware	February 27, 2017 3:30 PM
Building the Internet of Tools With CyVerse: The Cloud Integrated RNA-Sequencing Platform fRNAkesneq Allen Hubbard PhD Student Bioinformatics & Systems Biology	March 6, 2017 3:30 PM
Programming Models and Tools for Bioinformatics Sunita Chandrasekaran Assistant Professor, Computer and Information Sciences University of Delaware	March 13, 2017 3:30 PM
Predicting Protein-Protein Interaction Using Deep Learning Techniques Li Liao Associate Professor, Computer & Info Sciences University of Delaware	March 20, 2017 3:30 PM
No Seminar	March 27, 2017
Statistical And Computational Approaches for a Multi-Omics Understanding of Heat Stress Across Organs Allen Hubbard PhD Student Bioinformatics & Systems Biology	April 3, 2017 3:30 PM
Computing Phenotypes from Electronic Health Records Tim Bunnell Director, Center for Pediatric Auditory and Speech Sciences and Bioinformatics Core Facility Head, Speech Research Lab Alfred I. DuPont Hospital for Children	April 10, 2017 3:30 PM
Rethinking drug treatment rationale with biomedical mechanism-based phenotype descriptions Casey Overby Assistant Professor, Department of Medicine Divisions of General Internal Medicine and Health Sciences Informatics Johns Hopkins University School of Medicine	April 17, 2017 3:30 PM
Dynamics and evolution of translational regulation Premal Shah Assistant Professor, Department of Genetics Rutgers University	April 24, 2017 3:30 PM
Comparison of Allele Specific Expression in Various Tissues of Chickens Joseph Tomlinson MS Student Bioinformatics & Computational Biology	May 1, 2017 3:30 PM
Sufficient Dimension Reduction with Simultaneous Variable Selection in Application to Tumor Diagnosis Shanshan Ding Assistant Professor, Department of Applied Economics and Statistics University of Delaware	May 8, 2017 3:30 PM

Fall 2016

Summer Internship @ Google Cambridge Jia Ren MS Student Computer & Information Sciences Summer Internship @ IBM Almaden Research Center Lei Huang PhD Student Computer & Information Sciences	September 12, 2016 3:30 PM
Development of a Scalable Method for Creating Food Groups Using the NHANES Dataset and MapReduce Michael Wyatt II PhD Student Computer & Information Sciences	September 19, 2016 3:30 PM
Using Machine Learning Techniques to Analyze Electronic Health Records for Patients Risk Stratification Claudine Jurkovitz Senior Physician Scientist Value Institute, Christiana Care Health System Moumita Bhattacharya PhD Student Computer & Information Sciences	September 26, 2016 3:30 PM
GenPro Summer Internship: Enhancing Functional Annotation of Methylation Sites Maddy MacDonald PhD Student Bioinformatics & Systems Biology Summer Internship at Genome Profiling, LLC Julie Cowart PSM Student Bioinformatics	October 3, 2016 3:30 PM
Integrative Network Analytics for Insights Generation from Massive Healthcare Data Fei Wang Assistant Professor, Health Care Policy & Research Cornell University	October 10, 2016 3:30 PM
Looking to metabolism in order to revitalize our antibiotic medicine cabinet Mark Brynildsen Assistant Professor, Chemical & Biological Engineering Princeton University	October 17, 2016 3:30 PM
What makes T cells tick? Modeling the immune system across multiple spatio-temporal scales Gregoire Altan-Bonnet Investigator, Cancer and Inflammation Program Head, ImmunoDynamics Group NIH, National Cancer Institute	October 24, 2016 3:30 PM
In Search of the Gravitome: Candidate Gravity Responsive Gene Networks Irem Celen Bioinformatics & Systems Biology PhD Student	October 31, 2016 3:30 PM
System Genetics Approaches to Understand Metabolic Diseases Mete Civelek Assistant Professor, Biomedical Engineering University of Virginia	November 7, 2016 12:00 PM
Cryptic light-enhanced growth in heterotrophic bacteria Julie Maresca Assistant Professor Civil & Environmental Engineering Priscilla Hempel MS Student Bioinformatics & Computational Biology	November 7, 2016 3:30 PM
Identification and functional study of nucleosome-depleting factors Lu Bai Assistant Professor, Biochemistry & Molecular Biology Assistant Professor, Physics Penn State	November 14, 2016 3:30 PM
Fall Break	November 21, 2016
A Network Visualization of Dinaciclib and its Interactions with Different Proteins and Target Kinases Paolo Sicat PhD Student Bioinformatics & Systems Biology The Evolution of Biological Electron Transfer: Conservation of Sequence Determinants of the Reduction Potential in Bacterial Ferredoxins Mike Fajardo PhD Student Bioinformatics & Systems Biology	November 28, 2016 3:30 PM
Translating Cancer Genomics into Precision Oncology Francisco M. De La Vega Consulting Professor, Department of Genetics Stanford University School of Medicine	December 5, 2016 3:00 PM
Got Data? Building A Sustainable Data Ecosystem Dr. Francine Berman Chair, Research Data Alliance / US, and Edward P. Hamilton Distinguished Professor of Computer Science Rensselaer Polytechnic Institute	December 6, 2016 2:00 PM

Spring 2016

Accurate Scoring of Drug Conformations at the Extreme Scale Michela Taufer David and Beverly J.C. Mills Career Development Chair Computer and Information Sciences	February 8, 2016 3:30 PM
Vascular Trees and the Machine Learning Strategy on Manifold Hongyu Miao Associate Professor Department of Biostatistics School of Public Health, University of Texas Health Science Center at Houston	February 15, 2016 3:30 PM
No Seminar	February 22, 2016
Integrated Approach to Decipher Regulatory Networks in Eye and Craniofacial Morphogenesis and Their Associated Defects Salil Lachke Assistant Professor; Pew Scholar in Biomedical Sciences University of Delaware	February 29, 2016 3:30 PM
Comparative analysis of reproductive 21-nt phased siRNAs (phasiRNAs) in rice Saleh Tamim PhD Student Bioinformatics & Systems Biology Multiscale Investigation of Histone Modifications: Spatiotemporal Dynamics and Epigenetic Memory Levels Irem Celen PhD Student Bioinformatics & Systems Biology	March 7, 2016 3:30 PM
miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis Parth Patel PhD Student Bioinformatics & Systems Biology Phased, secondary siRNAs in non-grass monocots Atul Kakrana PhD Student Bioinformatics & Systems Biology	March 14, 2016 3:30 PM
Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides Ryan Moore PhD Student Bioinformatics & Systems Biology	March 21, 2016 3:30 PM
Spring Break	March 28, 2016
No seminar	April 4, 2016
Tying Genome Variation in Regulatory Regions to Neurodegenerative Phenotypes Terry Gaasterland Professor of Computational Biology and Genomics Director, Scripps Genome Center	April 7, 2016 2:00 PM
How to Interact with a Distinguished Seminar Speaker Michela Taufer David and Beverly J.C. Mills Career Development Chair Computer and Information Sciences Tom Hanson Professor ociate Director, Marine Biosciences Program	April 11, 2016 3:30 PM
Biological Switches and Modularity in Theory and Practice Ashok Prasad Assistant Professor, Chemical & Biological Engineering Colorado State University	April 18, 2016 3:30 PM
Tapping the Marine RNA Genome Pool Lisa Zeigler Allen Assistant Professor, Microbial and Environmental Genomics JCVI	April 25, 2016 3:30 PM
Digital biological signaling: pulsatile dynamics in the DNA damage response Eric Batchelor Head, Systems Biology Section NIH Stadtman Investigator Center for Cancer Research at the National Institutes of Health	May 2, 2016 3:30 PM
CANCELED Roger Nisbet Professor, Ecology, Evolution and Marine Biology University of California, Santa Barbara	May 9, 2016 3:30 PM
Excitable and other dynamic behaviors in migrating cells Pablo Iglesias Edward J. Schaefer Professor of Electrical & Computer Engineering Johns Hopkins University	May 16, 2016 3:30 PM

First Passage Times and Relaxation Times in Biological Stochastic Processes Anirvan Sengupta Professor Department of Physics and Astronomy Rutgers, The State University of New Jersey	December 7, 2015
Computational Approaches for Cancer: Insight into Recent Developments Eric Stahlberg HPC strategist NCI Center for Biomedical Informatics and Information Technology	November 30, 2015
fRNAkenseq: a Web-based RNA Sequencing Analysis Application Developed with the iPlant Collaborative Allen Hubbard PhD Student Bioinformatics & Systems Biology An Automated Thermo-align Approach for Identifying Template Specific Primers and Hybridization Oligos in (repetitive) Genomes Felix Francis PhD Student Bioinformatics & Systems Biology	November 16, 2015
From Data to Knowledge: The complex relationship between science and technology Anastasia Christianson Head of Translational R&D IT Bristol-Myers Squibb	November 9, 2015
Screening of NSD1 Inhibitors for Pediatric Acute Myeloid Leukemia Based on Compound Selectivity and Binding Affinity Melanie Salinas Professional Science Master's Student - Bioinformatics University of Delaware Data-Driven In silico Screening of Small molecule inhibitors for NSD1 protein Leon Qingliang Li Instructor, Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center	November 2, 2015
What if we ignore the random effects when analyzing RNA-seq data in a multi-factor experiment? Jing Qiu Assistant Professor Applied Economics and Statistics	October 29, 2015 2:00 PM
At the Intersection of the Laboratory and Big Data: Systems and People in Biopharmaceutical Research and Development Jim Brennan Technical Sales Specialist and Business Development LabWare, Inc.	October 19, 2015
Stochasticity and the Mechanism of Precision in the Vertebrate Segmentation Clock Ertugrul Ozbudak Associate Professor Department of Genetics Albert Einstein College of Medicine	October 12, 2015
Synthetic Biology: From Parts to Modules to Therapeutic Systems Ron Weiss Professor of Biological Engineering and Electrical Engineering and Computer Science Director, Synthetic Biology Center, Massachusetts Institutes of Technology	October 7, 2015 3:30 PM
Regulation of Transcription and RNA Processing in Single Cells: Understanding Heterogeneity in Gene Expression Dan Larson Head, Systems Biology of Gene Expression Center for Cancer Research at the National Institutes of Health	October 5, 2015
Establishing the Chinese Hamster Genome as the Reference for the CHO Community Maddy MacDonald PhD Student Bioinformatics & Systems Biology Mining for Datasets to be used in a DREAM Challenge Reza Hammond PhD Student Bioinformatics & Systems Biology	September 28, 2015
Chromosome Structure and Gene Regulation in C. elegans Sevinc Ercan Assistant Professor of Biology New York University	September 21, 2015
What It's Really Like To Be A Google Intern Michael Du PhD Student Computer & Information Sciences Working as a Ph.D. Student vs. as a Google Intern Gang Li PhD Student Computer & Information Sciences	September 14, 2015
Pan Teng Master's Student - Computational Sciences Concentration Center for Bioinformatics & Computational Biology University of Delaware Yubo Xu Master's Student - Computational Sciences Concentration Center for Bioinformatics & Computational Biology University of Delaware	May 18, 2015 3:30 PM
Following the Heart: Computational Methods in the Context of Cardiovascular Conditions Hagit Shatkay, PhD Associate Professor, Computer and Information Sciences University of Delaware	May 11, 2015 3:30 PM
From Retrieval to Discovery in Biomedicine Padmini Srinivasan, PhD Professor, Computer Science Department University of Iowa	May 4, 2015 3:30 PM
Genomes Galore: Big Data Challenges in the Life Sciences Srinivas Aluru, PhD Professor, School of Computational Science and Engineering Georgia Institute of Technology	April 30, 2015 10:30 AM
Genome-wide pathway analysis to decipher the shared genetic basis of neuropsychiatric disorders Phil Hyoun Lee, Ph.D. Psychiatric & Neurodevelopmental Genetics Unit and Analytic & Translational Genetics Unit Center for Human Genetic Research, Massachusetts General Hospital Department of Psychiatry, Harvard Medical School Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard	April 28, 2015 9:30 AM
Bioinformatics in Medicine: The Age of Omics Erin Crowgey PhD Student - Bioinformatics & Computational Biology Internship - Bioinformatics Consultant Advanced Clinical Biosystems Research Institute Cedars-Sinai, CA University of Delaware	April 20, 2015 3:30 PM
A mechanical "clock" serves as a master regulator of lung branching morphogenesis Jason Gleghorn, PhD Assistant Professor, Biomedical Engineering University of Delaware	April 13, 2015 3:30 PM
From flies to humans: Stochastic specification of color-detecting photoreceptors Robert Johnston, PhD Assistant Professor Department of Biology Johns Hopkins University	April 6, 2015 3:30 PM
Spring Break	March 30, 2015
Memory & Bacterial Growth in Fluctuating Environments Edo Kussell, PhD Associate Professor of Biology, Physics New York University (NYU)	March 23, 2015 3:30 PM
Beyond single pathogens: how the human microbiome impacts health and disease. Mihai Pop, PhD Associate Professor, Computer Science Department Center for Bioinformatics and Computational Biology University of Maryland	March 16, 2015 3:30 PM
Mathematical Modeling Tools for HIV Cure Strategies Allison Hill, PhD Research Associate, Program for Evolutionary Dynamics Harvard University	March 9, 2015 3:30 PM
Precision and Reproducibility in Development Thomas Gregor, PhD Assistant Professor of Physics Lewis-Sigler Institute for Integrative Genomics Princeton University	March 2, 2015 3:30 PM
Enabling Scalable Data Analysis of Large Computational Structural Biology Datasets on Distributed Memory Systems Michela Taufer, PhD David L. and Beverly J.C. Mills Chair of Computer and Information Sciences University of Delaware	February 23, 2015 3:30 PM
Integrative Multi-scale Analysis in Biomedical Informatics Joel Saltz, MD, PhD Cherith Professor and Founding Chair Department of Biomedical Informatics Stony Brook University	February 17, 2015 10:30 AM
Bioinformatics Core: CBCB Resources for Informatically Enabling Your Research Shawn Polson, PhD Research Assistant Professor, Computer & Information Sciences and Biological Sciences; Bioinformatics Core Coordinator, Center for Bioinformatics and Computational Biology University of Delaware	February 9, 2015 3:30 PM
WebGIVI: A Website Visualization of Gene and iTerm Liang Sun PhD Candidate Bioinformatics & Systems Biology VIROME and MgOl: Optimizing Functionality by Leveraging Metadata Barbra Ferrell Master's Student Bioinformatics & Computational Sciences	December 1, 2014 3:30 PM
How results from large scale genetic analysis inform on disease Benjamin Neale Assistant in Genetics, Analytic and Translational Genetics Unit, Massachusetts General Hospital Assistant Professor of Medicine, Harvard Medical School Associate Member, Program in Medical and Population Genetics Broad Institute of Harvard and MIT	November 24, 2014 3:30 PM
Regulatory Bioinformatics - Assessments Supporting Worldwide GMO Submissions Henry Mirsky, PhD Research Scientist / Regulatory Sciences - Bioinformatics DuPont Pioneer	November 17, 2014 3:30 PM
Origins and propagation of transcriptional noise in eukaryotic gene expression Sanjay Tyagi, PhD Public Health Research Institute Center New Jersey Medical School Rutgers, The State University of New Jersey	November 10, 2014 3:30 PM
Worms in Space: Epigenetic Response of C. elegans in Simulated Microgravity Chandran Sabanayagam Associate Scientist, Bioimaging Center Associate Professor, Biomedical Engineering DBI	November 3, 2014 3:30 PM
The role of water in cell mechanics, cell shape and cell motility Sean Sun, PhD Associate Professor, Mechanical Engineering Institute for NanoBio Technology Johns Hopkins University	October 27, 2014 3:30 PM
Simulating life - how computers are shaping biomedical research Martin Meier-Schellershein, PhD Chief, Computational Biology Section Laboratory of Systems Biology National Institutes of Health (NIH)	October 20, 2014 3:30 PM
Model-Based Engineering of Microorganisms Desmond Lun, PhD Associate Professor & Chair, Department of Computer Science Rutgers University	October 13, 2014 3:30 PM
Prevention and Rehabilitation for Post-Traumatic Osteoarthritis X. Lucas Lu, PhD Department of Mechanical Engineering, University of Delaware	October 6, 2014 3:30 PM
Science at Extreme Scale: Big Data and Big Compute Lucy T. Nowell, PhD Computer Scientist and Program Manager, ASCR Department of Energy's Office of Science	October 2, 2014 10:30 AM
More than skin deep: Exploring the connection between bacterial community diversity & pathogenic E. coli on pre-harvest cattle hides Ryan Moore PhD Student Bioinformatics & Systems Biology From Metagenomes to Marker Genes: Using Informatics and Genomics to Characterize Phage Populations Dan Nasko PhD Student Bioinformatics & Systems Biology	September 22, 2014 3:30 PM
What It's Really Like To Be A Google Intern Yifan Peng PhD Student Computer & Information Sciences Mining Metagenomes for Mycological Relevance - Finding Fungal Functions within Environmental Samples Joshua Herr, PhD Department of Microbiology & Molecular Genetics Michigan State University	September 15, 2014 3:30 PM
Alzheimer's Disease: A Genomics Approach Li-San Wang, PhD Associate Professor of Pathology and Laboratory Medicine University of Pennsylvania	September 8, 2014 3:30 PM

Pan Teng Master's Student - Computational Sciences Concentration Center for Bioinformatics & Computational Biology University of Delaware Yubo Xu Master's Student - Computational Sciences Concentration Center for Bioinformatics & Computational Biology University of Delaware	May 18, 2015 3:30 PM
Following the Heart: Computational Methods in the Context of Cardiovascular Conditions Hagit Shatkay, PhD Associate Professor, Computer and Information Sciences University of Delaware	May 11, 2015 3:30 PM
From Retrieval to Discovery in Biomedicine Padmini Srinivasan, PhD Professor, Computer Science Department University of Iowa	May 4, 2015 3:30 PM
Genomes Galore: Big Data Challenges in the Life Sciences Srinivas Aluru, PhD Professor, School of Computational Science and Engineering Georgia Institute of Technology	April 30, 2015 10:30 AM
Genome-wide pathway analysis to decipher the shared genetic basis of neuropsychiatric disorders Phil Hyoun Lee, Ph.D. Psychiatric & Neurodevelopmental Genetics Unit and Analytic & Translational Genetics Unit Center for Human Genetic Research, Massachusetts General Hospital Department of Psychiatry, Harvard Medical School Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard	April 28, 2015 9:30 AM
Bioinformatics in Medicine: The Age of Omics Erin Crowgey PhD Student - Bioinformatics & Computational Biology Internship - Bioinformatics Consultant Advanced Clinical Biosystems Research Institute Cedars-Sinai, CA University of Delaware	April 20, 2015 3:30 PM
A mechanical "clock" serves as a master regulator of lung branching morphogenesis Jason Gleghorn, PhD Assistant Professor, Biomedical Engineering University of Delaware	April 13, 2015 3:30 PM
From flies to humans: Stochastic specification of color-detecting photoreceptors Robert Johnston, PhD Assistant Professor Department of Biology Johns Hopkins University	April 6, 2015 3:30 PM
Spring Break	March 30, 2015
Memory & Bacterial Growth in Fluctuating Environments Edo Kussell, PhD Associate Professor of Biology, Physics New York University (NYU)	March 23, 2015 3:30 PM
Beyond single pathogens: how the human microbiome impacts health and disease. Mihai Pop, PhD Associate Professor, Computer Science Department Center for Bioinformatics and Computational Biology University of Maryland	March 16, 2015 3:30 PM
Mathematical Modeling Tools for HIV Cure Strategies Allison Hill, PhD Research Associate, Program for Evolutionary Dynamics Harvard University	March 9, 2015 3:30 PM
Precision and Reproducibility in Development Thomas Gregor, PhD Assistant Professor of Physics Lewis-Sigler Institute for Integrative Genomics Princeton University	March 2, 2015 3:30 PM
Enabling Scalable Data Analysis of Large Computational Structural Biology Datasets on Distributed Memory Systems Michela Taufer, PhD David L. and Beverly J.C. Mills Chair of Computer and Information Sciences University of Delaware	February 23, 2015 3:30 PM
Integrative Multi-scale Analysis in Biomedical Informatics Joel Saltz, MD, PhD Cherith Professor and Founding Chair Department of Biomedical Informatics Stony Brook University	February 17, 2015 10:30 AM
Bioinformatics Core: CBCB Resources for Informatically Enabling Your Research Shawn Polson, PhD Research Assistant Professor, Computer & Information Sciences and Biological Sciences; Bioinformatics Core Coordinator, Center for Bioinformatics and Computational Biology University of Delaware	February 9, 2015 3:30 PM
WebGIVI: A Website Visualization of Gene and iTerm Liang Sun PhD Candidate Bioinformatics & Systems Biology VIROME and MgOl: Optimizing Functionality by Leveraging Metadata Barbra Ferrell Master's Student Bioinformatics & Computational Sciences	December 1, 2014 3:30 PM
How results from large scale genetic analysis inform on disease Benjamin Neale Assistant in Genetics, Analytic and Translational Genetics Unit, Massachusetts General Hospital Assistant Professor of Medicine, Harvard Medical School Associate Member, Program in Medical and Population Genetics Broad Institute of Harvard and MIT	November 24, 2014 3:30 PM
Regulatory Bioinformatics - Assessments Supporting Worldwide GMO Submissions Henry Mirsky, PhD Research Scientist / Regulatory Sciences - Bioinformatics DuPont Pioneer	November 17, 2014 3:30 PM
Origins and propagation of transcriptional noise in eukaryotic gene expression Sanjay Tyagi, PhD Public Health Research Institute Center New Jersey Medical School Rutgers, The State University of New Jersey	November 10, 2014 3:30 PM
Worms in Space: Epigenetic Response of C. elegans in Simulated Microgravity Chandran Sabanayagam Associate Scientist, Bioimaging Center Associate Professor, Biomedical Engineering DBI	November 3, 2014 3:30 PM
The role of water in cell mechanics, cell shape and cell motility Sean Sun, PhD Associate Professor, Mechanical Engineering Institute for NanoBio Technology Johns Hopkins University	October 27, 2014 3:30 PM
Simulating life - how computers are shaping biomedical research Martin Meier-Schellershein, PhD Chief, Computational Biology Section Laboratory of Systems Biology National Institutes of Health (NIH)	October 20, 2014 3:30 PM
Model-Based Engineering of Microorganisms Desmond Lun, PhD Associate Professor & Chair, Department of Computer Science Rutgers University	October 13, 2014 3:30 PM
Prevention and Rehabilitation for Post-Traumatic Osteoarthritis X. Lucas Lu, PhD Department of Mechanical Engineering, University of Delaware	October 6, 2014 3:30 PM
Science at Extreme Scale: Big Data and Big Compute Lucy T. Nowell, PhD Computer Scientist and Program Manager, ASCR Department of Energy's Office of Science	October 2, 2014 10:30 AM
More than skin deep: Exploring the connection between bacterial community diversity & pathogenic E. coli on pre-harvest cattle hides Ryan Moore PhD Student Bioinformatics & Systems Biology From Metagenomes to Marker Genes: Using Informatics and Genomics to Characterize Phage Populations Dan Nasko PhD Student Bioinformatics & Systems Biology	September 22, 2014 3:30 PM
What It's Really Like To Be A Google Intern Yifan Peng PhD Student Computer & Information Sciences Mining Metagenomes for Mycological Relevance - Finding Fungal Functions within Environmental Samples Joshua Herr, PhD Department of Microbiology & Molecular Genetics Michigan State University	September 15, 2014 3:30 PM
Alzheimer's Disease: A Genomics Approach Li-San Wang, PhD Associate Professor of Pathology and Laboratory Medicine University of Pennsylvania	September 8, 2014 3:30 PM