Tools & Technology Seminar Series

 Thursday, Sep 20, 2018

Thursday, Sep 27, 2018

• “Assessing Breast Cancer Stem Cell Heterogeneity via Drop-Seq Single-Cell RNA Sequencing” - Michael Brooks (Hematology and Oncology)

Thursday, Oct 4, 2018

• TBA - Matt Cybulsky (Ionia Behavioral Insights)

Thursday, Oct 11, 2018

• “Development of computational tools and databases to study proteins and drugs in membranes" - Andrei Lomize (College of Pharmacy)

Thursday, Oct 18, 2018

• “Development of the System for Opioid Overdose Surveillance (S.O.S)” - Amanda Kogowski (Emergency Medicine)

Thursday, Oct 25, 2018

• "MTGO: data integration for protein network module identification" - Simone Marini (Computational Medicine & Bioinformatics)
  Tool Link: https://gitlab.com/d1vella/MTGO

Thursday, Nov 1, 2018

• TBA - Jian Kang (Biostatistics)

Thursday, Nov 8, 2018

• TBA - Ricardo D’O. Albanus (Computational Medicine & Bioinformatics)

Thursday, Nov 15, 2018

• “High throughput recoding and analysis of neuronal signals during behavior in rodents” - Brendon Watson and Tongyu Liu (Psychiatry)

Thursday, Nov 29, 2018

• TBA - Satish Narayanasamy (Electrical Engineering and Computer Science)

Thursday, Dec 6, 2018

• "ML-MATCH: A ML based atom parameterization program" - Murchtricia Charles (Computational Medicine & Bioinformatics)

Thursday, Dec 13, 2018

• TBA - Sardar Ansari 

Thursday, Jan 11, 2018 

• “Building cloud-computing tools for structural biology” - Michael Cianfrocco 

Thursday, Jan 18, 2018 

• "TnseqDiff: identification of conditionally essential genes in transposon sequencing studies” by  Lili Zhao (Biostatistics)

Thursday, Jan 25, 2018

•  “SAIGE: Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies” by Wei Zhou (DCMB)

Thursday, Feb 01, 2018

• "Deep Approaches to Forecasting Physiological Time-Series" by  Ian Fox (Electrical Engineering and Computer Science)

Thursday, Feb 08, 2018

• "Probabilistic computing and drug discovery in the pharmaceutical industry" by Gerry Higgins (DCMB)

Thursday, Feb 15, 2018

• "The ERN at UM: A Enterprise Research Notebook Collaboration Platform.” by Debra McCaffrey (Health Information Technology & Services)

Thursday, Feb 22, 2018

• “Towards the identification of invasive gene signatures in epithelial cancers” by  Koh Meng Aw Yong (Hematology/Oncology)

Thursday, Mar 01, 2018

•  "Using dplyr to wrangle data in R" by Matthew Flickinger (Center for Statistical Genetics)

Thursday, Mar 08, 2018

• “Designing drug combination therapies using INDIGO” by  Sriram Chandrasekaran (Biomedical Engineering)

Thursday, Mar 15, 2018

• “The RUV Package: Tools to Remove Batch Effects and other Unwanted Variation” by Johann Gagnon-Bartsch (Statistics

Thursday, Mar 22, 2018

• “Demo of deep learning in biomedical data.” by Yuanfang Guan (DCMB)

Thursday, Mar 29, 2018

• “VerifyBamID 2.0: Ancestry-agnostic detection and estimation of sample contamination from DNA sequence data.”  by Fan Zhang (DCMB)

Thursday, Apr 05, 2018

• "A versatile toolbox for droplet-based single-cell mRNA sequencing" by  Katsuo Kurabayashi (Mechanical Engineering, Electrical Engineering and Computer Science)

Thursday, Apr 12, 2018

• “Binner, a tool for annotation of degenerate features in untargeted LC-MS metabolomics data” by Alla Karnovsky, Hani Habra, Bill Duren (Computational Medicine & Bioinformatics)

Thursday, Apr 19, 2018

• "Conda, Snakemake, and Jupyter: An open-source tech stack for reproducible research." by Chris Gates (Bioinformatics Core)

Thursday, Jan 19, 2017

• “Nascent RNA Bru-seq technologies”-  Mats Ljungman

Thursday, Jan 26, 2017

• "Interactive Programming Tools Powered by Deep Learning Models" - Xin Rong

Thursday, Feb 02, 2017

• "Archive and Share Your Data with Deep Blue Data" - Amy Neeser, Jake Carlson, Scott Martin

Thursday, Feb 09, 2017

• “Decoding gene regulatory grammar across species: the Human-Mouse Gene Regulatory Module Browser at U of M" - Adam Diehl

Thursday, Feb 16, 2017

• "Convolutional Neural Networks for Biomedical Image Analysis" - Alex Kalinin

Thursday, Feb 23, 2017

• "Vertex models and self-organization in epithelia: A view from the retina" - David Lubensky

Thursday, Mar 02, 2017

• “Using R and the mlr package to develop and evaluate machine learning models” -Karandeep Singh

Thursday, Mar 09, 2017

• “From molecules to development: how biological oscillators function and coordinate.” - Qiong Yang

Thursday, Mar 16, 2017

• “The Big Data Effort in Radiation Oncology: Data Mining or Data Farming?” - Charles Mayo

Thursday, Mar 23, 2017

• “Mixed-solvent molecular dynamics for structure based drug design” - Sarah Graham

Thursday, Mar 30, 2017

• "BAMQL: a query language for extracting reads from BAM files."   - Akima George

Thursday, Apr 06, 2017

• “Identifying regulatory logic in a curated collection of E. coli expression data sets.”  - Rucheng Diao

Thursday, Apr 13, 2017

• “Simplifying Analysis of Mobile, Fitbit and Genetic Data Collection using Data Virtualization in the Intern Health Study” - Srijan Sen, Jamie Estill

Thursday, Apr 20, 2017

• “Cross application data exploration through R Shiny” - Keqiang Li

Thursday, Apr 27, 2017

• "Probing the accessible genome:  Using chromatin accessibility data to predict genome-wide transcription factor binding and residence time." - Ricardo Albanus

Thursday, Sep 21, 2017

• “An Algorithm for Cellular Reprogramming” - Indika Rajapakse 

Thursday, Sep 28, 2017

• "Tools and Topics in Topological Data Analysis with Applications in Biomedical Science and Engineering" - Nguyen (Josh) Vo 

Thursday, Oct 05, 2017

•  "LASER server: exploring ancestry of your sample using genotypes or sequence read data" - Daniel Taliun 

Thursday, Oct 12, 2017

• “High performance computing and statistical analysis of medical claims data” - Kerby Shedden 

Thursday, Oct 19, 2017

• “Tools for Volumetric Segmentation and Grouping” - Brent Griffin

Thursday, Oct 26, 2017

• "Contact-assisted ab initio structure prediction of proteins” - Golam Mortuza

Thursday, Nov 02, 2017

• “Disorder Atlas: A tool for standardizing intrinsic disorder calculations” - Santiago Schnell 

Thursday, Nov 09, 2017

•  "Using Google's TensorFlow for Medical Imaging Analysis" - Mitch Fernandez 

Thursday, Nov 16, 2017

• “Nephroseq 5: Using Agile software development methodology to rewrite a gene expression data mining webapp.”  - Becky Reamy 

Thursday, Nov 30, 2017

• "Seekmer: a fast hybrid approach to quantify splicing isoforms with high confidence."  - Hongjiu Zhang 

Thursday, Dec 07, 2017

• "Introduction to the National Library of Medicine Unified Medical Language System" - Tyler Nix

Thursday, Dec 14, 2017

• "Identifying differentially expressed genes and estimating gene expression heritability in RNAseq studies with MACAU" - Xiang Zhou 

Dec 15, 2016

• “Combining comparative genomics and graph databases to improve and streamline population and ecosystem meta-omics analyses.” - Kevin Meyer

Dec 01, 2016

• Title TBA - Mitch Fernandez

Nov 17, 2016

• MSFragger: Fast and comprehensive peptide identifications through index-based database search” - Andy Kong

Nov 10, 2016

• CANCELLED

Nov 03, 2016

• "LocusZoom.js: Visual Interactive Plotting of GWAS Results in JavaScript/d3" - Christopher Clark

Oct 20, 2016

•  “Accelerating Protein-Ligand Docking Using FFTs on GPUs” - Xinqiang Ding

Oct 13, 2016

• “Identify pleiotropic genes in genome-wide association studies for multivariate phenotypes with mixed measurement scales” - James Yang

Oct 06, 2016

• “CRIMSON: An integrated computer modeling framework for subject-specific cardiovascular simulation” - Alberto Figueroa

Sep 29, 2016

• “Advanced Research Computing at Michigan” - Brock Palen

Sep 22, 2016

• “Predicting Individual Outcomes for Rapid Intervention (PRIORI) mHealth monitoring in Bipolar Disorder” - Melvin McInnis

Sep 15, 2016

•  “annotatr: Associating genomic regions with genomic annotations” - Raymond Cavalcante

Apr 28, 2016

• "PubChem: Connected Data and Information on Small Molecules" - Ye Lab
  Related Resource: PubChem

Apr 21, 2016

• "Nephroseq: A gene expression data mining application for kidney disease" - Becky Steck and Ross Patterson
  Related Resource: Nephroseq Website

Mar 31, 2016

• "Reactome Functional Interaction Network and its Application in Cancer Research" - Guanming Wu
  Related Resource: Reactome Website

Mar 17, 2016

• "Next Generation Imputation Methods" - Sayantan Das
  Related Resource: Minimac3

Mar 03, 2016

• "MATLAB and Simulink: Simulation Tools for Scientific Computing" - Negar Farzaneh and Kayvan Najarian

Feb 18, 2016

• "Variable selection in survival analysis with high-dimensional covariates" - Kevin He

Feb 11, 2016

• "SEAD: Data management, publishing and archiving services" - Margaret Hedstrom
  Related Resource: SEAD Website

Feb 4, 2016

• "Outcome Modeling In Radiotherapy and Oncology: Listening to the Data" - Issam El Naqa

Jan 21, 2016

• "Three habits to bridge research code and sustainable software" - Chris Gates

Jan 14, 2016

• "vt - a short genetic variant calling and analysis tool" - Adrian Tan
  Related Resource: vt

Dec 17, 2015

• "Ligand-Based Virtual Screening for G Protein-Coupled Receptors" - Wallace Chan
  Related Resource: Zhang Lab/GLASS

Dec 10, 2015

• "Omics approaches to study the ecology of uncultivated viruses" - Melissa Duhaime

Dec 3, 2015

• "Identification and characterization of genic HPV integration events in oropharynx and oral cavity tumors" - Lada Koneva

Nov 19, 2015

• "DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics" - Chih-Chiang Tsou

Nov 5, 2015

• "Identification and interpretation of psoriasis susceptibility loci" - Alex Tsoi

Oct 29, 2015

• "Developing integrated online tools for protein structural dynamics and evolutionary analysis" - Shashank Jariwala

Oct 22, 2015

• "Identification of expanded repeat sequences in Illumina NGS exome data from ataxia patients" - Jun Li, Margit Burmeister

Oct 15, 2015

• "Using Computational and Bioinformatics Tools to Analyze Single Molecule Fluorescence Data" - Nils Walter

Oct 8, 2015

• "Sparse Screening for Big Biomedical Data" - Jie Wang 
  Related Resource: Ye Lab Software

Oct 01, 2015

• "CoolMap-based visualization and analysis of omics data" - Keqiang Li
  Related Resource: coolmap.org

Sep 24, 2015

• "SPECtre: spectral coherence-based classification of actively translated transcripts from ribosome profiling sequence data" - Tony Chung
  Related Resource: Mills Lab Software

Sep 10, 2015
"Chromosome conformation capture to interrogate the 3D genome" - Haiming Chen

May 22, 2015

• "Unit-free and robust detection of differential expression from RNA-Seq data" - Hui Jiang

May 14, 2015

• "Multimodal Sentiment Analysis" - Rada Mihalcea

May 07, 2015

• "Recent development in tools for homology inference, alignment and phylogenetic reconstruction" - Ya Yang

Apr 30, 2015

• "EpiGWAS: Moving from association to predicted function on an increasingly automated basis" - Ari Allyn-Feuer

Mar 26, 2015

• "LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach" - Damian Fermin
  Related Resource: Nesvizhskii Lab Software

Mar 19, 2015

• "Formulating multi-scale hybrid models to describe M. tuberculosis infection" - Elsje Pienaar

Mar 12, 2015

• "Big Data and Data Science: Hype or Reality" - Brian Athey

Mar 5, 2015

• "Massively parallel assays for functional interpretation of mutations" - Jacob Kitzman

Feb 26, 2015

• "Computational Protein Design" - David Shultis

Feb 19, 2015

• "Brain: The Next Frontier in Personalized Pain Medicine and Technology" - Alex DaSilva

Feb 12, 2015

• "#DeepLearning: The End of Machine Learning and Signal Processing" - Alex Kalinin

Feb 05, 2015

• "ConceptMetab: Exploring relationships among metabolite sets to identify links among biological concepts" - Snehal Patil and Raymond Cavalcante

Jan 29, 2015

• "Mining social media to analyze dissemination of health-related information and concerns" - V. G. Vinod Vydiswaran and Yang Liu

Jan 22, 2015

• "ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures" - Jungkap Park and Kazuhiro Saitou
  Related Resource: ROTAS

Jan 15, 2015

• "Linear Programming Tools for Scheduling Trainees in Healthcare" - Billy Pozehl

Dec 11, 2014

• "Synthetic Biology and the iGEM Competition"-  - Josh Abramson

Nov 20, 2014

• "OntoFox and Ontobee: Tools to support ontology reuse, browsing, and integration"-  - Oliver He

Nov 13, 2014

• "MetScape: A Multi-Purpose Cytoscape App for Metabolomic Network Analysis"-  - Bill Duren

Oct 30, 2014

• "IsoPred : Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data"-  - Ridvan Eksi

Oct 02, 2014

• "Template Based Modeling of Protein Complexes"-  - Brandon Govindarajoo

Sep 25, 2015

• "RAREMETAL: fast and powerful meta-analysis for rare variants"-  - Shuang Feng

Sep 18, 2014

• "Update on technology and bioinformatics for small genome resequencing"-  - Jim Cavalcoli

May 29, 2014

• "An Overview of NCBI Tools"-  - Marci Brandenburg

May 22, 2014

• "Modeling Biological Pathways by Redefining Referencing using PubMow.org"-  - Jon Mowers

May 08, 2014

• "Visualization Services and Support in the Library"-  - Justin Joque

May 01, 2014

• "A Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver for Electrostatics of Solvated Proteins"-  - Robert Krasny

Apr 03, 2014

• "Tethering with an ER/K linker: tuning distance and interactions between proteins"-  - Sivaraj (Shiv) Sivaramakrishnan

Mar 27, 2014

• "Computational Prediction of Sudden Cardiac Death following Acute Coronary Syndrome"-  - Alexander Van Esbroeck

Mar 20, 2014

• "Resolving Complex Structural Genomic Rearrangements Using a Randomized Approach"-  - Xuefang Zhao

Mar 13, 2014

• "An Introduction to Weka: Data Mining Software in Java"-  - Craig Biwer

Mar 06, 2014

• "An overview to some of the IT resources available to U-M Medical School staff, students, and faculty"-  - Aaron Bookvich

Feb 27, 2014

• "Nucleotide-dependent Transitions of the α-subunit of Heterotrimeric G-proteins Probed with Multiscale Molecular Simulations"-  - Xinqiu Yao

Feb 20, 2014

• "Targeted next generation sequencing of cancer using Ion Torrent technology"-  - Scott Tomlins

Feb 13, 2014

• "Best practices for quantifying allele-specific expression from RNA-seq data"-  - Kraig Stevenson

Feb 06, 2014

• "Epicode: combinatorial epigenetic patterns as quantitative predictors of chromatin biology"-  - Marcin Cieslik

Jan 30, 2014

• "SOCR Infrastructure for Technology-enhanced Trans-disciplinary Health Research & Science Education"-  - Ivo Dinov

Dec 19, 2013

• "METHYLSIG: A Whole Genome DNA Methylation Analysis Pipeline" - Yongseok Park

Dec 23, 2013