Tools & Technology Seminar Series

Thursday, Jan 21, 2021

• “Fitting a Square Peg in a Round Hole...Adding EEG Data to a Social Science Data Repository” - Amy Pienta (ICPSR)

Thursday, Jan 28, 2021

• “ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks” - Yang Li (Computational Medicine & Bioinformatics)

Thursday, Feb 04, 2021

• “Quetzal: a library for integrating distributional, demographic and coalescent models” - Arnaud Becheler (Ecology and Evolutionary Biology)

Thursday, Feb 11, 2021

• "MiCV - single-cell analysis at the push of a button" - Nigel Michki (Biophysics) 

Thursday, Feb 18, 2021

• "metabCombiner: Alignment of Disparately Acquired LC-MS Untargeted Metabolomics Datasets." - Hani Habra (Computational Medicine & Bioinformatics)

Thursday, Feb 25, 2021

• TBA - Veera Baladandayuthapani (Biostatistics; Computational Medicine & Bioinformatics)

Thursday, Mar 04, 2021

• TBA - Ryan Crawford (Computational Medicine & Bioinformatics)

Thursday, Mar 11, 2021 

• “F-Seq2: improving the feature density based peak caller with dynamic statistics” - Nanxiang (Samuel) Zhao (Computational Medicine & Bioinformatics)

Thursday, Mar 18, 2021

•  "Building a Software Pipeline for Developing and Evaluating Time-Series Machine Learning Models Using Electronic Health Record Data" - Jie Cao (Computational Medicine & Bioinformatics)

Thursday, Mar 25, 2021

• “RegulomeDB 2.0: Prioritization of regulatory SNPs affecting transcription factor binding” - Shengcheng Dong (Computational Medicine & Bioinformatics)

Thursday, Apr 01, 2021

• “Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons” - Xiaoqiong Wei (Molecular and Integrative Physiology)

Thursday, Apr 08, 2021

• “Identification of Collateral Lethal Metabolic Targets for Precision Medicine in Cancer” - Abhinav Achreja (Biomedical Engineering)

Thursday, Jan 16, 2020

• "Statistical analysis of spatial expression pattern for spatially resolved transcriptomic studies" - Jiaqiang Zhu

Thursday, Jan 23, 2020

• “C2Metadata: Automating the Capture of Data Transformation from Statistical Scripts in Data Documentation” - Jie Song

Thursday, Jan 30, 2020

• “U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies” - Zheng Gao

Thursday, Feb 06, 2020

• "Data-Driven Solutions to Challenges in Biophysics" - Aaron Frank

Thursday, Feb 13, 2020

• “Protein folding by a contact-guided replica-exchange Monte Carlo simulation using deep learning technology.”  - Wei Zheng

Thursday, Feb 20, 2020

• "Hardware Accelerated Systems for Next-Generation Sequencing Analysis" - Arun Subramaniyan
  BWA-MEM (on github)

Thursday, Feb 27, 2020

• "Creating a scalable toolkit for the analysis of expanded Brainbow images with nTracer." - Logan Walker

Thursday, Mar 05, 2020

• “Integrative Statistical Modeling Approaches for Imaging-Genetics Data” - Shariq Mohammed

Thursday, Mar 12, 2020

• “Ontoanimal tools for extensible ontology development, browsing, query, and data FAIRness” - Oliver He

Thursday, Mar 19, 2020

• CANCELLED 

Thursday, Mar 26, 2020

• "PALMER: Identification and characterization of occult mobile element insertions using long-read sequencing technology."   - Arthur Zhou 

Thursday, Apr 02, 2020

•  "An Accurate and Interpretable Computational Model for Predicting Nucleosome Resolution Chromatin Contact Maps." - Fan Feng

Thursday, Apr 09, 2020

• "An Accurate and Interpretable Computational Model for Predicting Nucleosome Resolution Chromatin Contact Maps." - Nicholas Wang 

Thursday, Apr 16, 2020

• "Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning." -  Chao Gao

Thursday, Sep 17, 2020

• "Fast and robust ancestry prediction with FRAPOSA" - David Zhang (Biostatistics)

Thursday, Sep 24, 2020

• “From millions of images of SARS-CoV-2 infected cells to drug mechanism of action.” - Matt O’Meara (Computational Medicine & Bioinformatics)

Thursday, Oct 08, 2020

• “Spacekime Analytics” - Ivo Dinov (School of Nursing; Computational Medicine & Bioinformatics)

Thursday, Oct 15, 2020

• “Chemical Synthesis in the Information Age.” - Timothy Cernak (Medicinal Chemistry; Chemistry)

Thursday, Oct 22, 2020

• “Translationally active cell-free expression for building synthetic cells.” - Allen Liu (Mechanical Engineering; Biomedical Engineering; Biophysics)

Thursday, Oct 29, 2020

• "CaliPro: a calibration protocol for complex mathematical models in biology" -  Louis Joslyn (Computational Medicine & Bioinformatics)

Thursday, Nov 05, 2020

• “Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing” - Kai Wang (Computational Medicine & Bioinformatics)

Thursday, Nov 12, 2020

• "BAGSE: A Bayesian Hierarchical Model for Gene Set Enrichment Analysis" - Abhay Hukku (Biostatistics)

Tool Link: https://github.com/xqwen/bagse

Thursday, Nov 19, 2020

• “Quantitative Data Extraction and Computational Modeling of Cell Signaling from Single-Cell, Time-Lapse Imaging” - Patrick Kinnunen and Ray Asare (Chemical Engineering)

Thursday, Dec 03, 2020

• “SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes.” - Kevin Amses (Ecology and Evolutionary Biology)

Thursday, Dec 10, 2020

• TBD - Karnovsky Lab (Computational Medicine & Bioinformatics)

Thursday, Jan 17, 2019

Thursday, Jan 24, 2019

Thursday, Jan 31, 2019

Thursday, Feb 07, 2019

Thursday, Feb 14, 2019

Thursday, Feb 21, 2019

Thursday, Feb 28, 2019

Thursday, Mar 07, 2019

Thursday, Mar 14, 2019

Thursday, Mar 21, 2019

Thursday, Mar 28, 2019

Thursday, Apr 04, 2019

Thursday, Apr 11, 2019

Thursday, Apr 18, 2019

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, Sep 20, 2018

Thursday, Sep 27, 2018

• “GuanRank:  Generalizing right-censored data into standard regression problem through complete ranking” - Daniel Quang (Computational Medicine & Bioinformatics)

Thursday, Oct 4, 2018

• “Beyond the Screen: How Voice Technology Drives Incremental Improvements in Healthcare” - 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

• "Multi-omics integration for precision medicine." - Simone Marini (Computational Medicine & Bioinformatics)
  Tool Link: https://gitlab.com/d1vella/MTGO

Thursday, Nov 1, 2018

• “Scalar-on-image regression via soft-thresholded Gaussian processes.”  - Jian Kang (Biostatistics)

Thursday, Nov 8, 2018

•  “Mining information from the accessible genome: Accurately predicting transcription factor binding from ATAC-seq data using BMO.” - Ricardo D’O. Albanus (Computational Medicine & Bioinformatics)

Thursday, Dec 13, 2018

• “Deep Learning Tools for Pattern Discovery in Electronic Health Records” - Sardar Ansari 

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 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 Dino

Dec 19, 2013

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