The DCMB Tools and Technology Seminar Series will be presented via a Zoom Live Stream each Thursday, at 12 noon EST.
Each seminar highlights a tool or technology, that is under development or in current use, that is of interest to department and University researchers. These seminars are streamed live using Zoom and are also archived and made available for future viewing on the DCMB YouTube Chanel:
Next Seminar
Thursday, Jan 28, 2021
“ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks” - Yang Li (Computational Medicine & Bioinformatics)
Live Stream via ZOOM
Winter 2021 - Tools & Technology Seminar Schedule and Video Archive
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)
Tools & Technology Seminar Archive
2020
Thursday, Jan 16, 2020
- "Statistical analysis of spatial expression pattern for spatially resolved transcriptomic studies" - Jiaqiang Zhu
Thursday, Jan 23, 2020
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
Thursday, Feb 20, 2020
- "Hardware Accelerated Systems for Next-Generation Sequencing Analysis" - Arun Subramaniyan
BWA-MEM (on github)
- "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
Thursday, Apr 09, 2020
- "An Accurate and Interpretable Computational Model for Predicting Nucleosome Resolution Chromatin Contact Maps." - Nicholas Wang
Thursday, Apr 16, 2020
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)
2019
Thursday, Jan 17, 2019
- “Integrating Imaging Phenotype with Genomics for Cancer: Case Studies in Radiomics, Pathology Informatics, and Drug Discovery” - Arvind Rao (Computational Medicine & Bioinformatics, Radiation Oncology)
Thursday, Jan 24, 2019
- “Data and Workflow Management with the signac Framework” - Vyas Ramasubramani (Chemical Engineering)
Thursday, Jan 31, 2019
- “Exploring bias in ATAC-seq experiments with ataqv, an interactive quality control tool for ATAC-seq data” - Peter Orchard (Computational Medicine & Bioinformatics)
Thursday, Feb 07, 2019
- "lilikoi: Metabolomics Personalized Pathway Analysis Tool" - Fadhl Alakwaa (Computational Medicine & Bioinformatics)
Thursday, Feb 14, 2019
- “Transcription Factor Network Drives Prostate Cancer Drug Resistance” - Patricia Schnepp (Urology)
Thursday, Feb 21, 2019
- “BAMnostic: an OS-agnostic toolkit for genomic sequence analysis” - Marcus Sherman (DCMB)
Thursday, Feb 28, 2019
- “CT-Based Analytical Techniques for Quantifying Lung Disease” - Craig Galban (Radiology, Biomedical Engineering)
Thursday, Mar 07, 2019
- "Dynamic protein modules and metabolic networks from time-course proteomics and metabolomics" - Ho-Joon Lee (Molecular & Integrative Physiology)
Thursday, Mar 14, 2019
- CANCELLED
Thursday, Mar 21, 2019
- “Database Integration and Digital Phenotyping to Improve Perioperative Care: Tools Used by the Multicenter Perioperative Outcomes Group” - Michael Mathis (Anesthesiology)
Thursday, Mar 28, 2019
- “The Carpentries at Michigan: Building a Community of Practice Around Data Analysis” - Patrick Schloss (Microbiology & Immunology)
Thursday, Apr 04, 2019
- "Computational tools for studying epithelial morphogenesis" - Idse Heemskerk (Cell and Developmental Biology)
Thursday, Apr 11, 2019
- “Efficient algorithms for resampling-based hypothesis testing in genomic data analysis.”- Hui Jiang (Biostatistics)
Thursday, Apr 18, 2019
- “Factors to consider when implementing nonnegative matrix factorization approaches” - Josh Welch (Computational Medicine & Bioinformatics)
Thursday, Sep 19, 2019
- "ML-MATCH: A ML based atom parameterization program" - Murchtricia Charles (Computational Medicine & Bioinformatics)
Thursday, Sep 26, 2019
- “Change Detection for preventive medicine” - Cristina Mitrea (Computational Medicine & Bioinformatics)
Thursday, Oct 03, 2019
- "Optimizing Glasso: Why Implementation Matters." - Bill Duren (Computational Medicine & Bioinformatics)
Thursday, Oct 10, 2019
- “Exploring bias in ATAC-seq experiments with ataqv, an interactive quality control tool for ATAC-seq data” - Peter Orchard (Computational Medicine & Bioinformatics)
Thursday, Oct 17, 2019
- “A Unified Workflow to Identify Structures and Changes in Protein-Protein Interactions from Crosslinking-Based Mass Spectrometry” - Catherine Barnier
Thursday, Oct 24, 2019
Thursday, October 31, 2019
- “TAIJI: Approaching Experimental Replicates-Level Accuracy for Drug Synergy Prediction” - Hongyang Li
Thursday, November 07, 2019
- "Collaborative Inference: A new statistical paradigm to overcome data sharing barriers" - Peter Song
Thursday, November 21, 2019
Thursday, December 05, 2019
- “Quantitative Morphological Characterization of Pharmacologic Effects using Cell Painting in the Context of Non-Alcoholic Fatty Liver Disease” - Jonathan Sexton
Thursday, December 12, 2019
2018
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
- “Assessing Breast Cancer Stem Cell Heterogeneity via Drop-Seq Single-Cell RNA Sequencing” - Michael Brooks (Hematology and Oncology)
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
2017
Thursday, Jan 19, 2017
- “Nascent RNA Bru-seq technologies”- Mats Ljungman
Thursday, Jan 26, 2017
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
Thursday, Feb 23, 2017
Thursday, Mar 02, 2017
Thursday, Mar 09, 2017
Thursday, Mar 16, 2017
Thursday, Mar 23, 2017
Thursday, Mar 30, 2017
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
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
Thursday, Dec 14, 2017
2016
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
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
Feb 11, 2016
- "SEAD: Data management, publishing and archiving services" - Margaret Hedstrom
Related Resource: SEAD Website
Feb 4, 2016
Jan 21, 2016
Jan 14, 2016
- "vt - a short genetic variant calling and analysis tool" - Adrian Tan
Related Resource: vt
2015
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
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
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
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
Feb 12, 2015
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
2014
Dec 11, 2014
- "Synthetic Biology and the iGEM Competition" - Josh Abramson
Nov 20, 2014
Nov 13, 2014
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
May 29, 2014
- "An Overview of NCBI Tools" - Marci Brandenburg
May 22, 2014
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
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
Feb 20, 2014
- "Targeted next generation sequencing of cancer using Ion Torrent technology"- - Scott Tomlins
Feb 13, 2014
Feb 06, 2014
- "Epicode: combinatorial epigenetic patterns as quantitative predictors of chromatin biology"- - Marcin Cieslik
Jan 30, 2014
2013
Dec 19, 2013
- "METHYLSIG: A Whole Genome DNA Methylation Analysis Pipeline" - Yongseok Park