The Computational Genomics Office at the IGB identifies and provides resources to support computational aspects of research at the Institute. Contact us at cg@igb.illinois.edu and see below for more.
Training
Genomics data analysis short course
The IGB Computational Genomics, in collaboration with HPCBio, will be piloting a four-session short course in genomics data analysis. The goal is to provide a conceptual framework for how to learn bioinformatics. This framework will be illustrated with bulk and single-cell RNA-seq analyses using the R programming language. The course will assume knowledge at the level of the HPCBio workshops. Email cg@igb.illinois.edu to attend.
The course will meet on the following Mondays from 12:00 - 1:00 pm CT. Preliminary syllabus:
|
Date |
Location |
Description |
|
2/6/2023 |
IGB 607 |
Topics: Concepts and framework of bioinformatics, formulating data analyses Exercises: Identify literature examples of genomic analyses, apply framework to examples |
|
3/6/2023 |
Topics: Discussion of literature examples, canonical data analysis strategies Exercises: Individually formulate analysis questions of interest, obtain and preprocess relevant data |
|
|
4/3/2023 |
IGB 607 |
Topics: R and R workflow, identify canonical data analysis strategies, bulk RNA-seq tutorial Exercises: Another bulk RNA-seq tutorial, single-cell RNA-seq tutorial |
|
5/1/2023 |
IGB 607 |
Topics: Guided analyses of individually formulated questions Exercises: Publish paper |
Matching students with computational projects
We are piloting a program to help themes at the IGB identify students of all levels to work on computational projects. Themes can generate text for job ads, which we will use to recruit and screen candidates from across campus. The ad generator and further instructions can be found here.
Students who are interested in learning more about genomics can check out IGB's MOOC called Genomics: Decoding the Universal Language of Life.
Research
Spatial Omics Initiative
The IGB recently established this initiative to advance research in spatial omics at the University of Illinois. See here for more information.
Directory
Illinois researchers are pushing the frontiers of computational omics and bioinformatics in many different directions. Find below this amazing cast of computational scientists with highly varied interests and expertise.
Mehmet Ahsen
Business, CIMED
https://giesbusiness.illinois.edu/profile/mehmet-ahsen
Medical Decision Making; Computational Biology
Md Tauqeer Alam
Veterinary Clinical Medicine
https://experts.illinois.edu/en/persons/md-tauqeer-alam
Infectious Diseases Genomics; Bacterial Genomics; Metagenomics
Charles Blatti
NCSA, CIMED
https://publish.illinois.edu/blatti/
Integrative omics data analysis
Colleen Bushell
NCSA, CIMED
Scientific Visualization; Visual Analytics; User Experience
Gustavo Caetano-Anolles
Crop Sciences
https://cropsciences.illinois.edu/people/profile/gca
Interaction of plants and microbes; Evolution of biological networks; Function and structure in proteins and ncRNA; Evolution of macromolecular structure
Julian Catchen
Evolution, Ecology, and Behavior
http://catchenlab.life.illinois.edu/
Genome evolution; Structural variation; Population Genomics
Roy Dar
Bioengineering
http://dar.bioengineering.illinois.edu/
Biophysics; Systems Biology; Noise Biology; Drug Screening; Virology
Lee DeVille
Mathematics
https://faculty.math.illinois.edu/~rdeville/
Mathematical biology, Biophysical modeling, Neuronal networks
Mohammed El-Kebir
Computer Science
https://www.el-kebir.net/
tumor phylogenies; copy-number aberrations and their evolution; migration history of metastatic tumors.
Chris Fields
High Performance Computing in Biology group (HPCBio), Roy J Carver Biotechnology Center
https://hpcbio.illinois.edu/people
Applied bioinformatics; bioinformatics training; genomics analysis workflows and pipelines; Bioinformatics infrastructure; microbiome analysis
Jiawei Han
Computer Science
http://hanj.cs.illinois.edu/
Biological text mining
Matt Hudson
Crop Sciences
https://cropsciences.illinois.edu/people/profile/mhudson
Plant and animal genomics; population genomics; genetic basis of crop traits; interactions of plants with pathogens and pests
Ravishankar Iyer
Electrical and Computer Engineering
https://depend.csl.illinois.edu/
Personalized healthcare analytics, and hardware and software systems for healthcare.
Paul Jensen
Bioengineering
http://jensenlab.net/
Infectious diseases; Accelerating microbiology; design new therapies
Halil Kilicoglu
I School
https://ischool.illinois.edu/people/halil-kilicoglu
Biomedical informatics; natural language processing; literature-based knowledge discovery
Luidmilla Mainzer
NCSA
https://www.linkedin.com/in/liudmila-sergeevna-mainzer-98854625
Computational genomics; sequence bioinformatics; high performance computing for biology;
Sergei Maslov
Bioengineering, Physics
https://bioengineering.illinois.edu/people/maslov
Bioinformatics; Biomolecular modeling; Cancer biology; Cancer genomics
Olgica Milenkovic
ECE
http://publish.illinois.edu/milenkovic/
Compression, gene regulatory networks, Gene prioritization
Naveen Naidu Narisetty
Statistics
https://stat.illinois.edu/directory/profile/naveen
high dimensional data analysis; model selection; Bayesian computation; large-scale computational models; functional data; quantile modeling.
Jian Peng
Computer Science
https://jianpeng.web.engr.illinois.edu/
Functional and Structural Genomics; Cancer Genomics; Pharmacogenomics; Neurodegenerative Diseases
Sandra Rodriguez-Zas
Animal Sciences
https://ansc.illinois.edu/directory/rodrgzzs
Genetics, Genomics, and Bioinformatics; Immunophysiology and Behavior; Meat Science and Muscle Biology; Nutrition; Production and Environment Management; Reproductive Biology
Ilan Shomorony
Electrical and Computer Engineering
www.ilanshomorony.com
Algorithms for genome assembly, Metagenomics, Information Theory, Data Science and Machine Learning
Diwakar Shukla
Chemical and Biomolecular Engineering
https://chbe.illinois.edu/directory/profile/diwakar
Molecular Engineering; Molecular Modeling and Simulations; Biophysics
Saurabh Sinha
Computer Science
https://www.sinhalab.net/
Regulatory Genomics; Systems Biology; Neurogenomics; Cancer genomics.
Jun Song
Physics
https://physics.illinois.edu/people/directory/profile/songj
integrative genomics; transcription factors; chromatin structure; non-coding RNAs; gene regulation in development and diseases; cancer genomics; physics-inspired machine learning
Jimeng Sun
Computer Science
https://cs.illinois.edu/about/people/faculty/jimeng
Data and Information Systems; Bioinformatics and Computational Biology; Artificial Intelligence
Shulei Wang
Statistics
https://sites.google.com/view/shulei-wang/
microbiome data analysis, high dimensional statistics, statistical machine learning
Tandy Warnow
Computer Science
http://tandy.cs.illinois.edu/
phylogenomics (genome-scale phylogeny estimation); multiple sequence alignment; metagenomics; Statistical estimation, applied probability, machine learning, graph algorithms
Chengxiang Zhai
Computer Science
http://czhai.cs.illinois.edu/
Health informatics; Biological text mining
Sihai Dave Zhao
Statistics
https://stat.illinois.edu/directory/profile/sdzhao
Statistical genomics; High-dimensional statistics; Survival analysis
Ruoqing Zhu
Statistics
https://stat.illinois.edu/directory/profile/rqzhu
Personalized Medicine; Survival Analysis
