Precision Medicine

Centers, Initiatives, and Institutes

CSL researchers are involved in a number of major centers and strategic partnerships that seek to advance medicine.

CompGen Initiative

• Ravi Iyer, co-director (CSL)
• Gene Robinson, co-director (the Carle R. Woese Institute for Genomic Biology [IGB])
• Victor Jongeneel, associate director (IGB and NCSA)

The CompGen initiative seeks to combine the collective strengths of Illinois’ genomic research with its prowess in large-scale parallel systems and big data to develop new technology that enables future genomic breakthroughs. As part of the initiative, researchers aim to build an instrument that allows scientists to manage and process genomic information and algorithm development. The new technology could enable a better understanding of the basic processes of life, illumination of how evolution works, and customized treatments for diseases, among other discoveries. 

BD2K Center

• Jiawei Han, PI and director (CS)
• Victor Jongeneel, executive director (IGB, NCSA)
• Saurabh Sinha, co-PI (CS)
• Jun Song, co-PI (BioE and Physics)
• Richard Weinshilboum, co-PI (Mayo Clinic)

CompGen is the home of a National Institutes of Health (NIH) Center of Excellence for Big Data Computing, which is part of an NIH Big Data to Knowledge (BD2K) initiative. The Center leverages the latest computational techniques for mining corporate or Internet data to enable the intuitive analysis and exploration of biomedical big data.

Illinois Mayo Alliance

Individualized medicine is the promise of advances in genetics, computing, and nanotechnology. In the belief that translating these advances into real-world applications requires strong collaboration between leading research and clinical partners, the University of Illinois and Mayo Clinic have formed a strategic alliance to promote a broad spectrum of collaborative research, the development of new technologies and clinical tools, and the design and implementation of novel education programs.

Faculty

Numerous CSL faculty and senior researchers are looking at various aspects of computing and data processing as they relate to precision medicine, especially with respect to the need to handle massive data sets quickly and efficiently and convert the data into useful, actionable knowledge. In pursuing this research, CSL personnel are partnering with subject matter experts from numerous units on campus and beyond.

The lists below are not meant to be exhaustive, but they do speak to the breadth of expertise and technology dimensions being brought to bear on the issues.

CSL Faculty

Roy Campbell (CS): Complex computer system organization and software engineering

Andreas Cangellaris (ECE): Design of high-frequency/high-speed integrated electronic components, circuits, and systems

Deming Chen (ECE): GPU computing and optimization, and the design of novel computing platforms

Minh Do (ECE): Visual information representation, image and multidimensional signal processing, and computational imaging

William D. Gropp (CS): Parallel computing, scientific computing, scalable numerical algorithms, programming models for scientific computing

Wen-mei Hwu (ECE): Architecture, compilation, and microarchitecture of high-performance parallel computer systems

Ravi K. Iyer (ECE): Reliable and secure networks and systems, and computing for genomics research

Zbigniew Kalbarcyzk (ECE): Reliable and secure networks and systems

Yi Lu (ECE): Distributed systems and networking, and inference on graphical models

Steven S. Lumetta (ECE): Cluster computing, parallel computing, user-level communication, validation and reliability, and computational genomics

Olgica Milenkovic (ECE): Bioinformatics, nonlinear compressive sensing with quantization, and fault-tolerant sensing algorithms and information theory

Klara Nahrstedt (CS): Quality of service management, QoS-aware service composition for advanced multimedia applications, and translation and mapping engines for QoS parameters

Rob A. Rutenbar (CS): Silicon accelerator architectures for computationally difficult tasks

William H. Sanders (ECE): Architecting of reliable & secure systems, stochastic modeling, and performance evaluation of distributed systems

Shobha Vasudevan (ECE): Algorithms for data analytics and graph analytics, and embedded systems validation and security

Venugopal V. Veeravalli (ECE): Signal processing for big data, information theory, and detection and estimation theory

Tandy Warnow (CS): Large-scale and complex estimation problems in phylogenomics and metagenomics

 

Partners – faculty and senior researchers

CSL faculty work with numerous partners in this sector. It is a great strength of CSL that when you approach CSL, you open connections to a vast network of experts both within CSL and beyond. Below are individuals to be found on the Urbana campus. The list is not meant to be exhaustive; new connections are continually being made.

Carl R. Woese Institute for Genomic Biology

• Isaac Cann (Animal Sciences)
• Reza Farivar (CS)
• Bruce Fouke (Geology)
• John Gerlt (Biochemistry)
• Andrew Leakey (Plant Biology)
• Stephen Long (Plant Biology, Crop Sciences)
• Gene E. Robinson (Entomology)
• Lisa J. Stubbs (Cell and Developmental Biology)

College of Engineering

• Nigel Goldenfeld (Physics)
• Jiawei Han (CS)
• John Hart (CS)
• Julia Hockenmaier (CS)
• Ting Lu (BioE)
• Jian Ma (BioE)
• Sergei Maslov (BioE)
• Dan Roth (CS)
• Jun Song (BioE and Physics)
• Marianne Winslett (CS)
• ChengXiang Zhai (CS)
• Saurabh Sinha (CS)

College of Agricultural, Consumer and Environmental Sciences

• Matthew Hudson (Crop Sciences)
• Alfred Roca (Animal Sciences)
• Sandra Rodriguez-Zas (Animal Sciences)
• Karen E. Sears (Animal Biology)
• Bryan White (Animal Sciences)

College of Liberal Arts and Sciences

• Ping Ma (Statistics)
• Ruby Mendenhall (Sociology and African American Studies)
• William W. Metcalf (Microbiology)
• Barry Pittendrigh (Entomology)
• Rachel Whitaker (Microbiology)
• Wenxuan Zhong  (Statistics)

College of Medicine (UIC regional campus)

• Bruce R. Schatz (Medical Information Science

National Center for Supercomputing Applications

• Donna Cox (also Art & Design)
• C. Victor Jongeneel
• Volodymyr Kindratenko
• Liudmila Mainzer