College of Liberal Arts & Sciences

Past News

Bioinformatics PhD program approved

March 16, 2009

The PhD granting program in Bioinformatics has been approved by the Board of Regents. The program is based in The Center for Bioinformatics and involves faculty at KU Lawrence, KU Medical Center, and Stowers Institute. The Bioinformatics faculty members are recognized world-class leaders in bioinformatics, computational biology, information technology, and life sciences. More information will be available soon on the program site.

Winning worldwide CASP competition: Yang Zhang does it again!

October 27, 2008

Assistant Professor of Bioinformatics Yang Zhang wins the server section of the Critical Assessment of Structure Prediction (CASP) contest again, the second time in a row, repeating his extraordinary achievement at 2006 CASP (see News). CASP is a biannual worldwide competition in blind protein structure prediction, in which the organizers solicit new protein structures from the experimentalists and offer the sequences to the community of modelers for blind prediction. The CASP competition is the most high-profile event in computational structural biology and bioinformatics. Yang’s repeated success in the automated server predictions, across all structure prediction categories, with a clear margin from the rest of the participating teams, solidifies his leadership in the computational structure prediction field. Our congratulations on this extraordinary occasion, which has become familiar, to Yang and his team members!

John Karanicolas joins The Center for Bioinformatics faculty

June 25, 2008

John Karanicolas

The Center for Bioinformatics is pleased to announce Dr. John Karanicolas as its newest faculty member. Dr. Karanicolas is an expert at using structure-based methods to design new protein-protein interactions. He looks forward to applying this expertise to study the interactions between cytokines and their receptors: predicting cytokine/receptor specificities, and redesigning with altered specificity. Dr. Karanicolas additionally validates computational predictions and designs through experimental characterization.

Dr. Karanicolas was granted a PhD from The Scripps Institute in 2003. He carried out his graduate studies in the laboratory of Professor Charles L. Brooks III, where he studied protein folding through analysis of molecular dynamics simulations.

He has since completed a postdoctoral fellowship in the laboratory of Professor David Baker, at the University of Washington. Here, Dr. Karanicolas carried out theoretical and/or experimental aspects of several design projects, including altering the allosteric mechanism of integrin signal transduction and designing a peptide to inhibit tau fibril formation. His postdoctoral accomplishments culminated in his design of a de novo protein-protein interface from two proteins with no natural affinity for each other.

Dr. Karanicolas stresses his enthusiasm to apply protein design methodology as an effective means to deconstruct the complexity in a system of particular biomedical interest, cytokine signaling. Carefully designed molecules will reduce cytokine signaling to a series of single well-defined responses, allowing clear delineation of these complex pathways and leading to a new class of therapeutics.

Dr. Karanicolas joins the Center at the rank of assistant professor, with a joint appointment in the Department of Molecular Biosciences.


Yang Zhang is awarded Sloan fellowship

February 19, 2008

Assistant Professor Yang Zhang became the second faculty member of the Center to be awarded prestigious Alfred P. Sloan Research Fellowship. Dr. Zhang's research interests are in modeling of protein structure and interactions. Starting in 2005, Dr. Zhang has successfully developed his research program in the Center to become one of the recognized leaders in the field. The Center is extremely proud of Dr. Zhang's achievement.


Wonpil Im becomes Alfred P. Sloan fellow

February 22, 2007

The Center for Bioinformatics congratulates Assistant Professor Wonpil Im with a prestigious fellowship award from the Alfred P. Sloan foundation. Wonpil's research focuses on computer simulations of protein structure and function. The Sloan fellowship is an extraordinarily competitive award, involving nominations for the very best young scientists. Selection of Wonpil Im from this remarkable group of nominees is an indication of the high esteem in which his work is regarded in the scientific community.


Yang Zhang wins worldwide CASP competition

September 14, 2006

Critical Assessment of Structure Prediction (CASP) is a biannual worldwide competition in blind protein structure prediction. In this competition, the organizers solicit new unpublished protein structures from the experimentalists and offer the sequences to the community of modelers for blind prediction. The CASP competition is the most high-profile event in computational structural biology and bioinformatics.

The Center for Bioinformatics is extremely proud and excited that one of its own, Assistant Professor Yang Zhang, won this year CASP7 in the most important and prestigious category - automated server predictions. The automated predictions do not involve human intervention, thus allowing objective evaluation of the prediction methodologies. As such, they are the most respected ones by the scientific community.

The prediction season ended in August and, as of September 13, most of the CASP7 targets (experimental structures) have been released. Based on a variety of automated evaluations, the Zhang-Server performed significantly better than all other automated servers in the field. Although the evaluation results are still not official, Zhang’s significant lead (5-10% better than the second best computer server of other groups) guarantees his first place.

Dr. Zhang just completed his first year (!) on the faculty as an assistant professor and we at the Center are wondering what to expect from him in the future! The Center invites all the colleagues to join us in congratulating him with this huge success.


A new addition to the Center faculty – Dr. Gennady Verkhivker

August 1, 2006

Gennady Verkhivker

The Center for Bioinformatics is announcing the recruitment of Dr. Gennady Verkhivker, a world leading scientist in modeling of biomolecular interactions, structure-based drug design, bioinformatics and computational pharmacogenomics. Dr. Verkhivker earned his PhD in theoretical physical chemistry from the Institute of Physical Chemistry, Russian National Academy of Sciences in 1986. He subsequently received there postdoctoral training and rose to the rank of a Group Leader in Theoretical Chemistry. Dr. Verkhivker continued pursuing his scientific interests in the laboratory of Prof. Ron Elber at the Department of Chemistry, University of Illinois at Chicago in 1990-1992. Upon starting his industrial career at Agouron Pharmaceuticals in 1993, Dr. Verkhivker established a distinguished professional record in pharmaceutical industry. He played a leading role in establishing computer-aided drug design technology and building the largest computational group in pharmaceutical industry. Dr. Verkhivker has held various research and management positions of increasing responsibility at Agouron Pharmaceuticals, Warner-Lambert, Pfizer Global Research and Development and served most recently as an Associate Research Fellow and Group Leader in the Department of Computational Chemistry at Pfizer Global R&D, La Jolla Laboratories. His distinguished research accomplishments and pharmaceutical industry experience have been highly regarded in the academic world. Dr. Gennady Verkhivker was appointed as an Adjunct Full Professor of Pharmacology at the Department of Pharmacology, University of California, San Diego and the UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences. Dr. Verkhivker is a highly distinguished scientist who is widely recognized for his research and important contributions in areas of computational chemistry, bioinformatics and computational biology with numerous high-profile publications in top peer-reviewed journals and presentations at many prestigious international conferences. Dr. Verkhivker is extremely active in the national and international scientific community, organizing many international symposia and workshops. He has been a reviewer of numerous scientific papers in leading journals and a member of review panels in major granting agencies.

Dr. Verkhivker joins The Center for Bioinformatics in October, as Full Professor with Tenure, with a joint appointment in the Department of Pharmaceutical Chemistry.


Research group of Dr. Wonpil Im is designated as an official developer of CHARMM

November 8, 2005

The research group of Dr. Wonpil Im has been designated as an official developer group of CHARMM (Chemistry at HARvard Macromolecular Mechanics,, a celebrated program for macromolecular dynamics and mechanics. Its development began in the research group of Professor Martin Karplus at Harvard University and continues throughout the world with contributing developers. CHARMM performs standard molecular dynamics and energy minimization with the potential energy functions for proteins, nucleic acids, and lipids. In addition, CHARMM can be used for various chemical and conformational free energy calculations with many types of restraints. It also provides versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories.

During his graduate and postdoctoral studies, Dr. Im has been involved in development and implementation of several modules in CHARMM such as:
- Poisson-Boltzmann EQuation solver (PBEQ module)
- Generalized Solvation Boundary Potentials (GSBP module)
- Generalized Born with a simple SWitching function (GBSW module)

CHARMM is available to academic users in full source form, plus extensive documentation and test input scripts, through Harvard University. A license for CHARMM can be obtained by inquiring to: 

Professor Martin Karplus, Department of Chemistry & Chemical Biology, Harvard University 
12 Oxford St, Cambridge, MA 02138 


The Center recruits Yang Zhang as its new faculty member

May 8, 2005

The Center for Bioinformatics is announcing the recruitment of Dr. Yang Zhang as its new faculty member. Dr. Zhang is a world-class expert in large-scale high-throughput protein modeling and structural aspects of protein interactions. His recruitment is an important step in the Center’s effort to build up its strength in this strategic research area. Dr. Zhang joins the Center in August, as assistant professor, with a joint appointment in the Department of Molecular Biosciences.

Dr. Zhang received his PhD in Physics at the Central China Normal University in 1996. He spent two years as the Alexander von Humboldt research fellow at Free University of Berlin, Germany. After a subsequent postdoctoral research in the Chinese Academy of Sciences, he joined the group of Jeffrey Skolnick at the Danforth Center. His most recent appointment has been on the faculty of the Center of Excellence in Bioinformatics at the University of Buffalo.


Wonpil Im joins the faculty of The Center for Bioinformatics

April 15, 2005

Wonpil Im

The Center for Bioinformatics is happy to announce that Dr. Wonpil Im of the Scripps Research Institute joins the Center in August 2005. Dr. Im is an outstanding researcher with top-level credentials in modeling of membrane proteins and physicochemical aspects of molecular biology. The Center is fortunate to acquire his unique expertise in this critical area of structural bioinformatics and computational biology.

Wonpil Im received B.Sc. and M.Sc. degrees in Chemistry from Hanyang University, Seoul, in 1994 and 1996. He received Ph.D. degree in Biochemistry from Weill Medical College of Cornell University in New York in 2002 (Professor Benoit Roux), focusing on theoretical study of ion permeation and selectivity in OmpF porin and its mutants by molecular dynamics simulations, Grand Canonical Monte Carlo - Brownian Dynamics, and Poisson-Nernst-Planck electrodiffusion theory. In 2002 he became a member of the group of Professor Charles L. Brooks, III at the Scripps Research Institute, where he has been working on insertion, folding, and assembly of membrane proteins and peptides by utilizing and extending generalized Born electrostatics theory. His research at KU will focus on the applications of theoretical and computational methods to chemical and physical problems in biology. Dr. Im joins the Center in the rank of assistant professor, with a joint appointment in the Department of Molecular Biosciences.


Recruitment of Director, Dr. Ilya Vakser

June, 2004

Ilya VakserThe University of Kansas is happy to announce the recruitment of Dr. Ilya Vakser of SUNY Stony Brook as the Director of the newly created Center for Bioinformatics. Dr. Vakser will assume his position on January 30, 2005. He is an internationally recognized expert in bioinformatics and computational biology and a leader in the field of modeling protein interactions and structural description of genomes.

Dr. Vakser earned his PhD in biophysics at Moscow State University in 1989 and received further training at the Weizmann Institute, Washington University, and the Rockefeller University. He served on the faculty of the Medical University of South Carolina as an assistant and associate professor and SUNY Stony Brook as an associate professor. Dr. Vakser will join KU as a full professor, with a joint appointment in the Department of Molecular Biosciences.

Dr. Vakser is the author of many scientific papers resulting from research funded by the National Institutes of Health, the National Science Foundation, and other funding agencies. He combines his research with scientific community-wide activities as an organizer of international conferences and a member of many advisory and steering committees.

The recruitment of Dr. Vakser comes at the time of the Kansas Economic Growth Act, which will allocate $500 million over the next ten years to Life Sciences research in Kansas. The KU Bioinformatics initiative under the leadership of Dr. Vakser will evolve into an interdisciplinary center, which will combine world-class research with graduate education, and become an international hub of activities in bioinformatics and computational biology.

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