Kihara Bioinformatics Laboratory News

July 2008

• Prof. Changsoon Park, Chung-Ang University, Korea, has visited us and discussed collaborative research projects. Welcome back, Prof. Park.
• David La's book chapter on Predicting binding interfaces of protein-protein interactions was accepted.
• A NSF proposal "Information transfer in biological systems" (Kihara: co-PI) was awarded.

June 2008

• A letter published on Science, "The emerging world of wikis" by Jim C Hu et al.
• Sparsh joined for summer reseach. Welcome, Sparsh!
• Received a grant from Purdue Research Foundation through Computer Research Center, Purdue!
• "PFP: Automated prediction of gene ontology functional annotations with confidence scores" by Troy Hawkins, meghana Chitale, Stanislav Luban & D. Kihara accepted for Proteins.
• David La passed his prelim.

May 2008

• Our EcoliHub project was reported on the Purdue News and NIH NIGMS!
• "Rapid comparison of properties on protein surface" by Lee Sael, David La, Bin Li, Raif Rustamov & D. Kihara accepted for Proteins.
• "ESG: Extended similarity group method for improved automated protein function prediction" by Meghana Chitale, Troy Hawkins, Changsoon Park & D. Kihara accepted for a talk at AFP/Biosapiens 2008!
• Welcome, Matt and Gregg, for summer research.
• Congratulations for graduation, Preston!

April 2008

• "Automated prediction of protein function from sequence" by Meghana Chitale, Troy Hawkins & Daisuke Kihara, a chapter in "Prediction of Protein Structure, Functions and Interactions", Janusz Bujnicki (ed.), John Wiley & Sons, Ltd.

March 2008

• "Threading without optimizing weighting factors for scoring function" by Yifeng D. Yang, Changsoon Park & D. Kihara accepted for Proteins: Structure, Function, and Bioinformatics.
• Prinyanka has received 2008 Howard Hughes Undergraduate Research Internship. Congratulations!

Februrary 2008

• "Fast protein tertiary structure retrieval based on global surface shape similarity" by Lee Sael, Bin Li, David La, Yi Fang, K. Ramani, R. Rustamov & D. Kihara accepted for Proteins: Structure, Function, and Bioinformatics. Visit also 3D-Surfer website.

January 2008

• 3D-Surfer, a server for rapid protein 3D structure search is released. For a user-uploaded, or selected PDB file, the server searches protein 3D structures with a similar surface shape in the entire PDB database in less than a minute. The conventional RMSD can be also computed to retrieved structures. Characteristic local surfaces, i.e. pockets and protrusions, are identified by our VisGrid algorithm.
• "Combining gene sequence similarity and textual information for gene function annotation" by Luo Si, D. Yu, D. Kihara, & F. Yi, accepted for Information Retrieval.
• We welcome Professor Changsoon Park from Chung-Ang University, Seoul, Korea, as visiting professor in our lab.
• "New paradigm in protein function prediction for large scale omics analysis" by T. Hawkins, M. Chitale & D. Kihara, accepted for Molecular BioSystems.

December 2007

• GenPortrait, a software for visualizing and comparing genome sequences is upgraded to version 2.0! It can be also used for comparing metagenomics data.
• Meghana passed her qual1 exams!

November 2007

• EcoliPredict database ver. 2.0 is released. EcoliPredict is a database of computational predictions of E. coli genes and genome. Current version contains protein 3D structure models computed by different programs with quality assessment information. EcoliPredict is intetegrated in and searchable from EcoliHub, E.coli hub data resource.
• Hao has been awarded YeungKyung Woo Achieve Excellence travel award from Dept. Biological Sciences, Purdue University.
• Hao receives Student Travel Grant to the 52nd Annual Meeting of the Biophysical Society from Biophysical Society.

October 2007

• Welcome, Qiong and Alisa for rotation!
• Welcome Rupal!

September 2007

• We welcome Dr. Vishwesh Venkatraman in our group!
• "Estimating quality of template-based protein models by alignment stability" by Hao Chen & Daisuke Kihara, accepted for Proteins: Str. Funct. Bioinformatics.
• Delegation from Harbin Institute of Technology, China, have visited our lab.

August 2007

• We welcome new members in our group, Wen Jun Poh and Stephen Ueng, and Priyanka Surana.
• Professor Changsoon Park visited our lab.

July 2007

• "Characterization of local geometry of protein surfaces with the visibility criterion" by Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani & Daisuke Kihara, accepted for Proteins: Str. Funct. Bioinformatics.
• "Tracing lineage in multi-version scientific databases" by Mingwu Zhang, Daisuke Kihara & Sunil Prabhakar, accepted for IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE) 2007.

June 2007

• Rayan joined us as summer intern from Cachan, France. Welcome, Rayan!
• Ju Hyung joined our group. Welcome!
• De'Rael joined our group as a summer intern from Georgia. Welcome, De'Rael!

May 2007

• Troy's abstract has been accepted for an oral presentation at AFP/Biosapiens 2007 meeting at ISMB, Vienna, July 19-20, 2007. The talk is entitled "Enriching functional knowledge in proteomics data using high-throughput PFP prediction" by T. Hawkins, M. Chitale & D. Kihara. The PFP protein function prediction server is here.
• David La passed the qualifying exam. Congrats!
• Dr. Ikuo Uchiyama visited our lab.
• Sael passed Qual2 exam. Congrats!
• Hao's abstract was selected for an oral presentation in the Indianapolis Bioinformatics Conference. Good job, Hao, and let's get well prepared!
• Jiyeon joined our group. Welcome!
• Rex has graduated CS dept. Congratulations!

April 2007

• Bin passed Qual2 exam! Congrats!
• Troy received Umbarger Outstanding Graduate Student Reserach Award, Dept. of Biological Sciences, Purdue Univesity. Congratulations!
• Preston received Honarable Mention at High Performance Computing Community Poster Session, Purdue Univeristy. Great job, Preson!

March 2007

• Preston has received 2007 Howard Hughes Undergraduate Research Internship. Congratulations!

February 2007

• "Salient critical points for meshes" by Liu Y.-S., Liu M, D. Kihara & K. Ramani accepted for ACM Solid and Physical Modeling Symposium 2007 (SPM2007).

January 2007

• Meghana has joined our group. Welcome!
• Rex has joined our group. Welcome!
• Preston continues to work with us with DURI (Discovery Park Undergraduate Research Internship).

December 2006

• Bin has passed qualifying exam. Congratulations!

November 2006

• PFP was ranked the top in the head to head performance comparison in the function prediction category in the CASP7 contest! Invited for a round table discussion of function prediction in the CASP7 meeting held in Asilomar.
• Dr. Jarek Meller visited our group.
• "Comparative genomics of small RNAs in bacterial genomes" by S.Luban & D. Kihara accepted for Omics.
• Yifeng passed his prelim! Congratulations!

October 2006

• Justin got a job in Chicago (and may work in Japan?). Congratulations!
• "Function prediction of uncharacterized proteins" by T. Hawkins & D. Kihara accepted for J. Bioinformatics and Computational Biology.

September 2006

• Hao Chen passed the prelim!
• Aditi Gupta started rotation with us. Welcome!
• Dr. Ruth Nussinov visited our group.
• The second acorn for us ! - we received the Seed of Success Award from Purdue University for the NIH funded EcoliHub project.

August 2006

• A reseacher from Ajinomoto Co. Inc. has visited out group.
• Steve, Preston, and Robert joined us. Welcome!

July 2006

• Troy will be supported by NIH Molecular Biophysics Training Grant Fellowship!
• The NIH award to the EcoliHub database project was announced in College of Science News!

June 2006

• "EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences" by J. Hu, Y.D. Yang & D. Kihara, accepted for BMC Bioinformatics.

May 2006

• Two of our works, Troy Hawkins and David La were selected for oral presentations at the Third Annual Indiana Bioinformatics Conference!
• Sael successfully passed her qualifing exams. Congrats!
• Stan, Tan and Jairav have graduated. Congratulations!
• Troy gave a seminar at Georgia Tech.
• Howard joins our group this summer. Welcome, Howard!

April 2006

• Received an NSF grant on Finding DNA/Protein motifs (D. Kihara, co-PI).
• Received a grant on protein structure modeling from a private company.(D. Kihara, PI).

March 2006

• Dr. Hiroshi Kihara from Kansai Medical Univ., Japan visits us on March 24, and give a seminar on "Role of alpha-helical burst appeared in the early stage of protein folding" at G-424, 4-5pm.
• "Statistial potential-based amino acid similarity matrices for aligning distantly related protein sequences" by Y.H.Tan, H. Huang & D. Kihara accepted for Proteins: Struct. Funct. Bioinformatics.

February 2006

• Prasad Siddavatam started Biology rotation with us. Welcome!
• David La received the 1st Place at the Sigma Xi Graduate Poster Competition with the poster entitled "Bridging geometric protein surface features and phylogenetic information for rapid identification of protein-protein interaction interfaces" by D. La, D. Liversay and D. Kihara. Congratulations!
• "Enhanced automated function prediction using distantly related sequences and contextual association by PFP" by T.Hawkins, S. Luban & D. Kihara, accepted for Protein Science The PFP server is available here.

January 2006

• Received an NIH grant on EcoliHub Database (D. Kihara, co-PI).
• Yuhao Lin got a job in Eli Lilly. Congratulations!
• A peer-reviewed paper accepted for publication on Cancer Informatics! "Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools." by D. Kihara, Yifeng D. Yang, & Troy Hawkins.
• Greg Ziegler started Biology rotation with us. Welcome!

December 2005

• We received the Seed for Success Award from Purdue University!
• David La formally has joined our group!
• Chetak got a job in Chicago. Congratulations!

November 2005

• 4 poster presentations accepted at International Conference on Genome Informatics, Yokohama Japan.

October 2005

• Yen Hock Tan nominated for CRA Award from CS Dept, Purdue.
• David La will start Biology rotation with us. Welcome!

September 2005

• Otto got a job in Indy. Congratulations!
• Now we received NIH R01 grant!

August 2005

• The second peer-reviewed paper accepted for publication on Nucleic Acid Research! "Potentials and Limitations of Current Motif Discovery Algorithms" by Jianjun Hu, Bin Li, and Daisuke Kihara
• Athurva Gore's "BioQ: A 3D Querying Engine for Proteins" received a top poster award at SURF (Summer Undergraduate Research Fellowship) Poster Presentation

July 2005

• The success of the PFP server is now featured in a news article in the Department of Computer Science Purdue University
• The success of the PFP server is now featured in the July issue of the newsletter of College of Science, Purdue University

June 2005

• Our PFP server for protein function prediction performed the best in the Automatic Function Prediction Special Interest Group (AFP-SIG)
• Luis Avila from St. Edwards University will stay with us for eight weeks with us. Welcome!

May 2005

• We received Purdue Alumni Association Faculty Incentive Grant
• Troy Hawkins passed the preliminary examinations. Congratulations!
• Dr. Weidong Tian from Buffalo Center of Excellence in Bioinformatics (Skolnick Lab) visited us.
• Katie Krajnak from Indiana Academy of Science will stay with us for two weeks as a summer intern. Welcome!
• Troy Hawkins's work on protein function prediction is accepted for oral presentation in ISMB for the Automated Function Prediction Special Interest Group meeting

April 2005

• Department of Biological Sciences, Purdue University Award and Recognition Reception recipients include:

  • Daisuke Kihara (PRF Summer Faculty Grant)
  • Troy Hawkins (Outstanding Graduate Teaching Assistant)
  • Stan Luban (Purdue/Howard Hughes Medical Institute Summer Internship)
  • Yen Hock Tan (Purdue/Howard Hughes Medical Institute Summer Internship)
  • Adam Boyko (Outstanding Graduate Teaching Assistant)

• Ei Ei Phyu received Howard Hughes fellowship for undergraduate research in Bioinformatics

• Troy Hawkins received the 2005 Outstanding Graduate Teaching Assistant Award in the Department of Biological Sciences, Purdue University
• The first paper from our group was accepted for publication in Protein Science! "On the effect of the long-range interactions on the secondary structure formation of proteins" by Daisuke Kihara
• Ei Ei Phyu, Yen Hock Tan, and Stan Luban's Howard Hughes Awards is now featured in a news article in the Department of Computer Science, Purdue University
• Yen Hock Tan's picture at the Undergraduate Research Poster Presentation, College of Science & College of Agriculture, Purdue University is on the front page of Local section of April 13th Journal and Courier
• Stan Luban's poster received Outstanding Research Award at the Undergraduate Research Poster Presentation, College of Science & College of Agriculture, Purdue University
• Otoniel Venezuela received Graduate School Incentive Grant
• Dr. Yasuo Hata from Institute for Chemical Research, Kyoto University, Japan visited us
• Yen Hock Tan's scholarship from Hewlett-Packard during the Department of Computer Science, Purdue University Awards banquet is now featured in a news article in the Department of Computer Science, Purdue University
• "PFP: Automatic annotation of protein function by relative GO association in multiple functional contexts" by Troy Hawkins and Daisuke Kihara accepted for poster presentation at ISMB 2005

March 2005

• Troy Hawkins's PFP server accepted for the AFP 2005 server submission challenge at ISMB conference
• Received a message from CASP6 Organizer: "Dear CASP6 predictor, Your group (P0530) submitted the best or nearly the best prediction for the following targets: D1_T0239". Congratulations CASP6 structure prediction team of Otoniel Venezuela, Yen Hock Tan, and Daisuke Kihara!
• Dr. Min Joong Jeong from Computational Biology Research Center, Tokyo visited us. He will give a seminar entitled "Decision Support System for Design Optimization and Fragment Assembly for Protein Structure Optimization"
• Daisuke Kihara received PRF Summer Faculty Grant
• Stan Luban and Yen Hock Tan received Howard Hughes Summer Internship
• Yifeng Yang will start PULSe rotation with us. Welcome!

January 2005

• Congratulations to Hao Chen for his success in his first committee meeting!
• Congratulations to Bin Li and family for his first child, Meixiang Li (Grace)!
• Hyun Chul Lee will start PULSe rotation with us. Welcome!

December 2004

• Stan Luban's Honorable Mention in the 2005 Outstanding Undergraduate Award Program of the Computing Research Association (CRA) is now featured in a news article in the Department of Computer Science, Purdue University

September 2004

• "Genome Function Research Handbook" was published by Yodosha Publishers, Toyko, Japan with a chapter entitled "Biomolecular Structure Databases" written by Daisuke Kihara

March 2004

• Stan Luban's Howard Hughes Summer Internship is now featured in a news article in the Department of Computer Science, Purdue University