Group Members

Jump to current members, undergraduate students, collaborators, alumni.


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Current members

Daisuke Kihara

Principal Investigator
email: dkihara@purdue.edu

Genki Terashi

Assistant Research Scientist
email: gterashi

Yuki Kagaya

PostDoc
email: ykagaya

Tsukasa Nakamura

PostDoc
email: nakamurt

Tunde Aderinwale

Computer Science Graduate Student
email: taderinw

Charles Christoffer

Computer Science Graduate Student
Former NIH T32 Mol. Biophys. Trainee
email: christ35

Farhanaz Farheen

Computer Science Graduate Student
email: ffarheen

Swagarika Giri

Computer Science Graduate Student
email: giri2

Nabil Ibtehaz

Computer Science Graduate Student
email: nibtehaz

Anika Jain

Biological Sciences Graduate Student
email: jain488

Devashish Prasad

Computer Science Graduate Student
email: prasadd

Ananth Shreekumar

Computer Science Graduate Student
email: ashreeku

Emilia Tugolukova

Biological Sciences Graduate Student
email: etugoluk

Jacob Verburgt

Biological Sciences Graduate Student
NIH T32 Mol. Biophys. Trainee
email: verburgt

Xiao Wang

Computer Science Graduate Student
MolSSI Software Fellow
email: wang3702

Yuanyuan Zhang

Computer Science Graduate Student
email: zhang038

Zicong Zhang

Computer Science Graduate Student
email: zhan1797

Undergraduates

Ritwik Jain

Han Zhu

Razan Alkawai

Yunhan Huang

Kunal Mahatha

Vijay Bharadwaj

Ethan Chen

Vo Ngoc Nhi

Visiting Professors

Mahmoud A. A. Ibrahim

Associate Professor
Head of CompChem Lab, Minia University, Egypt

Visiting Scholars

Harini Kannan

Indian Institute of Technology Madras, Tamil Nadu, India

Deepanshu Mody

Birla Institute of Technology and Science Pilani, Hyderabad, India

Manuel Zumbado Corrales

Costa Rican Institute of Technology (ITCR), Costa Rica

Chethiya Galkaduwa

University of Kelaniya, Sri Lanka

Collaborators

Takatsugu Hirokawa Professor AIST, Tokyo, Japan
Kenichiro Imai Research scientist Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology
Wen Jiang Professor Purdue University, Department of Biological Sciences
Woong-Hee Shin Assistant professor Sunchon National University, Department of Chemistry Education, Korea
Atilla Sit Assistant Professor Eastern Kentucky University, Department of Mathematics and Statistics, Kentucky
Yuji Sugita Professor RIKEN, Japan
Min Xu Assistant Research Professor Carnegie Mellon University, Department of Computational Biology

Alumni

K. Ramanathan Associate Professor VIT University, Dept. of Biotechnology, India Dec. 2018 - June 2019
Saeed Salem Associate Professor North Dakota University, Dept. of Computer Science August - Dec. 2018
Kujin Kim Professor Kyungpook National University, School of Computer Science and Engineering, Korea April - Dec. 2018
Xinyuan Zhou Assistant Professor Changsha University, Dept. of Computer Science and Technology, China March - Dec. 2015
Catherine Rayon Professor Universite de Picardie Jules Verne, Dept. of Biology, France Jan-May 2012
Hangchan Lee Associate Professor Hansung University, Dept. of Multimedia Engineering, Seoul, Korea Jan-May 2009
Changsoon Park Professor Chung-Ang University, Dept. of Statistics, Korea Jan-Feb 2008
Zhiqiang Jackie Huang Huazhong Agricultural University, China August 2017 - May 2018
Uttamkumar Samanta West Bengal State Univ., India Oct 2012 - May 2013, May-June, 2018
Mateusz Kurcinski Warsawa University, Chemistry, Poland Mar 2010 - Mar 2011
Daipayan Sarkar postdoc researcher Michigan State University July 2019-April 2021
Woong-Hee Shin chemistry, assistant professor, Sunchon National University, Korea August 2014-March 2019
Hyungrae Kim physics Kyonggi University, Korea Sep 2011-Aug 2016
Jian James Zhang chem. engineering, research scientist Zymoworks Inc. Aug 2014-May 2015
Amit Roy physics, comp. Str. Biologist NIH Rocky Mountain Laboratories Dec 2013-Dec 2014
Atilla Sit applied math, assitant professor Eastern Kentucky University, Dept. of Mathematics and Statistics Sep 2012-July 2014
Bingjie Hu Med Chem & Mol Pharmacology, scientist Merck > Eli Lilly Sep 2013-May 2014
Xiaolei Zhu chem eng, assistant professor Anhui Univ., China Jul 2012-June 2014
Yi Xiong CS, assistant professor Shanghai Jiaotong Univ., China Jan 2012-Dec 2013
Youn Im Choi statistics, research scientist Dept. of Statistics, Chung-Ang Univ., Korea Mar 2012-Mar 2013
Sael Lee CS, research scientist Samsung Advanced Institute of Technology, currently associate professor at Ajou University, Korea Aug 2010-Jul 2011
Vishwesh Venkatraman comp chemistry, moved onto scientist INRIA, France Sep 2007-Jul 2009
Jianjun Hu CS, associate professor Univ. of South Carolina Sep 2004-Aug 2005
Eman Alnabati Ph.D. (CS) Assistant Professor at Umm Al-Qura University, Saudi Arabia. July 2022
Lyman Monroe Ph.D. (Biol) Los Alamos National Lab. May 2022
Sai Raghavendra Maddhuri Venkata Subramaniya Ph.D. (CS) Facebook/Meta May 2022
Luong Minh Nguyen M.S. (CS) Microsoft May 2022
Aashish Jain Ph.D. (CS) Salesforce Aug. 2021
Siyang Chen M.S. (CS) Amazon May 2021
Xusi Han Ph.D (PULSe) Wells Fargo May 2020
Ziyun Ding Ph.D (PULSe) Convergent Genomics Inc > Varian > Roche Dec 2019
Lenna X. Peterson Ph.D (PULSe) Schrödinger Inc May 2017
Qing Wei M.S. (CS) Amazon May 2017
Ishita K. Khan Ph.D (CS) Ebay Aug. 2016
Juan Esquivel-Rodriguez Ph.D (CS) Google > Associate professor at Instituto Tecnologico de Costa Rica July 2014
Yoichiro Togawa M.S. (Biol) Self Defence Force, Japan May 2014
Meghana Chitale Ph.D (CS) Epic May 2013
Chao Yuan M.S. (Biol) Amazon May 2012
David La Ph.D (Biol) David Baker Lab, Univ. Washington, Seattle > DeepMind Dec 2011
Bin Li Ph.D (CS) La Jolla Institute for Allergy & Immunology, California Dec 2011
Sael Lee Ph.D.(CS) Continued as postdoc until July 2011 > Samsung Advanced Institute of Technology, Korea > assist. prof at SUNY Korea > BK Assoc. Prof at Seoul Nat. University > Associate Professor, Ajou University July 2010
Hao Chen Ph.D.(Biol) Bioinformatics analyst, Craig Venter Institute > bioinformatics sicentist at New York University > WuXi NextCODE May 2010
Yifeng David Yang Ph.D (Biol) statistical consultant at Equifax > Fifth Third Bank May 2010
Troy Hawkins Ph.D. (Biol) research assistant professor at IUPUI, Indianapolis > res. scientist at Eli Lilly > Head, Computer Sciences, Elanco > Vice President, BiomEdit Oct 2008
Tong Qi Statistics Feb 2018 - May 2019
Mengmeng Zhu PULSe May 2015 - Spring 2018
Israa Al-Qassem CS Jan. - Dec. 2017
Keisuke Yanagisawa Tokyo Inst. Tech, Japan Aug - Dec. 2017
Shiqi Yang Animal Sci Fall 2016
Xuejiao Kang CS Aug 2012-May 2015
Xin Cheng CS Aug 2013-Aug 2014
Kristen Johnson CS Aug 2013-Aug 2014
Hongyun Gao Dalian Univ. of Tech, Dept. of Math. Sci, China Aug 2012-Dec 2013
Mario Alfy Messih King Abdullah Univ., Saudi Arabia July-Aug 2011
Michal Jamroz Warsaw University, Chemistry, Poland Oct 2010-May 2011
Mingjie Tang CS Aug 2010-Aug 2011
Farrukh Arslan ECE Aug 2008-Dec 2009
Padmasini R. Chakravarthy Electrical and Computer Engineering (ECE) Aug 2008-Dec 2009
Rayan Chikhi CS, summer intern from ENS Cachan Britanny, France June-Aug 2007
Kean Tan Statistics, MS Aug 2010-May 2011
Otoniel Venuzuela Computer Science, MS May 2004-Aug 2005
Michael Gillogly CS, Purdue Aug 2009-Apr 2010
Rohan Narasimha CS Summer 2020 - Fall 2021
Yilin He Shandong University, China, CS Summer 2019
Yiwei Zhang Renesselaer Polytechnic Institute, CS Summer 2019
Yingfeng Lu Shanghai Jiao Tong University, China, CS Summer 2019
Rohith Ravindranath CS Spring 2019
Sean Flannery CS Spring 2019 - Summer 2019
Aditi Acharya Engineering Fall 2017 - Spring 2019
Hareesh Gali CS Fall 2017 - Spring 2019
Aung Myat CS Spring 2018 - Fall 2018
Qifen Chen CS Spring 2018 - Fall 2018
Matin Hormati CS Fall 2018
Vidhur Kumar CS Fall 2018
Shantanu Nair CS Fall 2018
Nikita Rajaneesh CS Fall 2018
Yibin Wu CS Fall 2018
Govind Girish CS Fall 2017 - Fall 2018
Kavya Nagalakunta CS Fall 2017
Dan Ntala Biol Spring - Fall 2017
Yuhong Zha CS Fall 2017- Spring 2018
Xi He Biol Fall 2017- Spring 2018
Caleb Belth CS Fall 2015- Spring 2018
Xiao Wang Xi'an Jiaotong U., China Summer 2017
Hao Zhu Beijing U. Posts & Tel. Summer 2017
Simeng Liao Nankai U, China Summer 2017
Varun Gupta CS Fall 2017
Hannah Zentner CS Fall 2017
Kevin Shim Biol Spring 2017
Natalie Oda Biol Spring 2017
Matthew Muhoberac CS Spring 2017
Alexandre Dias Fed. U. Lavras, Brazil Summer 2016
Morgan Farrell Biol Summer 2016
Alexandre Engstrom Biol Spring 2016
Aditya Vaidyam CS Spring 2015-Spring 2017
Brian Lembong Biol Summer 2016-Spring 2017
Hayley Chan MCMP Fall 2015-Spring 2017
Siddharth Prabhu BME Fall 2016-Spring 2017
Sarah Rodenbeck Biol/CS Spring 2016-Spring 2017
Andrew Walden Biol Summer 2016-Spring 2017
Josh McGraw Biol Summer 2015-Summer 2016
Tiange Dong Biol Spring 2013-Fall 2015
Eric Petit Biol Fall 2014-Fall 2015
Ray Ji Biol Fall 2014-Fall 2015
Tianmu Hu Biol Fall 2014-Fall 2015
Andrew Walden Biol/CS Fall 2014-Fall 2015
Ryan Hancock Industrial Engng. Summer 2015
Hanfu Zhang CS, Tsinghua Univ., China Summer 2015
Weichuan Luo Biol Fall 2013- Spring 2015
Tommy Lee Biol Spring 2015
Qing Wei CS Spring 2014-Fall 2014, cont.to grad
Charles Christoffer CS/Math Spring 2014-Summer 2015, cont.to grad
Yue Wang Stat Spring 2014-Summer 2015
Qing Zu Stat Summer-Fall 2014
Karan Dua IIT, Roorkee, India Summer 2014
Fangyuan Hou CS Summer 2013-Spring 2014
Yuqian Chen Biochem Spring -Fall 2013
Grant Gumina CS Spring 2013 -Spring 2014
Linzi Chen Bio/Stat Spring 2013 -Spring 2014
Arthi Anand Bio Spring 2013 -Fall 2013
Wen Sun Bio Fall 2013
Lillian Liu CS Spring 2012 -Spring 2014
Joel Crist Bio Summer 2013
Aanchal Kanodia VNIT-Nagpur, India Summer 2013
Minxian Li CS, Beijing Univ. of Chem. Tech Fall 2012 -Spring 2013
Xiaowei Hong CS Fall 2012 -Spring 2013
Yanan Tao Bio Fall 2012 -Spring 2013
Guanqun Mao CS Fall 2012 -Spring 2013
Linsheng Shen Bio Fall 2012 -Spring 2013
Chang Liu Math Fall 2012 -Spring 2013
Vianney Gonzalez Math Fall 2012 -Spring 2013
Sam Yap Bio Spring 2012 -Spring 2013
Shawn Deboth Bio Spring 2013
Wuwei Zhang CS Spring 2013
Alex Gao Stat Fall 2012
Liuning Wang Stat Fall 2012
Yingfei Ma Stat Spring 2011 -Spring 2012
Su Lin Ooi CS Fall 2011 -Summer 2012
Kara Kahue CS, SROP Summer 2012
Danny Antakli Bio Summer 2012
Benjamin Basnagel Bio Spring 2011 -Spring 2012
Yang Shen Bio Spring 2012
Roshna Agrawal CS Spring 2010 -Summer 2011
Xin Lu Tan Stat Fall 2010 -Spring 2011
William Hoffman Bio Spring 2010 -Spring 2011
Sanmeet Kanhere CS Summer 2010 -Spring 2011
Mi-Sun Kong Bio Fall 2010 -Fall 2011
Zilong Zhou Math Fall 2011
Shing Jay Ong CS Spring 2011
Shucong Zhang CS Spring 2011
Daniel Lee BioMed Eng Spring 2011
Gaonan Zhang Bio Spring 2011
Qiting Wu Bio Spring 2011
Hayun Lee Bio Spring 2011
Liyun Fan Bio Spring 2011
Yilong Jin CS Spring 2011
Satwica Yernini Vellore I. Tech., India Spring 2011
Shriphani Palakodety CS Fall 2009 -Spring 2010
Matt Herron Bio/CS Summer 2008 -Spring 2010
Sajat Jain CS Fall 2009 -Fall 2010
Abram Magner CS/Math Spring 2009 -Spring 2010
Kunal Modi CS Fall 2009 -Fall 2010
Wei-Chia Sun CS Fall 2010
Shuai Liu CS Fall 2010
Yidi Wang Bio Fall 2010
Malvika Mathur Bio Fall 2008 -Spring 2010
Sangwook Lee CS Fall 2009 -Spring 2010
Nicket Gupta CS Fall 2009 -Spring 2010
Priyanka Surana Bio Fall 2007 -Spring 2010
Paul Tuck CS Summer 2009 -Spring 2010
Gabriel Martinez CS Spring 2010
Gunjan Raghav CS Spring 2010
Gregg Thomas Bio Summer 2008 -Fall 2009
Devin Luckett Bio Fall 2008 -Spring 2010
Roy Ren CS Summer 2009
En-hsun Liu CS Summer 2009
Shen Liang CS Summer 2009
Subhash Atluri CS Summer 2009
Seven Ahrendt Bio/CS Fall 2008 -Spring 2009
Rupal Trivedi Bio Fall 2007 -Spring 2010
Emily Flynn Bio Fall 2008
Jared Bannister CS/Math Fall 2008
Sparsh Shekhar CS Summer 2008
Preston Spratt Bio Fall 2006 -Spring 2008
Jennifer S. Reeve CS Summer 2004 and 2011
Steven Ueng CS Fall 2007
De'Rael Darling Marc/AIM Summer 2007
Steve Krawczyk Bio Fall 2006-Spring 2007
Rex Chang CS Spring 2007
Yen Hock Tan CS 2004-2006
Jairav Desai CS, DURI 2005-2006
Robert Helms Bio Fall 2006
Howard Chang CS Summer 2006
Jiyoung Lee Bio Fall 2005
Ei Ei Phyu CS Spring/Fall 2005
Luis Avila Marc/AIM Summer 2005
Yuhao Lin Comp. Eng Spring 2005
Brian Trisler CS Spring 2005
Jonathan Williford CS Fall 2004
Joel Hayburst CS Fall 2004
Rodney Weaver CS Spring/Fall 2004
Antonius Sardjito CS Summer 2004
Irvan Sutiono CS Summer 2004
Jasmine Williams Marc/AIM Summer 2004
C.Sujjapong Comp. Eng Summer 2004
Danny Varghese CS Spring 2004
Brian Seckinger CS Spring 2004
Jason Pardieck CS Spring 2004
Stan Luban Biol/CS Spring 2004-Spring 2006
Katie Kranjak Indiana Academy of Science Summer 2005

Openings

Postdoctoral Positions

Qualified candidates should hold a PhD in Physics, Computer Science, Biology, Chemistry, Doctor of Engineering, or in a related field. The primary area sought is protein tertiary structure modeling & prediction, protein docking, and protein global/local shape comparison and search. Experience in electron microscopy or tomography data analysis, and 3D shape retrieval are plus. Fluent programming skill and good communication skills are essential. Highly motivated and creative candidates with a strong record of publication are encouraged to apply. Send curriculum vitae and contact information of three references to: dkihara@purdue.edu . Postal mail should be sent to: Dr. Daisuke Kihara, Department of Biological Sciences, Purdue University, Hockmyer Hall of Structural Biology, 249 S. Martin Jischke Drive, West Lafayette, IN 47907.

Graduate students

Highly motivated graduate students in the departments of computer science, biological sciences, PULSe program at Purdue are encouraged to contact Dr. Kihara. Available projects include protein 3D shape comparison, docking, 3D structure prediction, function prediction, and DNA sequence analyses (motif search, small RNA detection). Please note that usually research assistantship is only offered after working at least one semester as an independent study to prove productivy. Previous experience in bioinformatics is desirable but not necessary. Programming skill is not a requirement at the beginning if you are not CS major as long as you are eager to learn it in the first year.

Undergraduate Students

If you are interested in computational work in biology, you are almost always welcome to our group. We have worked with over twenty undergraduate students, and have a good record of scientific achievments with them, including publishing full research papers, research presentation in conferences, entering graduate programs. Feel free to contact Dr. Kihara.

Summer internship with pay

Not offered.