Group Members
Jump to current members, undergraduate students, collaborators, alumni.
See more pictures here
For information on openings see here.
Current members
Daisuke Kihara
Principal Investigator
email: dkihara@purdue.edu
Genki Terashi
Assistant Research Scientist
email: gterashi
Yuki Kagaya
PostDoc
email: ykagaya
Farhanaz Farheen
Computer Science Graduate Student
email: ffarheen
Swagarika Giri
Computer Science Graduate Student
email: giri2
Yunhan Huang
Computer Science Graduate Student
email: huan1482
Nabil Ibtehaz
Computer Science Graduate Student
email: nibtehaz
Anika Jain
Biological Sciences Graduate Student
email: jain488
Kafi Khan
Computer Science Graduate Student
email: khan555
Shu Li
Computer Science Graduate Student
email: li3916
Kai Ling
Computer Science Graduate Student
email: ling59
Boyuan Liu
Computer Science Graduate Student
email: liu3852
Emilia Tugolukova
Biological Sciences Graduate Student
email: etugoluk
Jacob Verburgt
Biological Sciences Graduate Student
NIH T32 Mol. Biophys. Trainee
email: verburgt
Yuanyuan Zhang
Computer Science Graduate Student
email: zhang038
Zicong Zhang
Computer Science Graduate Student
email: zhan1797
Han Zhu
Computer Science Graduate Student
email: zhu773
Undergraduates
Pranav Punuru
Min Lu
David Huang
Javad Baghirov
Joon Hong Park
Visiting Professors
Visiting Scholars
Collaborators
| Fadi Bou-Abdallah | Professor | Department of Chemistry, The State University of New York |
| Uma Aryal | Research Associate Professor | Bindley Bioscience Center, Purdue University |
| Jose-Maria Carazo | Professor | Spanish National Center for Biotechnology, CNB-CSIC, Spain |
| Takatsugu Hirokawa | Professor | University of Tsukuba, Japan |
| Kenichiro Imai | Research scientist | Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology |
| Wen Jiang | Professor | Purdue University, Department of Biological Sciences |
| Masahide Kikkawa | Professor | Department of Cell Biology and Anatomy, University of Tokyo |
| Lukasz Kurgan | Professor | Virginia Commonwealth University, Department of Computer Science |
| Toshio Moriya | Associate Professor | Structure Biology Center, High Energy Accelerator Research Organization (KEK), Japan |
| Anindito Sen | Research Scientist | Microscopy and Imaging Center, Texas A&M University |
| Toshiya Senda | Professor | Structure Biology Center, High Energy Accelerator Research Organization (KEK), Japan |
| 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 |
| John Tesmer | Professor | Department of Biological Sciences, Purdue Univeresity |
| Min Xu | Assistant Research Professor | Carnegie Mellon University, Department of Computational Biology |
Alumni
| M. Michael Gromiha | Professor | IIT Madras, India | June - July 2022 |
| Mahmoud A. A. Ibrahim | Associate professor | Minia University, Egypt | Feb. 2022 - July 2022 |
| 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 |
| Yuxuan Chen | Shanghai Jiao Tong University, China | Feb. 2023 - Feb. 2024 |
| Manav Taluja | Vellore Institute of Technology, Vellore, India | Sep. 2023 - Jan. 2024 |
| Uzma Ramzan | University of Punjab, Pakistan | Oct. 2022 - Jun. 2023 |
| Chethiya Galkaduwa | University of Kelaniya, Sri Lanka | Oct. 2022 - Feb. 2023 |
| Harini Kannan | Indian Institute of Technology, Madras, India | May 2022 - Jan. 2023 |
| Deepanshu Mody | Birla Institute of Technology and Science, India | Jun. - Dec. 2022 |
| Manuel Zumbaro Corrales | Costa Rica Institute of Technology | Jan. - Feb. 2020, Aug. - Nov. 2022 |
| Archit Gupta | SRM Institute of Science and Technology, India | Mar. - Aug. 2022 |
| Sadam Munawar | University of Agriculture Faisalabad, Pakistan | Sept. 2020 - Mar. 2021 |
| Zhiqiang Jackie Huang | Huazhong Agricultural University, China | Aug. 2017 - May 2018 |
| Uttamkumar Samanta | West Bengal State University, India | Oct. 2012 - May 2013, May - Jun., 2018 |
| Mateusz Kurcinski | Warsawa University, Poland | Mar. 2010 - Mar. 2011 |
| Tsukasa Nakamura | postdoc researcher | High Energy Accelerator Research Organization, Japan | April 2022-June 2024 |
| 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 |
| Charles Christoffer | Ph.D. (CS) | Purdue RCAC | Dec. 2023 |
| Xiao Wang | Ph.D. (CS) | Postdoc at University of Washington | Dec. 2023 |
| Devashish Prasad | M.S. (CS) | Nabla Bio Inc. | May 2023 |
| Tunde Aderinwale | Ph.D. (CS) | Amazon | May 2023 |
| 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 |
| 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 |
| Luong Minh Nguyen | CS | |
| 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 |
| Iman Mevaa | Biol | |
| Razan Alkawai | CS | Summer 2021 - Spring 2022 |
| Yunhan Huang | CS | Fall 2021 - Summer 2022 |
| Ritwik Jain | IIT Kharagpur | Summer 2021 - Summer 2022 |
| Han Zhu | CS | Summer 2021 - Summer 2022 |
| Kunal Mahatha | BIT Sindri | Fall 2021 - Fall 2022 |
| Vo Ngoc Nhi | Biol | Fall 2021 - Fall 2022 |
| Ethan Andrew Chen | Chem | Fall 2021 - Fall 2022 |
| Sandokan Shahini | Biol | Summer 2021 |
| Rohan Narasimha | CS | Summer 2020 - Spring 2022 |
| Vijay Bharadwaj | CS | Fall 2019 - Spring 2022 |
| Logan Borders | CS | Fall 2020 - Spring 2021 |
| Param Talwalkar | CS | Spring - Summer 2021 |
| Devon Herr | CS | Spring - Summer 2021 |
| Anurupa Karmakar | NIT Durgapur | Summer 2020 |
| Yifan Deng | CS, Wuhan U. | Summer 2020 |
| David H. Kim | Biol | Summer 2020 |
| Jacob Moore | CS | Summer 2020- |
| Abhinam Adari | CS | Summer 2020 |
| Manish Kannan | CS | Summer 2020 |
| Hanwen Gu | CS | Summer 2020 - Spring 2021 |
| Hao Wu | CS | Summer 2020 - Spring 2021 |
| Pinaki Mohanty | CS | Spring 2020 - Spring 2021 |
| Nguyen Do | CS | Spring 2020 |
| Joseph Veltri | CS | Spring 2020 |
| Adrian Gerard Raj | CS | Spring 2019 - Spring 2020 |
| Nirali Rai | CS | Spring 2019 - Spring 2020 |
| David Rivera | Biol | Fall 2019 - Spring 2020 |
| 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.