Group Members

Director


Dr. Homayoun Valafar
Lab Director

Dr. Valafar received his B.S., M.S. and Ph.D. in Electrical and computer engineering from Michigan technological university and Purdue (M.S. & Ph.D.) in 1988, 1990 and 1995 respectively. Following his graduation he received two post doctoral fellowship appointments with Drs. Peter Albersheim and James Prestegard in the areas of structure determination of carbohydrates and computational methods of protein structure determination. Before joining USC as an assistant professor he served as the bioinformatics project coordinator at the Southeast Collaboratory for Structural Genomics (SECSG).


Postdoctoral researchers


Linkel Boateng, Ph.D
Post Doc

Linkel Boateng has a B.S. in Chemical Engineering from Kwame Nkrumah University of Science and Technology in Ghana. He received his M.S. in Civil Engineering from North Carolina A&T State University and his PhD in the same field from the University of South Carolina (USC) in 2015. Before coming back to USC, he served as a Post-doctoral Fellow at Clemson University’s department of Chemical and Biomolecular Engineering. His research interests include atomistic and process simulations of environmental systems, membrane-based water treatment processes, and application of nanotechnology in water treatment. He is currently investigating protein structure and dynamics using molecular dynamics simulations.


Graduate Students


Nick Boltin
Doctoral Student

Nicholas Boltin received his B.S in Audio Engineering in 2005 from Appalachian State University. In 2010, Nick returned to school for a degree in Biomedical Engineering, with a view toward a career in research. As an undergraduate at the University of South Carolina he developed an instrument for blood detection to be used in forensic science at the State Law Enforcement Division. He also wrote several programs for data collection, analysis and instrument control. Nick works with National Instruments and is the LabVIEW student ambassador for USC. Now in his second year as a PhD candidate in Biomedical Engineering, he is developing software applications for triaged patients during mass causality events.

Devaun McFarland
Doctoral Student

Devaun received his Bachelor of Science degree as a double major in Mathematics and Computer Science from St. Lawrence University in 2009, with McNair and senior research focused in Graph Theory. In spring semester of 2010, Devaun became part of the University of South Carolina's (USC) Graduate Community. He completed his Masters' work at USC in 2012, obtaining a Masters in Engineering and Computing (ME). He is currently working toward his PhD in the department of Computer Science and Engineering at the University of South Carolina as well. His research experiences are in the fields of imaging, mobile applications, web applications, and most current, bioinformatics; here Devaun focuses on Active Site Identification. He joined the Computational Biology Research Lab in 2013.


Hanin Omar
Doctoral Student

Hanin Omar received her her Bachelor’s Degree in Computer Science from The University of Jordan in 2007. She returned to school in 2011 to pursue her graduate studies at University of South Carolina, she is currently a P.H.D student in the Computer Science and Engineering department there. She joined the Computational Biology Research Lab in 2014 and is currently focousing on De Novo RNA sequence assembly and protein dynamics research.


Casey Cole
Doctoral Student

Casey Cole received her B.S. in Computer Science from The University of South Carolina. She has continued her studies in the Doctoral Program at USC. She is a recipient of the Rothberg Fellowship and the Presidential Fellowship. She joined the Computational Biology Lab in 2013 as an undergraduate researcher. Her current projects include protein structure calculation and protein dynamics.


Kenneth Nesbitt
Doctoral Student

Kenneth earned a B.S. in chemistry from the University of South Carolina where he studied iron transport in prokaryotic systems as a recipient of the Howard Hughes Undergraduate Research Fellowship. He then moved to the University of North Carolina where he earned an M.S. in biochemistry while working on the biochemistry and electrophysiology of ion channels. Upon graduation, Kenneth worked for a few years as an analytical chemist and a microbiologist before returning to school to study computer science. Since joining the Valafar lab, he has been studying protein folding via pdpa.


Mohammed Behbooei
Doctoral Student

Mohammed received his B.Sc. in computer engineering from Polytechnic of Tehran having exemplary projects done at the intersection of artificial intelligence and robotics. He joined USC in the fall of 2015 and has already received an M.Sc. in computer science. He is currently pursuing a PhD in computer science with a focus on Artificial Intelligence and Sensory Networks. He is a former professional footballer.



James Brubaker, MS
Doctoral Student

James completed his undergraduate studies at University of Illinois at Urbana-Champaign, and his Master's work at University of Illinois at Springfield. He is currently interested in engineering software for scientific research, and enjoys reading about the history of computers, computing culture, and science in general.


Undergraduate Students


Bethany Janos
Undergraduate Student

Bethany Janos is an undergraduate student from the University of South Carolina currently pursuing a bachelor's in Biomedical Engineering with a minor in Computer Science. She plans on pursuing a master's degree in either Computer Science or Biotechnology. She is currently working on Android development with Dr. Valafar.


Diego Valdes
Undergraduate Student

Diego is currently pursuing an undergraduate degree in Computer Science from the University of South Carolina. He is presently assisting in the development of an Android application that will assist nurses during mass causality events



Caleb Parks
Undergraduate Student

Caleb is currently looking to earn a Bachelors in Computer Science at the University of South Carolina. He is a member of the Honors and college and on the Deans List. His project calculates the root mean square deviation between the x, y, z coordinates of proteins. It also rotates proteins to minimize the rmsd and creates a file that prints the proteins in the PDB, Protein Data Bank, format.





Chris Bowling
Undergraduate Student

Chris Bowling is currently an undergraduate at the University of South Carolina pursuing a bachelor's degree in Computer Science with a minor in Mathematics. After graduation, he plans to pursue a master's degree in Software Engineering. He joined the Computational Biology Research Lab in the Spring 2017 semester and is currently working on Android development.




Visiting Scholars


Greg Avsyuk
Rogue Scholar

Greg Avsyuk is an undergraduate student at Rensselaer Polytechnic Institute. He is currently pursuing a bachelor's degree in Computer Science and Mathematics. With the help of Dr. Valafar, he was able to learn about Android development and contribute to several projects. After graduation he plans on working in the software development industry.



Former Postdoctoral researchers


Arjang Fahim, Ph.D
Post Doc

Arjang came to US in 2002. His B.S is in Computer Software Engineering with emphasis on designing large-scale LANs. After working in various positions such as software developer, software architect and project manager, he decided to pursue a Ph.D degree in computer science at University of South Carolina. Currently he is working as research assistant at Dr. Valafar's lab. His research is in classification and refinement of protein structure using NMR data.

Rishi Mukhopadhyay
Postdoctoral researcher

Rishi Mukhopadhyay received his B.S. in Computer Science from Cornell University's College of Engineering in 2005. During this time he was funded by the NSF REU program at Oakland University for the summers of 2002 and 2003 where he researched and published in the area of content-based image retrieval. Following his graduation he came to get his PhD at the University of South Carolina where he was a Rothberg Fellow in Bioinformatics from 2005-2007.


Stephanie Jiménez Irausquin
National Science Foundation (NSF) Postdoctoral Fellow

In 2002, Stephanie Irausquin received her Bachelor’s Degree with honors in Exercise Science from the University of South Carolina. She returned to the University of South Carolina in 2005 as a student in the Professional Science Master’s Program and subsequently obtained a P.S.M. Degree with an emphasis in Bioinformatics in 2007, as well as a Doctoral Degree in Biological Sciences in 2010. In August 2012 she was awarded an NSF Postdoctoral Fellowship for Transformative Computational Science using CyberInfrastructure (CI TraCS) for which she proposed a Novel RDC Analysis Pipeline for Determination of Protein Structure and Dynamics.



Former Graduate Students


Hao (Emily) Ji
Doctoral Student

Hao (Emily) Ji received her Bachelor’s Degree in Computer Science from National University of Defense Technology in 2003 and Master of Business Administration in Business school from Central South University in 2008. She was working as a research associate in College of Pharmacy before she became a Ph.D. student in Computer Science at University of South Carolina in 2014. She is currently working on research in cancer genomics and high-throughput screening data analysis.

Matthew Fawcett
Doctoral Student

Matthew Fawcett received his B.S. in Computer Science from Clemson University in 2000. He then received his M.S. in Mathematics from Clemson University in 2002. His research involved ray tracing and computer graphics. He returned to school in 2006 to pursue his P.h.d in Computer Science. He is currently working on research in protein sidechains and protein refinement.

Paul Shealy
Doctoral Student

Paul Shealy received his B.S. in Computer Science from Clemson University in 2002, where he was a Palmetto Fellow. He received his M.S. in Computer Science from Duke University in 2004. His thesis research at Duke focused on object tracking in videos. He also performed research on tolerating hard faults in microprocessors as part of the FaultFinder project. He is currently pursuing a Ph.D. in computer science at USC, where he is a Rothberg Fellow in bioinformatics.

Mikhail Simin
Doctoral Student

Mikhail came to America from Russia in 1998 with his family. He graduated an American high school and entered USC in 2004. He received his B.S. from University of South Carolina in 2008, in Electrical Engineering with emphasis on semiconductor devices. His last year in Electrical Engineering he acted as the president of student branch of IEEE. Entering graduate school he switched over to Computer Science and chose a research field in bioinformatics. At the moment he is researching protein folding with limited RDC data for Dr. Valafar.

Chris Schmidt
Masters Student

Chris recieved his B.S. in Computer Information Systems from the University of South Carolina in 2009. He is currently pursuing a M.S. in Computer Science and Engineering. Chris's work focuses on maintaining and updating REDCAT as well as integrating REDCAT with VMD. Chris has also worked on a java-based interface for Xplor-NIH scripting.

Dr. Xijiang Miao
Doctoral Graduate

Xijiang Miao specializes in computational biology. He has a BS in Computer Science and Engineering from Xian Institute of Technology and a Master's in Computer Science from Beijing University of Posts and Telecommunications. He completed his MS in Biology, University of South Carolina, with a thesis in phylogenetic analysis (2004, P.J.Waddell supervisor) and his Ph.D in Computer Science, also at USC, with a dissertation in protein structure classification (2007, H.Valafar supervisor).

Ryan Yandle
Masters Graduate

Ryan Yandle received his B.S. in Computer Information Systems from the University of South Carolina in 2007. He is currently pursuing a M.S. in Computer Science. Ryan's current work is focused on PDPA. Ryan is a native of South Carolina and a Boy Scouts of America Eagle Scout. He is an avid outdoorsman who enjoys hunting, fishing, and camping. He has begun work at Microsoft in the Microsoft Office Division.

Former Undergraduate Students


Helen Carr
Undergraduate Student

Helen Carr is an undergraduate student from the University of South Carolina currently pursuing a bachelor's in Biomedical Engineering with a minor in Biology. She plans on pursuing a master's degree. She joined the Computational Biology Lab in Spring 2015 as an undergraduate researcher. She is currently working on De Novo RNA sequence assembly with Dr. Valafar.


Daniel Vu
Undergraduate Student

Daniel Vu is an undergraduate at the University of South Carolina. He is currently pursuing his B.S. degree in Computer Science with a minor in Music. Under Dr. Valafar's mentoring, he is working with other undergraduate students to find new ways to improve communication infrastructures in the medical field through the increased presence of smart phones and tablets.


Tyler Wagner
Undergraduate Student

Tyler started at York Technical College in Rock Hill, SC in Fall 2011 and transferred to the University of South Carolina in Spring 2013. He is currently pursuing a bachelor's degree in Computer Science with a minor in mathematics, and he intends to pursue a Masters after graduation. Tyler will then go and work in the aeronautical or aerospace industry.

Andrew Freix
Undergraduate Student

Andrew Freix is currently a Sophomore at USC pursuing a degree in Computer Science. He is a McNair Scholar from Fairfax, VA who has been working under Dr. Valafar since the spring of his Freshman year. He is a member of Beta Theta Pi, the club soccer team, and the improv team at USC. He plans on pursuing a job in Silicon Valley following his graduation.

Andreea Stoichita
Undergraduate Student

Andreea Stoichita is an undergraduate student at the University of South Carolina pursuing a bachelor's degree in Biomedical Engineering, with minor in Spanish. Andreea is a Palmetto Fellowship recipient and a member of the Tau Beta Pi engineering honor society. Also a premed student she plans on getting an MD degree after finishing her undergraduate studies. Andreea has conducted research in the area of bioinformatics and computational biology under her mentors Mikhail Simin and Dr. Homayoun Valafar.

Mark Williams
Undergraduate Student

Mark Williams is an undergraduate at the University of South Carolina. He is currently pursuing a bachelor's degree in computer science, and intends to pursue a Ph.D. after graduation. He has been conducting research over the past summer with his mentors, Dr. Homayoun Valafar and graduate student Paul Shealy, in the field of computational biology and bioinformatics.

Ahmed Khawaja
Undergraduate Student

Ahmed Khawaja is an undergraduate student at the University of South Carolina pursuing a bachelor's degree in Computer Engineering, with a minor in Mathematics. Ahmed is a pre-med student and plans on acquiring dual MD/PhD degrees after graduation. He has been conducting research with Dr. Homayoun Valafar in the field of protein structure validation and intends on moving to the problem of de novo protein structure prediction.

Dustin Dalton Brown
Undergraduate Student

Dalton started at USC Sumter in Fall 2008 and transferred to USC Columbia in Spring 2010. He is currently pursuing a Bachelors in Computer Science.

Melanie Santos
Undergraduate Student

Melanie Santos is an undergraduate student from Puerto Rico. She is studying Industrial Biotechnology at the University of Puerto Rico at Mayagüez Campus and after graduation she will pursue graduated studies in the area of biomedicine. During the summer, she has been working with Rishi Mukhopadhyay and Dr. Valafar on protein structure simulation.

Zach Swearingen
REU Undergraduate Student Funded by NSF

Zach Swearingen is an undergraduate at the University of South Carolina. He is working for a bachelor's degree in Computer Science, with minors in both Physics and Mathematics. He has been conducting research over the past summer with his mentors, Dr. Homayoun Valafar and graduate student Paul Shealy, in the field of computational biology and bioinformatics.

Parker Bush
Undergraduate Student

Parker Bush is an undergraduate at the University of South Carolina. He is currently pursuing a bachelor's of computer science, and intends to pursue his M.S. after graduation. He has been working with Paul Shealy and Dr. Valafar on the development of msTALI over the past year, and is currently working on deploying a version to the web.

Liz Timko
REU Undergraduate Student Funded by NSF

A graduate of the South Carolina Honors College, Elizabeth Timko has finished her bachelor's degree in Computer Science, with minors in both Mathematics and Business Administration. She has conducted research in the areas of computational biology and bioinformatics for the past year under her mentor, Dr. Homayoun Valafar. Her research topic in protein folding has led to a Magellan Scholarship in 2008, and her research results have recently been accepted for publication and presentation at BioComp08, a prestigious conference ranked in the top 5 percent of all computer science conferences. After receiving her undergraduate degree, Liz plans to continue on to a master's degree, also in Computer Science.

Sarah Deuell
Undergraduate Student

Sarah Deuell is an undergraduate student at the University of South Carolina Honors College. She is working toward a bachelor's degree in Computer Science and Mathematics. She just began working on research with her mentors Dr. Valafar, and Rishi Mukhopadhyay last year in the area of computational biology. She wants to go on to graduate school to receive a master's degree in Computer Science. She is a diver on the South Carolina Swimming and Diving Team, and also a member of Fellow Christian Athletes(FCA).



Other Past Undergraduate Students

  • J.D. White
  • Andrell Shaw (aka Zell)
  • Stephen Smith