Dr. Homayoun ValafarLab 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).
Linkel Boateng, Ph.D
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 included atomistic and process simulations of environmental systems, membrane-based water treatment processes, and application of nanotechnology in water treatment. During his work he investigated protein structure and dynamics using molecular dynamics simulations.
Positions available. If interested please contact Dr. Valafar at email@example.com.
Hanin OmarDoctoral 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.
Brendan Odigwe Received his Bachelor of Engineering degree in Computer Engineering from Covenant University, Ota, Ogun State, Nigeria in 2016. In the Spring of 2018, Brendan became of member of the University of South Carolina Graduate community and Joined the Computational Biology Research Lab shortly after. He earned a master’s degree in Software Engineering from the University of South Carolina and is now pursuing his doctorate in Computer Science with his research Focused on Computational Medicine and Bioinformatics. His current interests include the deployment of AI techniques as applicable in medicine as well as automated analysis of medical images. He is currently working on applying machine learning towards public health interventions involving diseases such as; Chronic Kidney Disease, Sickle Cell Anemia, and Heart Failure.
Chrisogonas Odhiambo joined the Valafar Lab in Spring 2019. His areas of interest include: AI, Machine Learning and Deep Learning, Big Data Services, Data Mining, Data Visualization, AI Robotics and related development, HPCs and Parallel Computing and Blockchain Technology. His current project in the Valafar Lab is "Detecting Smoking Events Using Smartwatch Technology" which employs sensors, AI and robust machine learning models to monitor smoking behavior and detect puffs and sessions. Currently he is working towards examining the feasibility of detecting smoking behavior using smartwatches and comparing the level of success of conventional self-reporting techniques vs the use of smartwatches to study smoking behavior. By extension, the study aims to estimate the amount of nicotine consumption by smokers. This data could be used in preventive measures. In addition, he is also working on techniques of converting sign language to regular speech and creation of Keras Tensorflow user tools to avail the power of AI and Machine Learning to even non-computer science experts.
Alaleh received her Bachelor of Science degree in Computer Engineering from Shiraz University, Shiraz, Iran in 2011. She also got her Masters in Artificial Intelligence from K.N.Toosi University of Technology, Tehran, Iran in 2015. Her research in KNTU was involved in using AI methods to find anomalies in computer network data. In Fall 2017 Alaleh joined USC as a PhD student. Her current interests include image processing, AI techniques in medicine as well as automated gesture detection.
Aaron Hein received his Bachelor’s degree in Computer Science from Baylor University in 2001. After working in Industry for 13 years, Aaron made the decision to go back to school in 2014. He earned a Graduate Certificate in Cyber Security and his Master’s degree from the University of South Carolina in 2016 and 2017 respectively while working full time. Aaron joined the Computational Biology Research Lab in 2019 and is interested in the prediction of protein structures using various machine learning techniques. He lives with his wife and children in Austin, TX.
Julian Rachele is a first-year Masters student focusing on Bioinformatics, and has been working in the Valafar lab since September 2018. His work involves optimizing the REDCRAFT/REDCAT suite and developing GUI software, but he also has experience with AI development, specifically in the Unreal Engine for the French Gendarmerie. His interests include language learning, cooking, and code.
Peyton Chandarana received his Bachelor's degree in computer engineering from the University of South Carolina in 2019. Peyton joined the Computational Biology Lab in 2020 and is researching protein similarities, particularly between SARS-CoV-1 and SARS-CoV-2. He is currently interested in computational biology, neuromorphic computing, and other topics that integrate computing into biological topics.
Niharika Pandala, Computer Engineering Student, has been working in Valafar Lab since summer 2019. She has been on a journey of erudition, exploring topics in the pulmonary domain, inspired by integrating healthcare and technology. The exploration encompassed a project addressing respiratory episodes that culminated in developing a missing pulse detector. Her research in the lab on the host-shutoff mechanism of SARS-CoV nonstructural protein-1 has earned her a publication with the ACM Conference on Bioinformatics, Computational Biology and Health Informatics 2020, and Magallen scholar award from USC Columbia. This voyage, coupled with an experience in the industry(Blue Cross Blue Shield, South Carolina) predicting COVID hospitalizations in asthma and type II diabetes patients and recent public sector experience as a statistical and research analyst, dealing with electronic lab data from COVID-19 testing sites and its reporting(Department of Health and Environmental Control, South Carolina) has facilitated her to seek more knowledge for solving public health problems. She is keen to explore the amalgamation of big data and precision medicine to study generic pulmonary symptoms to comprehend better the different maladies that affect the lungs by pursuing graduate studies in Bioinformatics. On leisure, Niharika enjoys singing and believes meditation helps to elevate consciousness successively, improving overall health.
JJ is a sophomore undergraduate majoring in Computer Science. He has been working in the Valafar for since summer of 2019. He currently works with the computation of small data analytics using Python and and the analysis of genetic data. His interests lie in working out, trying new foods, and learning to code.
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.
Arjang Fahim, Ph.D
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 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.
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.
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. She recieved her MS in Computer Science in 2018 and is projected to complete her Ph.D degree by Spring 2020. Her current projects include protein structure calculation, protein dynamics, genomic analysis and pattern recognition.
Edward Tsien received his BS in Computer Science from Augusta University and then worked as a software developer in the industry for 3 years as well as doing research at East China Normal University in AI and Computer Vision. In 2018, he began his combined Masters/PhD program at USC, and joined the Valafar Lab in 2019 with a focus on AI applications in medical imaging. His current interests are Convolutional Neural Networks, Computer Vision, Data Analytics, and information security.
Betsy graduated in Fall 2018 with a Masters in Computer Science. While in the Valafar Group she primarily worked on image processing of medical images.
Jun Chen worked in the Valafar Group from Spring 2017 to Fall 2018. His primary interest was deep learning with a special focus on the applications of deep learning to gesture detection.
Jared graduated in Spring 2019 with a Masters in Computer Science. While in the Valafar Group he primarily worked on transcriptome assembly/analysis, web development, and applied AI techiques in medicine.
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. He graduated in 2018 with his Ph.D in Biomedical Engineering and is currently employed by UofSC as an Instructor for Biomedical Engineering.
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. During his time in the Valafar lab, he had been studying protein folding via pdpa. Although he has moved on, he still remains in our thoughts and is missed.
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.
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.
Hao (Emily) Ji
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 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.
Chris Ott is a Masters student in the Valafar Group. His current interests include protien structure prediction, AI/ML techniques and improvement of data storage and retrevial.
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 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 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
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 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.
Justin is an undergraduate student majoring in CS. His current interests include optimization techniques and software engineering with respect to calculation of order tensors.
Jeff is an undergraduate student majoring in CS. His current interests include mathematical derivations of rotation operators. He is currently funded through the SURF grant.
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.
Colby is currently an undergraduate at the University of South Carolina pursuing a bachelor's degree in Computer Science. He joined the Computational Biology Research Lab in the Spring 2017 semester and worked primarily on Android development.
Blake is currently an undergraduate at the University of South Carolina pursuing a bachelor's degree in Computer Science. He joined the Computational Biology Research Lab in the Spring 2018 semester and worked primarily on Android development.
Joshua is currently an undergraduate at the University of South Carolina pursuing a bachelor's degree in Computer Science. He joined the Computational Biology Research Lab in the Spring 2018 semester and worked primarily on Android development.
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.
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
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.
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 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 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 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 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 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 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
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 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.
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 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.
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 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 Students: