Former 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
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 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.
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
Hanin OmarDoctoral
Student
Hanin Omar received 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
Doctoral Student
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
Doctoral Student
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.
Julian
Rachele
Masters Student
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
Masters Student
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.
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 the 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 the
most
current bioinformatics; here Devaun focuses on Active Site Identification. He joined the Computational
Biology
Research Lab in 2013.
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. 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
Doctoral Student
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 McCourt
MS
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
Doctoral Student
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 Gentry
MS
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.
Nick Boltin
Ph.D
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
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.
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
Brubaker
MS
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
Behbooei
MS
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
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
i Ph.D
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
Masters Student
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
Ph.D
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
Niharika
Pandala
Undergraduate Student
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
Satti
Undergraduate Student
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.
Justin
Taylor
Undergraduate Student
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
Russell
Undergraduate Student
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
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.
Colby Hill
Undergraduate Student
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 Edwards
Undergraduate Student
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 Rapoport
Undergraduate Student
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
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.
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
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.
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 Students:
- J.D. White
- Andrell Shaw (aka Zell)
- Stephen Smith
Dr. Homayoun ValafarLab Director - LinkedIn
Dr. Hamed AbdollahiPost Doc - 
Aaron HeinDoctoral Student - 
Ali FiroozDoctoral Student - 
Alireza BagheriDoctoral Student - 
Alaleh TorkjaziDoctoral Student - 
Lexington WhalenUndergraduate Student - 
Musa AzeemUndergraduate Student -