Bioinformatics Program

MSBS in Bioinformatics Alumni

ahmed pic

Ahmed S. Al-Khudhair

Thesis Advisor: Dr. Tammy Morrish
Thesis: "Inter-and-Intra-Populated Genetic Variations in Humans"

Ahmed successfully defended his thesis on November 4, 2014 and is currently pursuing a PhD in Molecular Medicine (MOME track) at UT. 
 
"While earning my master’s degree, I learned skills and knowledge on combining biological data to form a comprehensive picture of cellular activities. The field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. 
 
My next plans and professional objectives are very clear.
 
It is my desire to be a high profile researcher in the fields of genetics, molecular and cellular biology, gene microarrays, genomics and proteomics. The Masters program was my initial step." 
tomi

Oluwatomisin "Tomi" Atolagbe

Thesis Advisor: Dr. Guillermo Vazquez
Thesis: "RNA-sequencing analysis of polarized macrophages derived from wild-type mice with macrophage-specific loss TRPC3 function" 
 
Tomi successfully defender her thesis on July 11, 2017. She is now a Research Assistant in Dr. James Allison's Lab at the MD Anderson Cancer Center.
patrick

Patrick Brennan 

Thesis Advisor: Dr. Alexei Fedorov
Thesis Title: "An Investigation of Personal Ancestry Using Haplotypes"
 
Patrick successfully defended his thesis on July 13, 2017 and is now a Bioinformatics Analyst at Nationwide Children's Hospital in Columbus where he applies bioinformatics tools to pediatric cancer and rare diseases.
 
"The bioinformatics program has definitely helped with my career. In my experience, employers look for bioinformatics candidates with good programming experience. I started the program with no programming experience, but I learned a lot during my thesis with Dr. Fedorov. The programming knowledge gained during my thesis was enough  to qualify me for bioinformatics positions."
 heather  

Heather P. Brown

Thesis Advisor: Dr. R. Travis Tayler
Thesis: "Homology-Based Structural Prediction of the Binding
Interface Between the Tick Borne Encephalitis Virus Restriction Factor
TRIM79 and the Flavivirus Non-Structural 5 Protein
Heather successfully defended her thesis on December 1, 2016.  She is now an adjunct professor at Jackson College in Michigan.
 chakrabortty  

Sharmistha Chakrabortty, PhD 

Thesis Advisor: Dr. Alexei Fedorov 
Thesis: "SNPs and Indel Analysis in Human Genome using Computer Simulation and Sequencing Data"
 

She is now a graduate research assistant at Iowa State University.

 subha  

Subhanwita Ghosh

Thesis Advisor: Dr. David Kennedy
Thesis: "Regulatory Mechanisms of Cardiotonic Steroids in Chronic Kidney Disease"
 
Subhanwita successfully defended her thesis on July 10, 2017. 
 Deepti  

Deepti Gurung 

Thesis advisor: Dr. Robert Blumenthal
Thesis: "Evolution of recombination: RecBCD in Bacteria"
Contactdeepti.gurung@rockets.utoledo.edu

Deepti successfully defended her thesis on August 14, 2019. 
I am staying in University of Toledo (dedicating additional years of education and training), to pursue my doctorate degree in Cancer Biology. I am in Dr. Jing Yuan Liu's lab. My major project is to understand dynamics of my protein of interest, 14-3-3-𝞂, for the treatment of pancreatic cancer.  Our approach to solve this problem employs both computational and experimental methods. 
 Prabhjot  

Prabhjot Kaur 

Thesis advisor: Dr. Sadik Khuder
Thesis: "Identifying a Biomarker for Chronic Obstructive Pulmonary Disease"
 
Prabhjot successfully defended her thesis on July 9th, 2019.
 Caroline  

Caroline Lambert 

Thesis Advisor: Dr. R. Mark Wooten
Thesis: "Identification and Description of Burkholderia pseudomallei Protiens that bind Host Complement-Regulatory Proteins via in silico in vitro Analyses" 
 
Caroline successfully defended her thesis on August 1, 2018.
 Oluwatobi  

Oluwatobi "TOBI" Lasisi 

Thesis advisor: Dr. Sadik Khuder
Thesis: "Identifying a biomarker for Sjogren disease
 
Tobi successfully defended his thesis on July 8, 2019. He is now a Research Assistant at Wayne State University. 
 
"I work as a Research Assistant at the sleep research lab, department of Pulmonary & Critical Care and Sleep Medicine, School of Medicine Wayne State University. My PI is Dr Safwan Badr who is also the chair of the department. Most of our projects or researches are funded by NIH and the VA (Veteran Affairs). We conduct sleep research studies on patients with both obstructive and central sleep apnea; where we investigate several therapeutic interventions, one of which is the use of acetazolamide in addition to CPAP-Continuous positive airway pressure (goal standard) , to achieve better treatment outcome. 
I perform night studies which involves the use of spirometry, PSG (polysomnography) and ventilators. I conduct raw data analysis (my bioinformatics background has really helped) and also assist in manuscript writing."
 joseph  

Joseph S. Mainsah

Thesis Advisor: Dr. Alexei Fedorov
Thesis Title: "Determination of Early Human Intercontinental Migration
from Genomic IBD Segments Flow Analysis". 
 
Joseph successfully defended his thesis on September 27, 2016.
 Arnab  

Arnab Saha Mandal

Thesis Advisor: Dr. Alexei Fedorov
Thesis Title: "Computational Analysis of the Evolution of
Non-Coding Genomic Sequences"
 
Arnab successfully defended his thesis on June 24, 2013
and is currently a PhD Student in Bioinformatics at the 
Alberta Children's Hospital Research Institute for Child and
Maternal Health, University of Calgary.

"I always had an innate curiosity about applying programming skills
to biological problems, but I never had a career insight into this
multidisciplinary field. My admission to the MSBS program in bioinformatics provided an ideal platform. The coursework covered a comprehensive breadth of genetics, molecular biology, cellular signaling mechanisms, biostatistics etc. I co-authored four publications from Dr. Fedorov's lab, and received awards thereafter from University of Toledo as well as my current institution, the University of Calgary. The growing deluge of genomic datasets is creating an urgent need for experts in computer programming, biology, genetics, mathematics and statistics. As a result, bioinformatics skills are widely sought after in academia and industry. I am glad to have graduated from the bioinformatics program at UT, that helped me imbibe the skills, knowledge, tenacity and resilience to proceed forward."
 jenna  

Jenna McGowan

Thesis Advisor: Dr. Ritu Chakravarti
Thesis: The antigenicity of the 14-3-3zeta protein
 
Jenna successfully defended her thesis on July 26, 2018. She is currently a Research Assistant in Physiology and Pharmacology Department at the University of Toledo.
 diego  

Diego A. Morales 

Thesis Advisor: Dr. James Willey
Thesis: "A Bioinformatical Approach to COPD"
 
Diego successfully defended his thesis on October 19, 2016.

He is currently a Data Analyst at the University of Pennsylvania School of Medicine.

 Nabiyouni  

Maryam Nabiyouni, PhD

Thesis Advisor: Dr. Alexei Fedorov
Thesis: "Mega-scale Bioinformatics Investigation of Codon Bias in Vertebrates"
 
Maryam successfully defended her thesis on June 3, 2011.
She is currently a Senior Automation Scientist at Bluestar Genomics, inc. 

"I just completed my PhD in Bioengineering at the University of Toledo
College of Engineering under supervision of Dr. Sarit B. Bhaduri
where I investigated the biomedical applications of magnesium-phosphate
nanoparticles. My earlier bioinformatic dgree has definitely differentiated
me from other scientists in biological or computer sciences,
as it has given me the skills to understand both sides.
I feel privileged to have a degree in bioinformatics as in the era
of excessive biological information there is a growing need
for scientists with background in bioinformatics."
Rajan

Rajan "Raz" Paudel 

Thesis advisor: Dr. Alexei Fedorov
Thesis: "Study of lnRNA exon-intron structure conservation in human and mouse"

Rajan successfully defended his thesis on July 1, 2019.
He currently is employed at Agriplex Genomics as a Senior Data Analyst.
 
Rais

Theodor B. Rais, MD

Thesis Advisor: Dr. Alexei Fedorov
Thesis Title: "Conserved signals of non-coding RNA across 73 gene
associated with Autistic Spectrum Disorders"

Theodor successfully defended his thesis on April 24th, 2009.
Currently, Dr. Rais is an Associate Program Director for Residency Training
Program In Psychiatry, Ocean County Medical Center, Brick, New Jersey,
and a Professor of Psychiatry at Hackensack Meridian Health
Seaton Hall Medical School, South Orange, NJ, and a Professor of Psychiatry at Rowan Osteopathic Medical School, Stratford, NJ.
 
“The MSBS program helped me to have a more comprehensive
understanding of the medical field and stay updated with
the genomic psychiatry breakthroughs. I still find it difficult
to bridge between the Basic Science, people, and the clinicians
who want concrete improvements in patient care.”
yvette

Yvette Unoarumhi 

Thesis Advisor: Dr. Jyl Matson
Thesis title: "Evolution of a Bacteria Global Regulator-Lrp"
 
Yvette successfully defended her thesis on April 12, 2016.  
Yvette completed an Internship at Procter & Gamble in Cincinnati, OH
and is currently in the process of interviewing to find her new position.

"While at UT, I worked on the evolution of a global regulator;
Leucine responsive regulatory protein (Lrp), and it was a very
rewarding experience. The program is indeed challenging,
but in a rewarding way, and at the end it pays off. I am grateful for
the seasoned professors I worked with who constantly encouraged
me to do my best. Upon graduation, I was awarded the
Best Graduating Student in Basic Science Research award, in addition
to the publication of my research thesis in a scientific journal. 
Lastly, the BIPG program creates a unique opportunity with an edge."
cole

Cole J. White

Thesis Advisor: Dr. Heather Conti
Thesis Title: "Beta-Defensin3 Mediated Regulation of Transcriptional Changes During Oropharyngeal Candidiasis"
 
Cole successfully defended his thesis July 18, 2018.
 
"I am a fourth-year medical student at Ohio University Heritage College of Osteopathic Medicine. I am finishing my clinical rotation at Mercy St. Vincent Medical Center in Toledo, OH. I will be applying for an internal medicine residency position this fall."
yuriy

Yuriy R. Yatskiv 

Thesis Advisor: Dr. Alexei Fedorov
Thesis Title: "Haplotype Analysis of an Archaic Denisovan Genome"
 
Yuriy successfully defended his thesis on August 18, 2016.
 
He is currently pursuing an MBA degree at UT, College of Business and Innovation.
ahmad alimadadi

Ahmad Alimadadi

Thesis Advisor: Dr. Bina Joe
Thesis Title: "Application of Bioinformatics and Machine Learning Approaches  in Cardiovascular Medicine"

Ahmad successfully defended his thesis on July 21, 2020.
He is currently employed as an Associate Bioinformatics Specialist at La Jolla institute for Immunology. 
https://www.lji.org/faculty-research/labs/hedrick/#overveiw

"In this position I will be in charge of the analysis of NGS data in the field of immunology, cancer, and atherosclerosis. I may also get involved in the vaccine and COVID-19 research."

ammar

Ammar Eljack

Thesis Advisor: Dr. Sadik Khuder
Thesis Title: "Potential Genetic Biomarkers for Dilated Cardiomyopathy using Genomic Data"

Ammar successfully defended his thesis on May 1, 2020.
"Currently I'm doing cardiology fellowship at Baylor Scott and White, The Heart Hospital-Plano- Texas.

I have done with Internal medicine board at Beaumont Hospital Dearborn".

melissa

Melissa Curtis

Thesis Advisor: Dr. James Burkett

Thesis Title: "The effects of Developmental Pyrethroid Pesticide Exposure in Mouse Brain using Multiomics"

Melissa successfully defended her Thesis on April 22, 2021

"I'll be working as a Research Assistant after I graduate. I plan to apply for other Bioinformatic jobs that are in Ann Arbor, to get some industry experience. After about 6-12 months I'm going to start studying for the MCAT and preparing to apply for medical school as well."

Aryal

Sachin Aryal,

Thesis Advisor: Dr. Bina Joe

Thesis Title: "Applications of Artificial Intelligence/Machine Learning for Cardiovascular Diseases"

Sachin successfully defended his Thesis on June 25, 2021

 "I am starting Ph.D. program at the University of Toledo in department of Physiology and Pharmacology (Molecular Medicine track) from this fall. I will be working in Bioinformatics and Artificial Intelligence Lab within the department."

Dillon

John Dillion,

Thesis Advisor: Dr. Heather Conti

Thesis Title: "Head and neck radiotherapy induces a transcriptional profile associated with inflammation and damage"

John successfully defended his Thesis on April 30, 2021

"I will be moving on to my PhD with my advisor Dr. Heather Conti in the fall of this year."

joyetta

Joyeeta Dutta,

Thesis Advisor: Dr. Sadik Khuder

Thesis Title: "Identifying a Biomarker for Systemic Sclerosis Using Existing Genomic Data"

Joyeeta successfully defended her Thesis on April 20, 2021

 

Manandhar1

Ishan Manandhar,

Thesis Advisor: Dr. Bina Joe

Thesis Title: "Artificial intelligence-based clinical classification of diseases: Utilizing gut microbiota as a feature for supervised learning and diagnostic screening of inflammatory bowel disease"

Ishan successfully defended his Thesis on June 23, 2021

Alex

Alexander McCartney,

Thesis Advisor: Dr. Sadik Khuder

Thesis Title: "Identifying Multiple Sclerosis Biomarkers Using Existing Omics Data"

Alexander successfully defended his Thesis on April 1, 2021

"I'm applying for jobs in a few different fields. I'm thinking I may be going into teaching HS biology/physical science, but I'm not sure"

scott

Scott Miruzzi,

Thesis Advisor: Dr. Robert Smith

Thesis Title: "Bilirubin Exerts Hormonal Regulation on Transcription of Genes through Modulation of Key Coregulator Protein Recruitment"

Scott successfully defended his Thesis on April 19, 2021

Bhuwan

Bhuwan Rai,

Thesis Advisor: Sadik Khuder

Thesis Title: "Data Pooling to Investigate the Abundance of Gut Microbiome Composition in Autoimmune Disease"

Bhuwan successfully defended his Thesis on April 12, 2021

kaitlyn

Kaitlyn Zigulis,

Thesis Advisor: Randall Worth

Thesis Title: "Expression of FcgammaRIIA Across Species"

Kaitlyn successfully defended her Thesis on August 3, 2021
She is currently a Pathology Technician at ProMedica in Microbiology. 

Alex

Alex Joyce,

Thesis Advisor: Dr. Robert Smith

Thesis Title: Analysis of AKT1 activity in Alzheimer's
Disease and Schizophrenia though Kinopedia,
an interactive application for kinome array data

Alex successfully defeded his Thesis on April 1, 2022
He is currently in the Ph.D program at OSU. 

vineet

Vineet Reddy,

Thesis Advisor: Dr. Robert Smith/Dr. Rammohan Shukla

Thesis Title: Single Cell Transcriptomic-informed
Microcircuit Computer Modelling of Temporal
Lobe Epilepsy

Vineet successfully defended his Thesis on April 18, 2022

evelyn

Evelyn Bates,

Thesis Advisor: Dr. Robert Smith/Sinead O'Donovan

Thesis Title: Single Cell Transcriptomic-informed
Microcircuit Computer Modelling of Temporal
Lobe Epilepsy

Evelyn successfully defended her Thesis on April 20, 2022

 

 

 

 




































 

 









 
 



 
 


 

 

 

 

 
























 








 

 

 

  








 

 


  

 

  

 


 

 

  

 

 

 

 

 

 

 

 

 

 




 

 

 

 

 

 



 


 


 

 




  

 



  

 

 

 



 

 





 

 
 
 
 

 

 

 

 

 

 

 

 





 

 

 

 

Last Updated: 7/26/22