Current Members
Name Title
Abrar Albahrani Student intern
Nagavardhini Avuthu PhD Student
Jasjit Banwait Postdoctoral Research Associate
Adam Cornish PhD Student
Matthew Cserhati Bioinformatics programmer/data analyst
Babu Guda Professor & Principle investigator
Yeong Kim Assistant Professor
Duc Le Bioinformatics programmer/data analyst
Nitish Mishra Postdoctoral Research Associate
Meng Niu Bioinformatics programmer/data analyst
Sanjit Pandey Senior Bioinformatics programmer/data analyst
Siddesh Southekal PhD Student
Neetha Vellichirammal Instructor
Navodita Upadhyay Bioinformatics Programmer/Analyst
Kristen Wipfler PhD Student
Peng Xiao Assistant Professor


Faculty and Staff
Dr. Babu Guda Babu Guda, Ph.D.
Principal Investigator
Phone: 402-559-5954
CV

I moved to UNMC in 2010 as a Tenured Associate Professor in the Department of Genetics, Cell Biology and Anatomy, and as the inaugural Director of the Bioinformatics and Systems Biology Core, from the State University of New York at Albany . I was formally trained in both Molecular Biology and Computer Science. I received my PhD from Auburn University in 1997 in Molecular Biology and then got trained as a part-time student in computer science at Iowa State University and as a postdoc in computational biology at University of California, San Diego.  In 2004, I accepted a tenure-track position as an Assistant Professor at the Cancer Research Center of SUNY-Albany. I have published over 65 peer-reviewed research articles that cover a wide range of topics related to bioinformatics, systems biology and Big-Data (Omics) analyses including cancer genomics. As the primary advisor, I mentored or currently mentor three junior faculty, 5 postdocs, 10 PhD, 4 MS, 4 undergraduate  and 4 high-school students. My research has been continuously funded by NIH and other sponsors since 2004. In my spare time, I play tennis and volunteer for kids educational activities like science fairs and conducting the Bee Contests in Spelling, Math, Science, etc.

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Peng Xiao Peng Xiao, Ph.D.
Assistant Professor
Joined: 2014
Phone: 402-559-2083

I received a B.S. in Biochemistry and Molecular Biology from Hunan Normal University, China, and a Ph.D. in Biomedical Sciences - Human Genetics and Genomics from Creighton University in Omaha, Nebraska. During the Ph.D. study, I received an extensive training in human functional genomics and statistical genetics. After receiving the Ph.D., I had been working as an Assistant Professor in the School of Medicine at Creighton University for seven years. I have published 52 peer-reviewed papers, 30 meeting abstracts and two book chapters in the areas of human genomics and system biology. Currently, my research interests are in the fields of cancer genomics and biostatistics. My hobbies include Christian evangelization, badminton and tennis.

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Yeong Kim

Yeong Kim, Ph.D.
Assistant Professor
Joined: 2016
Phone: 402-559-4640

I studied biology at Yonsei University in Seoul, Korea for BS and MS, molecular biology at Cornell University, immunology at Indiana University Medical School, and computer science at Illinois Institute of Technology for MS and PhD degrees. Before joining UNMC as an assistant professor in the Department of Genetics, Cell Biology and Anatomy in 2010, I worked as a research scientist in bioinformatics and functional genomics at NorthShore Research Institute / University of Chicago from 2004 when I started to work on next generation sequencing. My major research area is computational cancer genomics, focusing on genomic variations in small/large scales by analyzing NGS data from various cancers, especially on non-coding regions such as promoters and enhancers. I am also interested in genomic instability caused by structural perturbation like kataegis and chromothripsis in cancer genomes. My current work involves the project for clinical application of exome variant data with the Breast Cancer Collaborative Registry at the Fred & Pamela Buffet Cancer Center.

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Neetha Vellichirammal Neetha Vellichirammal, Ph.D.
Instructor
Joined: 2016
Phone: 402-559-5925

Neetha received her PhD in 2010 from Rajiv Gandhi Center for Biotechnology (affiliated to Kerala University), India. Her PhD was in the genetics and pharmacogenomics of schizophrenia, a complex psychiatric disorder. During this study, she identified markers that can be used to predict the symptom spectrum and treatment response in this disorder. She then worked as a postdoctoral research associate at the University of Nebraska-Lincoln in the School of Biological Sciences and in the Department of Entomology. Her previous research at the University of Nebraska used transcriptomic and proteomic approaches to understand complex phenotypes and gene-environmental interaction in different non-model organisms. She also worked on identifying the impact of environmental stress on the developmental trajectory of non-model organisms. She is currently involved in identifying bio-markers for identifying cancer subtypes, prognosis and treatment predictions with a focus on fusion genes. She is also actively involved in STEM outreach programs and regularly volunteers for coordinating the Nebraska Science Olympiad.

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Nitish

Nitish Mishra, Ph.D.
Postdoctoral Research Associate
Joined: 2013
Phone: 402-559-5925

Before joining GCBA, UNMC I was postdoctoral fellow at The Samuel Roberts Noble Foundation, Ardmore, OK. Where I was working on project “Prediction of substrate specificity of membrane transporter proteins”. Objective of that project was to develop computational models to predict transporter protein as well as probable substrates specificities of predicted transporter proteins. I did my PhD from Institute of Microbial Technology, Chandigarh, India under supervision of Dr. G.P.S. Raghava. The title of my PhD thesis was “Development of in-silico method for searching of potential drug molecules and targets”. During PhD I developed several free tools and webservers in area of computer aided drug designing. Currently I am working on “genomic aberrations in pancreatic ductal adenocarcinoma”. Here I am looking role of SNP, indel, large scale structural variation and DNA methylation in pancreatic cancer. Overall goal of current project is to find out genomic aberrations which can play vital role in pancreatic ductal adenocarcinoma.

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Matthew Cserhati PhD BSc Matyas Cserhati, Ph.D., B. Sc.
Bioinformatics Programmer / Data Analyst
Joined: 2013
Phone: 402-559-5925

I received a PhD in biology and a BSc in computer science from SZTE-TTIK in Szeged, Hungary. My PhD thesis involved the development of a motif prediction algorithm in promoters of co-regulated genes in cereal plants. My BSc thesis was about the development of a dedicated database for holding information on drought-related genes in barley. At UNMC I am involved in the development of the NNTC database, which holds information on AIDS-related studies. I am also involved in several core projects, involving IPA analysis and gene analysis. I am also working on genome analysis of human compared to Neanderthal and Denisova. Hobbies include Christian apologetics, drawing, chess, target shooting, reading, and languages.

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Meng Niu Meng Niu, Ph.D.
Bioinformatics Programmer / Data Analyst
Joined: 2015
Phone: 402-559-5925

I received my B.S. and M.S degrees in Computer Science from Jilin University, China and Ph.D. in Bioinformatics from University of North Carolina at Charlotte. My Ph.D. research focuses on algorithm design and pipeline development for the next generation sequencing data analysis, in particular, ChIP-seq data from human and Drosophila.  After receiving the Ph. D., I worked at the Carolina Medical Center of Carolinas Healthcare System (CHS) as a Bioinformatician, where I developed analytical tools and databases for the proteomics core lab. I’m interested in TFBS/CRM prediction algorithm optimization and design.

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Duc Le Duc Le, B.Sc.
Bioinformatics Programmer / Database Designer
Joined: 2016
Phone: 402-559-5925

I graduated with a B.Sc. in Computer Science from University of Nebraska at Omaha and joined UNMC as a bioinformatics programmer/data analyst.  Before joining UNMC, I worked for several companies such as FirstComp Insurance Company, BoysTown, Mid-America Computing Corporation. I'm currently working on the CHARTER database project.  I’m a Huskers fan, and I love to watch college football.

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Sanjit Pandey Sanjit Pandey, M.S.
Senior Bioinformatics Programmer / Data Analyst
Joined: 2010
Phone: 402-559-5925

I graduated with Masters in Computer Science from University of Nebraska at Omaha and joined UNMC as a bioinformatics programmer/data analyst. I worked on identifying wrongly annotated proteins in the NCBI database as my graduate thesis. After working on different bioinformatics projects in the Bioinformatics and Systems Biology Core for almost 3 years, I started Ph.D in Biomedical Informatics at UNMC. I have always been interested in using different tools and techniques in computer science to solve biological problems. I am currently working in a project to identify and quantify organisms in metagenomic samples. Metagenomic samples collected from different environment contain multiple bacteria, fungus and viruses. Correctly identifying and quantifying them helps researchers identify the organisms causing the problem and plan for solution.

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Adam Adam S Cornish, B.S.
Ph.D. Student
Joined: 2013
I joined the Guda lab in August 2013. Prior to that, I graduated from UNO with a B.S. in bioinformatics which was followed by a three year stint as the primary bioinformatician for the UNMC Next Generation Sequencing (NGS) Core Facility. Recently I finished work on standardizing the analysis pipeline for whole exome data and had this research published in Biomed Research International. Currently I am working on creating a tool that uses NGS data from cancer patients to identify subclonal populations within tumors as well as identifying mutations specific to those subclones. In my free time I volunteer as the webmaster for Spielbound, the new board game cafe in Midtown Crossing, as well as the Omaha Jitterbugs, a non-profit that preserves the historicity of swing dancing through teaching and social dance.
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Kristen Wipfler

Kristin E Wipfler, B.S.
Ph.D. Candidate
Joined: 2013

Before joining UNMC, I graduated from UNL with a B.S. in Biochemistry. For my graduate work, I am performing an integrative molecular characterization of glioblastoma, the most common and deadliest type of primary brain tumor. This includes a comprehensive analysis of seven different data types from The Cancer Genome Atlas as well as integrative and pathway analyses. I am involved in several organizations at UNMC, including the Graduate Student Association (Alumni and Outreach Chair), the Graduate Student Grievance Resolution Committee, and the EMPOWER board (Public Relations/Social Media). Outside of UNMC, I do volunteer work in women’s rights advocacy and youth educational outreach.

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Nagavhardini Avuthu

Nagavardhini Avuthu, M.S.
PhD student
Joined: 2016

I am a 1st year Ph.D. student in prof. Babu Guda's lab. I received my M.S in Applied Microbiology from Sri Padmavati Mahila Viswavidyalam from India and Advanced Diploma in Bioinformatics from Madurai kammaraj university, India. After that I joined in Prof. Dharmalingam's lab at MKU, India and worked on bioinformatic tool and database development. Later as a research associate at ICRISAT, India, I worked on the project, “The molecular diagnosis and genetic variability in Fusarium oxysporum f. sp. ciceris (Foc) causing fusarium wilt of chickpea”, under supervision of Dr Mamta Sharma and developed a high density Foc DArT arrays to assess molecular diversity in Foc population. At ICRISAT, I was also involved in studying the effect of elevated CO2 concentration on Fusarium wilt disease of chickpea and developing a rapid detection method for fusarium wilt pathogen. My current project explores systems-level understanding of root metabolism in maize by comparative analysis of plant omics data and genetic variation, construction of predictive metabolic network models and databases of maize root systems biology datasets.

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Jasjit Banwait

Jasjit Banwait, Ph.D.
Postdoctoral Research Associate
Joined: 2016
Phone: 402-559-5925

Before joining UNMC, I received my Ph.D. in Information Technology (Concentration: Bioinformatics) degree from University of Nebraska at Omaha (UNO). The overarching goal of my dissertation work was to identify suitable miRNA(s) as a drug-substitute, which can be used in the treatment of complex diseases. Existing computational efforts primarily focused on the presence of miRNA binding sites in the 3’-untranslated region (3’-UTR) of an mRNA. The inverse relationship between level of miRNA and gene expression have yielded many false positives. Specifically, this research focused on optimizing the relationship between miRNA and mRNA using their sequence and structural features. To add into the existing complexity, an miRNA is capable of regulating multiple genes and, on the other hand, one gene can be regulated by multiple miRNAs. This target multiplicity attribute of miRNAs make these tiny regulators a great potential for gene regulation and in turn a useful therapeutic agent that can influence a number of important biological pathways or processes. This combinatorial and cooperative role of miRNAs in regulating a target gene(s) gives a new direction to the miRNA research. A working model that allows multiple miRNA and mRNA features to be integrated in optimizing miRNA-mRNA relation was demonstrated. Finally, and most importantly, my dissertation provided a novel approach to identify candidate therapeutic miRNAs for complex disease treatment. Besides Science, I volunteer as Instructor and Evaluator of Punjabi Language at Dallas, TX authorized by University of North Texas, Denton, TX.

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Siddesh

Siddesh Southekal, M.S.
Ph.D. student
Joined: 2017
Phone: 402-559-5925

Prior to joining UNMC, I completed my M.S in Life Science Informatics from University of Bonn, Germany. My Master thesis was in the area of Molecular Dynamics simulation of G-protein coupled receptors which was done at Forschungszentrum Jüelich, Germany. During my studies I also interned at the National University of Taiwan, University Hospital, Taiwan in the area of Pharmacoinformatics. My research skills were further honed while working as a Project Assistant at the Indian Institute of Science (IISc), India in the area of Mathematical Biology following which I worked in the area of Tissue repository and Cancer Genomics at Health Care Global, India. My current research interest lies in application of Bioinformatics in the area of Translational research.

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Navodita

Navodita Upadhyay, M.S.
Bioinformatics Programmer/Analyst
Joined: 2016
Phone: 402-559-5925

I graduated with Masters in Management Information System from University of Nebraska at Omaha. I received project management graduate certification from University of Nebraska, Omaha. I joined UNMC as a Bioinformatics Programmer/Analyst. I have a wide range of experience in database development, web development, project management field using latest tools and techniques. Currently, I am working on the Animal tracking database project and creating user friendly web interface application in .net framework.  My hobbies are: traveling and exploring new places, watching sports like basketball, tennis, soccer.

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Abrar

Abrar Albahrani, M.Sc.
Student intern
Joined: 2017
Phone: 402-559-5925

I graduated with a B.S. in Bioinformatics from University of Nebraska at Omaha, and a M.S. in Bioinformatics from Georgetown University. While completing my M.S. study, I presented my internship work, titled ‘Development of a Python Program for De-identification of Breast Cancer Patient Data’, that involved de-identify breast cancer data from PHI, such as names, dates, and medical record numbers, before upload to a database. I also volunteered at Dr. Habtom Ressom’s lab to work on RNA-seq data analysis by creating multiple workflows using Partek Flow, and pathway analysis and comparison of multi-omic data using IPA and Pathway Studio. In my spare time, I like to draw and crochet. 

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