Current Members
Name Title
Abrar Albahrani Student Intern
Nagavardhini Avuthu PhD Student
Adam Cornish PhD Student
Babu Guda Professor & Principle Investigator
Sankarasubramanian Jagadesan Post-Doctoral Associate
Duc Le Bioinformatics DatabaseSrv Administrator
Sujana Maddipati Student volunteer
Nitish Mishra Instructor
Meng Niu Bioinformatics Programmer/Data Analyst
Sanjit Pandey Core Assistant Director/ PhD Student
Siddesh Southekal PhD Student
Yuande Tan Post-Doctoral Associate
Ahmad Tanwir Radiology Research Associate/ M.S. Student
Neetha Vellichirammal Instructor
Peng Xiao Assistant Professor


Faculty and Staff
Guda_small.png 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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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.
Instructor
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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Niu.png 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. Right now I’m working in UNMC as a bioinformatics analyst for: clinical genetic testing including hereditary cancer testing and postnatal testing (MMI Human genetic lab); research analyses including RNAseq, miRNA-seq, variants-calling, single cell sequencing data analysis and etc. I’m mostly interested in working with neuron cells and cancer cell heterogeneity.

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Duc Le Duc Le, B.Sc.
Bioinformatics DatabaseSrv Administrator
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/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.
Core Assistant Director/ Ph.D. Student
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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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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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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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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Ahmad Tanwir, M.S. 
Radiology Research Associate/ M.S. Student
Join: 2018

 I graduated from University of Dhaka, Bangladesh with B. Pharm., and M. Pharm. degree in Pharmaceutical Science. Then, I joined bio-imaging core facility of University of Nebraska Medical Center as a Radiology Research Associate in 2013. After realizing that there is a huge opportunity of implementing data analysis, data modeling, database development techniques in that field, I enrolled into the M.S. in Biomedical Informatics of the University of Nebraska Medical Center in 2014. Currently I am working on the project, titled “Development of Preclinical Magnetic Resonance Imaging Relational Database and Interactive Analytical Tool for Diffusion Tensor Imaging”. The goal of this project is to develop a database and interactive tools that allow users to insert and extract quantitative DTI metrics without having to go through the complicated manual mapping process. The interactive tools will retrieve the data from the database, perform statistical analysis (t-test, ANOVA, and test of association) and generate graphs (histogram, bar diagram, scatter plot, box plot, time series plot) to present results.

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sankara

Sankarasubramanian Jagadesan, Ph.D.
Post-Doctoral Associate
Join: 2018
Phone: 402-559-5925

I received my B.S. degrees in Bioinformatics from Manonmaniam Sundaranar University, India. M.S. degree in Bioinformatics from Bharathiar University, India. I worked on Genome Information Resource: Thermoregulation of Camel under Cold/Heat stress. Later, I have joined Madurai Kamaraj University, India and did my Ph.D. in Microbiology and Interdisciplinary Genomics, (Major: Bioinformatics). My thesis entitled with Comparative genomics and phylogeny analyses of Brucella. I have an experience in analyzing the infectious disease with Bioinformatics methods. I was an expert in genome assembly, annotation, variant calling, and identification of novel genes from sequenced raw reads from any NGS platform. I am also interested in the emerging study of NGS and data analysis, GWAS, Database development and maintenance, Comparative genome analysis, SNP analysis, protein-protein interaction, host-pathogen interaction, docking and structural studies. I have a good knowledge in web designing and server maintenance. I joined the Prof. Babu Guda's lab in September 2018 and working in Metagenomics and data analysis.

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Sujana Maddipati, B.S
Student volunteer
Join: 2018

Prior to working in Dr. Guda’s lab, I completed my B.S. in Biology at Creighton University. While in undergrad, I worked in an Analytical Chemistry lab under Dr. Erin Gross. My research focused on development of a glucose biosensor for the detection of diabetes using the electrogenerated chemiluminescence technique. The biosensor used the chemiluminescent properties of a luminol and hydrogen peroxide reaction to determine glucose concentrations of standard solutions. Additionally, I was involved in a project focused on analyzing the efficiency of various biosensors based on the chemiluminescent properties of luminol and ruthenium complex titled A review of electrogenerated chemiluminescent biosensors for assays in biological matrices. Furthermore, I participated in the Summer Undergraduate Research Program at UNMC under Dr. Ann Anderson-Berry and Dr. Corrine Hanson where we assessed the nutrition of pregnant women and their access to food.

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Yuande.JPG

Yuande Tan, Ph.D.
Post-Doctoral Associate
Join: 2018
Phone: 402-559-5925

I received B.S. in agronomy from Hunan Agricultural University, M.S. in plant physiology from Zhongshan University, and PhD in animal molecular genetics from Southwest Agricultural University, respectively, in China. I taught and studied in biostatistics, genetics, molecular evolutionary genetics, and biological technology in China.  After coming in USA, I first worked in genetic linkage and epidemiology in The University of Texas at Houston. I developed genetic mapping functions, mapping method, and new epidemiological design and statistical test.  Later, I won master degree in biostatistics from The University of Texas at Houston and began to transfer to bioinformatics research in Baylor College of Medicine where I was working in identifying differentially expressed genes from transcriptomic data, doing genome-wide association analysis of complex diseases, and developed differential analysis methods. In addition, I also worked in numerical computation, numerical simulation, statistical and machine learning, and network. I joined the Prof. Babu Guda's lab in August 2018 where I am focusing on alternative splicing associated with cancers, statistical analysis of single-cell RNA-seq data, and developing new bioinformatics tools or methods.

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