Current Members
Name Title
Nagavardhini Avuthu PhD Student
Babu Guda Professor & Principal Investigator
Sankarasubramanian Jagadesan Post-Doctoral Associate
Nitish Mishra Instructor
Meng Niu Bioinformatics Programmer/Data Analyst
Sanjit Pandey Core Assistant Director/ PhD Student
Sahil Sethi PhD Student
Sushil Shakyawar Post-Doctoral Associate
Siddesh Southekal PhD Student
Yuande Tan Post-Doctoral Associate
Neetha Vellichirammal Instructor
Peng Xiao Core Operational Director


Faculty and Staff
Guda_small.png Babu Guda, PhD
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 the 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, PhD
Core Operational Director
Joined: 2014
Phone: 402-559-2083

I received a BS in Biochemistry and Molecular Biology from Hunan Normal University, China, and a PhD in Biomedical Sciences - Human Genetics and Genomics from Creighton University in Omaha, Nebraska. During my PhD study, I received extensive training in human functional genomics and statistical genetics. After receiving the PhD, 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, PhD
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 biomarkers 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, PhD
Instructor
Joined: 2013
Phone: 402-559-5925

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

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

I received my BS and M.S degrees in Computer Science from Jilin University, China, and PhD in Bioinformatics from the University of North Carolina at Charlotte. My PhD 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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Sanjit Pandey Sanjit Pandey, MS
Core Assistant Director/ PhD Student
Joined: 2010
Phone: 402-559-5925

I graduated with a Masters in Computer Science from the 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 a PhD 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 on a project to identify and quantify organisms in metagenomic samples. Metagenomic samples collected from different environments contain multiple bacteria, fungus, and viruses. Correctly identifying and quantifying them helps researchers identify the organisms causing the problem and plan for the solution.

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Nagavhardini Avuthu

Nagavardhini Avuthu, MS
PhD student
Joined: 2016

I am a 1st year PhD 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 Kamaraj University, India. After that, I joined Prof. Dharmalingam's lab at MKU, India, and worked on the bioinformatics 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 the systems-level understanding of root metabolism in maize by a 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, MS
PhD student
Joined: 2017
Phone: 402-559-5925

Prior to joining UNMC, I completed my M.S in Life Science Informatics from the 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 the application of Bioinformatics in the area of Translational research.

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Sankarasubramanian Jagadesan, PhD
Post-Doctoral Associate
Join: 2018
Phone: 402-559-5925

I received my BS degrees in Bioinformatics from Manonmaniam Sundaranar University, India. MS 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 PhD in Microbiology and Interdisciplinary Genomics, (Major: Bioinformatics). My thesis entitled Comparative genomics and phylogeny analyses of Brucella. I have experience in analyzing infectious diseases 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 of web designing and server maintenance. I joined Prof. Babu Guda's lab in September 2018 and working in Metagenomics and data analysis.

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Yuande Tan, PhD
Post-Doctoral Associate
Join: 2018
Phone: 402-559-5925

I received a BS in agronomy from Hunan Agricultural University, MS 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 the USA, I first worked in genetic linkage and epidemiology at The University of Texas at Houston. I developed genetic mapping functions, mapping methods, and new epidemiological design and statistical tests.  Later, I won a master's 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 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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Sahil Sethi, MS
PhD student
Joined: 2020

I graduated with a Bachelor’s in Bioinformatics from Jaypee University of Information Technology (India) and a Master’s in Biomedical Informatics from the University of Nebraska Omaha. While doing my master’s I worked on my thesis, titled “HLA Expression and HLA typing in Human Cancer”. After graduating, I went in to get some industry experience and had a chance to work as an Application Developer and Bioinformatician for various organizations. Soon after gaining enough experience, I decided to pursue a PhD in Biomedical Informatics from the University of Nebraska Medical Center.


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Shakyawar, Sushil K ,PhD
Post-Doctoral Associate
Joined: 2020

I received my PhD with a specialization in Computational Systems Biology and Metabolic Modelling from the University of Minho (Portugal). My PhD thesis was mainly focused on systems biology-based applications and metabolic network modeling to understand infection of parasite L. major in humans. The project was supported by European Marie Curie ITN at Silicolife Lda (Portugal). I completed MRes (Master of Research) in Computational Biology from the University of York (UK), and BTech in Biotechnology from Indian Institute of Technology Guwahati (India). During my postgraduation, I mainly explored machine learning applications for identifying drug-target interactions in human cancer. Previously, I undertook training in biotechnology, bioinformatics, and computational biology. At UNMC, my research objective is to understand different biological networks (e.g. gene-gene interactions, protein-protein interactions, metabolic interactions, etc.), which are key determinants of cellular behaviors at the system-level. I focus on machine learning methods, big data (omics) analysis and integration, and computational biology modeling to determine dynamical and topological characteristics of various networks, and understand the interplay between their functions.