Current Members

Name Title
Babu Guda Professor & Principal Investigator
Peng Xiao Assistant Professor, Core Operational Director
Meng Niu Assistant Professor
Nagavardhini Avuthu Post-Doctoral Associate
Sankarasubramanian Jagadesan Bioinformatics Scientist
Sahil Sethi Ph.D. Student
Sushil Shakyawar Post-Doctoral Associate
Avinash M Veerappa Instructor
Jai Chand Patel Post-Doctoral Associate
Rajashree Chakraborty Ph.D. Student
Ramanuja Simha Instructor
Nagasundaram Nagarajan Post-Doctoral Associate


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 Ph.D. 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 Ph.D., 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
Assistant Professor, 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 Ph.D. in Biomedical Sciences - Human Genetics and Genomics from Creighton University in Omaha, Nebraska. During my Ph.D. study, I received 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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Niu.png Meng Niu, PhD
Assistant Professor
Joined: 2015
Phone: 402-559-5925

I received my BS and M.S degrees in Computer Science from Jilin University, China, and a Ph.D. in Bioinformatics from the 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 humans 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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Nagavhardini Avuthu

Nagavardhini Avuthu, Ph.D.
Post-Doctoral Associate
Joined: 2016
Phone: 402-559-5925

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 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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subu

Sankarasubramanian (Subu) Jagadesan, Ph.D.
Bioinformatics Scientist
Joined: 2018
Phone: 402-559-5925

I received Ph.D. in Microbiology (Specialization: Bioinformatics and Genomics) in 2019 from Madurai Kamaraj University, India. My thesis is entitled Comparative genomics and phylogeny analyses of Brucella. I did my MS degree in Bioinformatics from Bharathiar University, India and BS degree in Bioinformatics from Manonmaniam Sundaranar University, India. 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, whole genome data analysis, server maintance and website creation.

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Sahil Sethi, M.S.
Ph.D. student
Joined: 2020
Phone: 402-559-5925

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 Ph.D. in Biomedical Informatics from the University of Nebraska Medical Center. My current thesis topic is Comparative analysis of transcriptomic profiles from SARS-CoV-2 and other human viral infections.

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Shakyawar Sushil K Ph.D.
Post-Doctoral Associate
Joined: 2020
Phone: 402-559-5925

I received my Ph.D. with a specialization in Computational Systems Biology and Metabolic Modelling from the University of Minho (Portugal). My Ph.D. 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 the 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.

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Avinash M Veerappa, Ph.D.
Instructor
Joined: 2021
Phone: 402-559-5925

I am a postdoctoral research associate at the University of Nebraska Medical Center. I was previously employed at New York University Langone Medical Center before receiving my Ph.D. and M.Sc. in Genetics from the University of Mysore. My research focus is primarily in computational genomics and involves the design of new tools and pipelines to model biological systems and to study the complexities of human diseases and disorders.

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Jai

Jai Chand Patel, Ph.D.
Post-Doctoral Associate
Joined: 2021
Phone: 402-559-5925

I am Jai Chand Patel joined as Postdoctoral Research Associate at UNMC in Professor Guda’s lab on October 1st, 2021. I completed my Ph.D. from DRDO (India) in 2021. During my Ph.D., I worked on developing a predictive model for hypoxia-induced pathologies using network biology, time series analysis, machine learning, and microarray analysis. I received my M.Sc (2014) and B.Sc (2012) from Kurukshetra University (India). Currently, I am working on development of machine learning models for survival prediction, subtyping and early diagnosis in different types of cancer. Primarily, I am focusing on integration of multi-omics cancer data from public repositories using deep learning models.

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rajashree

Rajashree Chakraborty, M.S.
Ph.D. student
Joined: 2022
Phone: 402-559-5925

Hello, I am a PhD student at Dr. Guda's lab. I pursued my bachelor's and master's degree in biotechnology from India. I have always been fascinated by computer science and its implication in every field. That is how as a biologist, I happened upon Dr. Guda's lab where he and his team research and analyze biological data computationally. This opened a whole new arena for me for which I am extremely grateful and excited for. Currently my research entails understanding in depth the molecular interactions of the pathophysiology of addiction.

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 ramanujasimha

Ramanuja Simha, Ph.D.
Instructor
Joined: 2022
Phone: 402-559-5925

My research background is in machine learning and computational biology. I received my PhD in Computer Science from the University of Delaware. For my PhD, I developed probabilistic graphical models for protein subcellular multi-localization. During my PhD, I interned at LinkedIn where I developed a pipeline to rank startup companies, and at GE Global Research where I developed a software to stratify cancer patients. I have since worked as a postdoctoral fellow at the University Health Network at the University of Toronto where I developed statistical pipelines for biomedicine and as a postdoctoral research associate at the Oak Ridge National Lab where I developed machine learning methods for computational biological applications. I have also been a Research Scientist at Adobe Research where I worked on developing deep reinforcement learning techniques for process scheduling.

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 nagasundaram

Nagasundaram Nagarajan, Ph.D.
Post-Doctoral Associate
Joined: 2022
Phone: 402-559-5925

I have completed PhD in Bioinformatics from VIT university, India. Before that I have completed master degree in Bioinformatics from Bharathiar university and bachelor degree in Biotechnology from Madurai Kamaraj university. My PhD thesis focused on analysing the effects of deleterious SNPs at structural and functional level of proteins. I have used molecular docking and molecular dynamics simulations approaches to understand the structural behaviour of Protein-Protein, Protein-DNA, Protein-Drug interactions in the presence of deleterious SNPs. Later joined in Hongkong Baptist University as postdoctoral fellow their gained experience in utilizing high performance cluster facilities for molecular modelling. Next as a principal investigator in DST-NPDF fellowship completed a project entitled “Insights the mechanism of ALK drug resistance in human lung cancer treatment and identification of potential inhibitors” sponsored by Department of Science and Technology (DST), Indian government. Then, worked as a “Research Fellow” at NTU Singapore in the department of medical humanities to analyses the human genomic data and involved in the development of machine learning methods to solve various biological problems. Recently was as a “Research Associate” in Indian council of medical research [ICMR] project at VIT university focused on antimicrobial drug resistant studies and further involved in various cancer WES and microbial WGS data analysis.

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