Babu Guda, PhD

Principal Investigator
Phone: 402-559-5954
Email
CV
GitHub

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.

Peng Xiao, PhD

Assistant Professor, Core Operational Director
Joined: 2014
Phone: 402-559-2083
Email

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 64 peer-reviewed papers, 32 meeting abstracts, and two book chapters in the areas of human genomics and system biology. Currently, as the Bioinformatics and System Biology Core operational director, I am an expert in Next-Gen sequencing-based data (whole genome-seq, exome-seq, RNA-seq, miRNA-seq, ChIP-seq, 16s & metagenomics, single-cell RNA-seq, etc.) and proteomics data analyses, as well as the downstream functional characterization of genes and gene products to understand the pathways and interaction networks. My hobbies include Christian evangelization, badminton, and tennis.

Sankarasubramanian (Subu) Jagadesan, PhD

Bioinformatics Scientist
Joined: Sep 2018
Phone: 402-559-5925
Email

I obtained my Ph.D. in Microbiology with a specialization in Bioinformatics and Genomics from Madurai Kamaraj University, India, in 2019. Prior to that, I earned my M.S. in Bioinformatics from Bharathiar University and my B.S. in Bioinformatics from Manonmaniam Sundaranar University, India. My research expertise lies in applying bioinformatics methodologies to analyze infectious diseases. I joined Prof. Babu Guda's lab in September 2018 and have since been actively involved in various areas of computational biology. My expertise includes NGS data analysis, GWAS, database development and maintenance, comparative genome analysis, SNP analysis, protein-protein interaction studies, host-pathogen interactions, genome assembly, annotation, variant calling, metagenome analysis, whole-genome comparisons, RNA-seq, ATAC-seq, scRNA-seq, and spatial transcriptomics. Additionally, I have a strong background in web development and maintenance, having developed R-based tools for metagenome and scRNA-seq data analysis. I also manage the lab server, ensuring its efficient operation and maintenance.

Sushil K Shakyawar, PhD

Instructor
Joined: Mar 2020
Phone: 402-559-5925
Email

My PhD work primarily focused on systems biology and metabolic network modeling, and supported by European Marie Curie ITN at Silicolife Lda and University of Minho, Portugal. Prior to this, I completed MRes (Master of Research) in Computational Biology from the University of York (UK), and bachelor’s degree in biotechnology from the Indian Institute of Technology Guwahati (India). With the diverse background and trainings in bioinformatics and machine learning (ML) acquired at various institutes, my current research at UNMC is centered on leveraging computational and machine learning techniques to advance the multiomics field. Specially, I specialize in ML-based modelling and bioinformatics approaches for analyzing and integrating multiomics data, disease subtyping, discovering molecular biomarkers, and developing prognostic models for human diseases including cancer.

Avinash M Veerappa, PhD

Instructor
Joined: Apr 2021
Phone: 402-559-5925
Email

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.

Jai Chand Patel, PhD

Post-Doctoral Associate
Joined: Oct 2021
Phone: 402-559-5925
Email

I joined as a Postdoctoral Research Associate at UNMC in Professor Guda’s lab on October 1st, 2021. I completed my Ph.D. from DRDO (India) in 2021, where I developed a predictive model for hypoxia-induced pathologies using network biology and machine learning. Primarily, I am focusing on integration of multi-omics cancer data from public repositories using deep learning models. Previously, I developed machine learning models for subtype prediction, and early diagnosis in different types of cancer, focusing on integrating multi-omics cancer data from public repositories using deep learning models. Currently, I am working on a genomic window project to create uniform matrix representations of cancer genomic data across chromosomes, with the aim of converting these matrices into images for use in Convolutional Neural Networks (CNN).

Rajashree Chakraborty, MS

PhD student
Phone: 402-559-5925
Email

I am a PhD student at Dr. Guda's lab. I pursued my bachelor's and master's degree in medical 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 unraveling the genomic and epigenomic vulnerabilities in substance use disorders (SUDs). I use various bioinformatics tools, pipelines and programming languages to gain insight on the complexities of SUDs.

Nagasundaram Nagarajan, PhD

Post-Doctoral Associate
Joined: 2022
Phone: 402-559-5925
Email

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.

Naresh V R Mutha, PhD

Post-Doctoral Associate
Joined: Sep 2023
Phone: 402-559-5925
Email

I am a postdoctoral researcher in bioinformatics at the University of Nebraska Medical center. My current research focuses on elucidating genetic architecture of Alzheimer’s diseases across different ethnicities by integrating GWAS with robust multio-mics using publicly available datasets. I received my PhD degree in Bioinformatics from the University of Malaya. Before joining UNMC I did my postdoctoral research at Vanderbilt University Medical Center and AIIMS-Bhubaneswar.

Sujith Manavalan, MS

PhD student
Joined: Jan 2023
Phone: 402-559-5925
Email

I am a Bioinformatics and Systems Biology Ph.D. candidate at UNMC, with a Master's degree in Genomics. Previously, I have investigated implications of Fusobacterium infection in early-stage tongue cancer, explored the role of microRNAs in tongue cancer metastasis, and studied molecular mechanisms of hormone therapy resistance in breast cancer. My skills encompass both computational techniques and molecular biology lab methods. My current research focuses on computational methods for molecular subtyping of cancer for improving prognosis and biomarker discovery. My work bridges bioinformatics, machine learning, and cancer biology, aiming to advance our understanding of cancer biology.

Saadyeh Rashidi, MS

PhD student
Joined: Feb 2024
Phone: 402-559-5925
Email

My name is Saadyeh (Saadya), and I am from Saqqez, Kurdistan, Iran. I studied Cell and Molecular Biology for my bachelor's degree at Kharazmi University and Molecular Genetics for my master's degree at Shahid Beheshti University. During my master's, I worked on an autoimmune disorder, henoch-schönlein purpura. My interest in bioinformatics developed during this time, and I began learning programming skills. I was privileged to be accepted into the BISB program at UNMC in 2023 and join Dr. Guda’s lab. My primary focus in Dr. Guda’s lab is on leveraging computational techniques to advance the field of proteomics. I aim to use machine learning for disease subtyping, biomarker discovery, and building prognostic models. I am grateful to have the opportunity to contribute to this cutting-edge research.

Swathi S Yakasiri, MS

PhD student
Joined: Jun 2024
Phone: 402-559-5925
Email

I have received my Bachelor's in Computer Applications and Master's in Computer Science from Acharya Nagarjuna University, India. I have been working as a Software Engineer for 8 years in the Healthcare domain, with experience in Python, Teradata, and various BI tools. I have always been passionate about biology and science since my childhood. I am grateful for this opportunity and am very excited to learn and research in neuroscience.

Kayode Raheem, MS

PhD student
Joined: Dec 2024
Phone: 402-559-5925
Email

I hold a Bachelor’s degree in Biochemistry from Adekunle Ajasin University, Akungba-Akoko, Nigeria, and a Master’s degree in Bioinformatics from COMSAT University, Islamabad, Pakistan. My research expertise spans cancer genomics and computational drug discovery, where I have designed personalized neoantigen mRNA vaccines for breast cancer using next-generation sequencing (NGS) data, developed the R Shiny cGEDs App for cancer drug-sensitivity analysis, and analyzed multi-omics datasets (RNA-seq, proteomics) to identify genomic biomarkers and potential drug targets. I have also employed structural bioinformatics techniques, including homology modeling, molecular docking, and molecular dynamics simulations, to study protein-ligand and protein-protein interactions. Currently, I am leveraging machine learning and deep learning models to advance the drug discovery process, focusing on predicting drug candidates and optimizing lead compounds for therapeutic applications..