University of Nebraska Medical Center



Nebraska Research Initiative (NRI) Core PI: Guda 07/01/12- Current
Bioinformatics and Systems Biology Core (BSBC)”
Funds provided by NRI to subsidize core services. BSBC provides bioinformatic data management and analysis services to over 100 independent PIs, both from and outside of Nebraska institutions.

Human Genetics Laboratory (HGL) Contract PI: Guda 07/01/15- Current
“MOU for providing bioinformatics support to HGL’s clinical diagnostic services”
HGL is a CLIA-certified laboratory that offers genetic diagnostic testing services for patients using a variety of gene panels. We support the bioinformatic analysis of next-gen sequencing data and the interpretation of genetic variants in patient samples.

2P01AG029531-06A1 (NIH/NIA) (PI: Bousfield) Guda (Subaward PI) 09/01/17–05/31/22
"The Aging Pituitary/Gonadal Axis"
This is a Program Project Grant (PPG) to study the role of FSH in bone loss. The Bioinformatics and Genomics Core provides support for ‘Omics-data’ generation and data analysis.

1R01MH110636-01A1(NIH/NIMH) (PI: Mirnics) Guda (Co-I) 06/01/17–05/31/22
"Vulnerability of DHCR7+/- mutation carriers to aripiprazoleand trazodone treatment"
The goal of this project is to test the vulnerability of the DHCR7+/- gene mutation carriers to aripiprazole (an atypical antipsychotic) and trazodone (an antidepressant) exposure.

3P30MH062261-15S1 (NIH/NIMH) (PI: Buch/Fox) Guda (Co-I) 04/01/16 – 03/31/22
“Chronic HIV Infection and Aging in NeuroAIDS (CHAIN) Center”
This is a Center grant to support investigators working on NeuroAIDS research. Guda (Co-I) provides bioinformatics support to analyze various ‘omics’ data generated by this project.

5P30CA036727-29 (NIH/NCI) (PI: Cowan) Guda (Core-Lead) 09/01/15 - 07/31/21
"UNMC Eppley Cancer Center Support Grant"
The mission is to coordinate basic research and clinical cancer research, patient care and educational programs, to facilitate application of new knowledge about the etiology, diagnosis, treatment and prevention of cancer and to improve health and quality of life.

NSF Nebraska EPSCoR (PI: Choobineh) Guda (Subaward PI) 06/06/16 – 05/31/21
“Center for Root and Rhizobiome Innovation (CRRI)”
This project will generate large volumes of omics datasets from analyses and measurements of root gene expression and metabolites, soil microbiota, and plant phenotypes. Computational algorithms will be used for predictive model construction for more efficient data mining.

1 U54GM115458-01 (NIH/NIGMS) (PI: Rizzo) Guda (Co-Director) 09/01/16 – 06/30/21
"Great Plains IDeA-CTR"
The goal of this project is to provide infrastructure, mentoring, resources and evaluation for building clinical and translational research programs for the IDeA-CTR network member institutions through the Biomedical Informatics (BMI) Key Component Activity (KCA).

2P20GM103427-14 (NIH/NIGMS) (PI: Turpen) Guda (Core-Lead) 05/01/14 – 06/30/20
INBRE-Nebraska Research Network in Functional Genomics
This is an Institutional Development Award (IDeA) to enhance the research capabilities of underfunded institutions through infrastructure development and partnerships.

1U24MH100925-01 (NIH/NIMH) (PI: Fox) Guda (Co-I) 05/01/13 – 02/28/18
National NeuroAIDS Tissue Consortium Data Coordinating Center (NNTC-DCC)
NNTC, a consortium of four brain banks has served the NeuroAIDS research community since 1998. Guda is a Co-I, who oversees the management of data (clinical/experimental) from NNTC and CHARTER projects, building databases, making the data accessible to researchers and supervising the DCC personnel.


FP Buffett Cancer Center Contract (PI: Guda) 02/01/15 – 06/30/17
Whole Genome Analysis of breast cancer patients
Integrative analysis of next-gen sequencing data (mostly ExomeSeq data, but also include RNAseq, array CGH, miRNA microarrays and MethylSeq data) from 1000 in-house collected breast cancer tumor/normal paired samples to identify somatic mutations and correlate their effects on the initiation and progression of breast cancer.

University of South Dakota (USD) (PI: Burrell) Guda (Co-PI) 06/01/16 – 05/31/17
“Developing a full-sequence genome of the medicinal leech (Hirudo medicinalis)”
USD Center for Brain & Behavior Research collaborates with UNMC to develop a full-genome sequence map for medicinal leech. Guda’s group will carry out de novo genome assembly to develop the reference draft and annotate the coding regions.

Nebraska Research Initiative (NRI) (PI: Kharbanda) Guda (Co-I) 07/01/15 – 06/30/17
“Role of betaine in preventing alcohol-induced gut dysbiosis”

To investigate if betaine prevents alcohol-induced gut dysbiosis and also if betaine could reverse the alcohol-induced changes in gut microbiota. Guda (Co-PI) is responsible for providing bioinformatics support for metagenomics data analysis in this project.

T32CA009476 (NIH/NCI) (PI: Black) Guda (Mentor) 07/01/15 - 06/30/17
Eppley Institute Cancer Biology Training Grant to Kristin Wipfler
“Integrative molecular characterization of glioblastoma
This is a prestigious award from the National Cancer Institute (NCI) and competition for these fellowships is rigorous.

UNMC Graduate Fellowship to Adam Cornish Guda (Mentor) 07/01/15 - 06/30/17
“Determining the clonal heterogeneity in tumors using exome sequencing data
This is a competitive fellowship awarded by UNMC graduate school to support up to 2 years of stipend for a full-time graduate student at UNMC

FP Buffett Cancer Center Pilot AwardPI: Guda 11/01/13 – 11/30/16
“Genomic profiling of breast cancer tumors using bioinformatics approaches”
Develop bioinformatic pipelines to analyze various types of NGS data including ExomeSeq, RNA Seq, and microarrays for over 1000 breast cancer patient samples treated at UNMC.

UNMC’s BMI Graduate Fellowship to You LiGuda (Mentor) 07/01/15 - 06/30/16
“A gene fingerprint-based algorithm for fusion genes detection from RNA-Seq short reads
This is a competitive fellowship awarded by the UNMC graduate school to support stipend for a full-time student in the Biomedical Informatics (BMI) graduate program

1R01GM086533-01A1 (NIH/NIGMS)PI: Guda 09/01/09 - 08/31/15
"Cataloging the Subcellular and Suborganellar Proteomes of Sequenced Genomes
Development of a novel method for predicting protein subcellular location, followed by experimental validation and development of an open-source software package and a web application.

MBEP Pilot Grant (FPB Cancer Center)PI: Guda 6/01/14 – 5/31/15
“Proteogenomic (Proteomics-Genomics) Integration of Breast Cancer Expression Data”
TCGA database provides different types of genomic and proteomic data from over 1000 breast cancer patients. The raw and/or processed data are not readily accessible in an understandable format by the biologists. This pilot project facilitates the development of a backend database and a web-based user-interface to query the TCGA data on breast cancer that can be eventually applied to other cancer data.

Nebraska Research Initiative (NRI) (PI: Eudy) Guda (Co-I) 08/01/14 – 07/31/15
“Establishment of Single Cell Genomics Technology for Nebraska Researchers”
This equipment grant supports the acquisition of the first single cell genomics instrumentation in the State of Nebraska. This includes the C1-Single-cell AutoPrep system, BioMark HD qPCR system and Access Array system for library preparation. Guda (Co-I) provides bioinformatic data analysis support for single-cell genomics data generated from this technology.

UNMC’s BMI Graduate Fellowship (Vural)Guda (Mentor) 07/01/13 - 06/30/15
“Molecular subtyping of breast cancers using NGS data and machine-learning methods”
This is a competitive fellowship awarded by the UNMC graduate school to support up to 2 years of stipend for a full-time student in the Biomedical Informatics graduate program.

Pancreas SPORE’s Pilot Grant (UNMC)PI: Guda 08/01/13 – 07/31/14
“Identification and characterization of pancreatic cancer subtypes using exome-sequencing data”
UNMC is the home of the Rapid Autopsy Program (RAP), which provides unique collection of specimens to be used to further research in pancreatic cancer. This project analyzes the Exome sequencing data from matched samples of pre-metastatic (Whipple), primary and metastatic tumors to determine the genomic variants that may be associated with the progression of pancreatic cancer.

Bukey Graduate Fellowship (Mohammed)Guda (Mentor) 07/01/12 - 08/15/14
“Development and application of a hierarchical machine learning method for enzyme classification”
This is a competitive fellowship awarded by UNMC graduate school to support up to 3 years of stipend for a full-time graduate student at UNMC.

1R15GM080681-01A1 (NIH/NIGMS)PI: Guda 03/01/08 - 03/31/11
An integrated approach to infer and validate domain-domain interactions in proteins
This is an AREA (Academic Research Enhancement Award) to develop a novel computational method for inferring functionally significant domain-domain interactions (DDIs) from protein-protein interactions, followed by their experimental validation using yeast-two-hybrid studies.

1UO1HG004571-01 (NIH/NHGRI)(PI: Tenenbaum) Guda (Co-I) 09/01/07 - 08/31/10
Comprehensive Identification of ENCODE RNA based on cis-regulatory elements
The objective of this project is to comprehensively catalog cis-regulatory elements/RBP-binding sites (CREBS) present in expressed ENCODE mRNA. Guda (Co-I) provided bioinformatics support for this project.

5T34-GM008807 (NIH/NIGMS) (PI: Rocha) Guda (Consultant) 08/01/04 - 05/31/10
California State University of San Marcos MARC U*STAR Program
Guda (Bioinformatics Consultant) was involved with the incorporation of preparatory courses in the undergraduate curriculum to enable students pursue graduate training and careers in bioinformatics.

NPACI/NSFPI: Guda 04/01/03 – 12/31/03
“Developing a Standalone Tool for Multiple Protein Structure Alignment Algorithm”
This award supported an REU (Research Experience for Undergraduates) summer student in the Guda lab to develop a standalone software package called CE-MC (Combinatorial Extension-Monte Carlo) that performs the alignment of multiple protein structures in the Protein Data Bank (PDB).