KBRIN-funded Next Generation Sequencing Projects

Title

Researcher

Inst.

Type

Year

LncRNA-dependent mechanism of DNA/RNA-binding proteins.

Ushida, Shizuka

UofL

RIP-Seq; 10 samples.

2017

Isolation and gene expression profiling of successfully regenerating hindbrain.

Gibbs, Kurt

MST

RNA-Seq; 6 samples.

2017

PCBs and changes in the microbiome during pregnancy and lactation.

Curran, Christine

NKU

16S RNA-Seq; 64 samples.

2017

Role of iron-sulfur cluster proteins in diabetes: shifting metabolism one sugar at a time.

Menze, Mike

UofL

RNA-Seq; 12 samples.

2017

Investigating β-caryophyllene-induced alterations in transcriptome profiles related to Identifying novel targets of Iroquois transcription factors in the vertebrate pharynx.

Frost, Chris

UofL

RNA-Seq 12 samples.

2017

Identifying novel targets of Iroquois transcription factors in the vertebrate pharynx.


Shifley, Emily

NKU

RNA-Seq;9 samples.

2017

Characterization of Chemo-Resistant Breast Cancer Cells Using RNA-seq.

Imbert-Fernandes, Joannis

UofL

RNA-Seq; DNA-Seq; 18 samples.

2017

Molecular mechanism by which circadian clock regulates gene expression.

Jacobshagen, Sigrid;

WKU

ChIP-Seq; 9 samples.

2017

Identification of point mutations in the Pu27 family G-quadruplex sequences.

Miller, Don

UofL

Amplicon-Seq; 25 samples.

2017

Microbial Ecology of Antibiotic Resistance in Louisville Environments.

Himes, Paul

UofL

16S RNA-Seq; 110 samples.

2017

Genome-wide CRISPR-Cas9 Screen to Identify Pathways that Determine Response to AS1411.

Bates, Paula

UofL

Amplicon-Seq; 15 samples

2017

 

Transcriptomics of the avian Iimmune response using RNA-seq.

Ashley, Noah

WKU

RNA-Seq; 16 samples

2016

Quantifying gene expression changes in Xenopus laevis spinal cord following crush injury.

Gibbs, Kurt,

Morehead State
University

RNA-Seq, 12-18 samples

2016

Whole genome CRISPR/Cas9 screen to identify genes required for survival of lung cancer cells on 3 dimensional ECM treated with cisplatin.

Beverly, Levi/Siskind, Leah

UofL

Amplicon-Seq; 10 samples.

2016

Metabolic inflexibility with obesity: Investigating molecular mechanisms that influence the metabolic health of women.


Maples, Jill

WKU

ChIP-Seq, 12 samples

2016

Comparative gene expression associated with inflammation and endoplasmic reticulum stress in diabetic kidney.

Pushpakuma, Sathnur/ Weber, Gregg

UofL

RNA-Seq, 12 samples

2016

Role of tudor gene in small piRNA biogenesis in Drosophila Brain.

Arkov, Alex

Murray State
University

miRNA-Seq, 6 samples.

2016

Quantify differentially abundant RNA transcripts in mouse kidney tissue with chronic alcohol consumption.

Merchant, Michael

UofL

RNA-Seq, 12 samples.

2016

Determine transcriptome response to endoplasmic reticulum stress in rat oligodendrocyte precursor cells.

Hetman, Michal

UofL

RNA-Seq, 12 samples

2016

Impact of G-quadruplex forming oligonucleotides from c-MYC promoter (Pu27).

Miller, Donald/ Rezzoug, Francine

UofL

RNA-Seq, 12 samples

2016

Comparative gene expression analysis in melanocytes driven by tumor cell-derived exosomes.

McMasters, Kelly/ Hao, Hongying

UofL

RNA-Seq, 9 samples

2016

Identification of molecular of targets of natural compound which inhibits breast cancer stem cells.

Damodaran, Chendil

UofL

RNA-Seq, 12 samples.

2016

Novel Interferon-stimulated gene pathway.

Chung, Donghoon

UofL

RNA-Seq, 6 samples.

2016

Manipulation of PMN gene expression during Yersinia pestis infection.

Lawrence, Matt

UofL

RNA-Seq, 12 samples.

2016

 

Variant detection of human respiratory syncytial virus

Bill Severson, Department of Microbiology

UofL

WGS/variant

2015

Comparison of SBKR-3 Single Cell vs. Cell Line SNP Detection Using AmpliSeqTM Cancer Hotspot Panel

Lori Millner, Department of Pathology and Laboratory Medicine

UofL

Cancer Hotspot

2015

Sequence and Variant Analysis of Pu27 Homologs using Amplicon Sequencing

Don Miller, Department of Medicine - Oncology

UofL

Custom Amplicon

2015

Analysis of Putative g-Quadruplex Forming Sequences Within the Mus musculus Papillomavirus

Alfred Jensen, Department of Medicine - Oncology

UofL

Bioinformatics

2015

Comparison of Methodologies for Differential Expression of a Mus musculus RNASeq Dataset Generated on the CeGeMM NextSeq-500

Alan Cheng, Department of Biochemistry and Molecular Biology

UofL

RNASeq

2015

Analysis of g-Quadruplex Forming Sequences Within the Manatee Papillomavirus

Alfred Jensen, Department of Medicine - Oncology

UofL

Bioinformatics

2015

Gut microbiota of APCmin and CCR2XAPCmin mice

Venkatakrishna Jala, Department of Microbiology

UofL

16s rRNA

2015

Pu27 Treatment Analysis Using RNA-Seq

Don Miller, Department of Medicine - Oncology

UofL

RNASeq

2015

Analysis of g-Quadruplex Forming Sequences Across 9 Rodent Papillomavirus Genomes

Joongho Joh, Department of Medicine - Oncology

UofL

Bioinformatics

2015

RNASeq Analysis of human neutrophils infected with F. alocis

Sylvia Uriatre

UofL

RNASeq

2015

Bind-N-Seq Analysis of Zink Finger Proteins

Moon-Soo Kim

WKU

Amplicon Sequencing

2015

Analysis of g-Quadruplex Forming Sequences Within Manatee Papillomavirus Strains 1,3,4

Alfred Jenson

UofL

Bioinformatics

2015

Transcriptome Study of Acinobacter baumanni ddrR Mutant vs WT cells

Janelle Hare

MSU

RNASeq

2015

Identification of host innate immune genes activated by pyrimidine depletion in cells

Donghoon Chung

UofL

RNASeq

2015

Transcriptome Assembly of Pelargonium X Hortorum

David Schultz

UofL

RNASeq

2015

RNASeq Analysis of Crystalline Sillica (CS) Promoting Lung Tumor Growth by Recruiting N2-Neutrophils

Hari Bodduluri

UofL

RNASeq

2015

Investigating the relationships between the various cellular compositions of ECTs and the tissue level activation of critical regulatory pathways relevant to myocardial function, remodeling, and angiogenesis

Fei Yi

UofL

RNASeq

2015

Immunomodulatory effects of Urolithin A on Macrophages

Venkatakrishna Jala, Department of Microbiology

UofL

RNASeq

2015

Gut microbiome analysis of colon cancer and IBD patients using an open reference

Venkatakrishna Jala

UofL

16s rRNA

2015

Pu27 Treatment Analysis Using RNA-Seq: A comparison of hg19 and hg38 using Ensembl Annotations

Don Miller, Department of Medicine - Oncology

UofL

RNASeq

2015

Identification of differentially expressed genes between two breast cancer cell lines: MDA231 and MDA231LN

Jino Park

UofL

RNASeq

2015

Hepatitis C variant detection, round II

Michael Hughes, Department of Surgery - General

UofL

Variant

2014

Ion AmpliSeqTM Comprehensive Cancer Panel Variant Detection

Donald Miller, Department of Medicine - Oncology

UofL

CCP

2014

Ion AmpliSeq TM Comprehensive Cancer Panel Variant Detection for Fanconi Anemia

Alfred Jenson, Department of Medicine - Oncology

UofL

CCP

2014

Role of PARP1 in Alternative Splicing

Yvonne Fondufe-Mittendorf, Department of Cellular and Molecular Biology

UK

RNASeq

2014

Mechanisms of soy glyceollin in brain

Cynthia Corbitt, Department of Biology

UofL

RNASeq

2014

Sex specific miRNA expression profiles in mice with left ventricular hypertrophy using pyrosequencing

Rebekah Waikel, Department of Biology

EKU

miRNA

2014

Transcriptional analysis of African green monkey cells with lentivirus treatment

Emilia Galperin, Department of Cellular and Molecular Biology

UK

RNASeq

2014

Gut microbiome analysis of colon cancer and IBD patients using a closed reference

Venkatakrishna Jala, Department of Microbiology

UofL

16s rRNA

2014

Legionella Variant Detection

Yousef Abu-Kwaik, Department of Microbiology

UofL

Variant

2013

Adenovirus Variant Detection

Sam Zhou, Department of Surgery - Oncology

UofL

Variant

2013

Hepatitis C variant detection

Michael Hughes, Department of Surgery - General

UofL

Variant

2013

Amplicon sequencing of equine encephalitis virus and SNPs detection

Donghoon Chung, Department of Microbiology

UofL

WGS/Variant

2013

De novo sequencing of Achebe bacteriophage

Claire Rinehart, Department of Biology

WKU

WGS/Variant

2013

De novo sequencing of Busterbird bacteriophage

Claire Rinehart, Department of Biology

WKU

WGS/Variant

2013

miRNA profiles of oral cancer cells after treatment with tobacco products

Wolfgang Zacharias, Department of Medicine - Oncology

UofL

miRNA

2013

Sex specific miRNA expression profiles in mice with Left Ventricular Hypertrophy

Rebekah Waikel

EKU

miRNASeq

2012

Transcriptome analysis of Acinetobacter baumannii

Janelle Hare

MoSU

RNASeq

2012

Growth Hormone Pathways in Zebrafish Auditory Hair Cell Regeneration using GH Antagonist

Michael Smith

WKU

RNASeq

2012

Using Next-generation Sequencing to Reveal the Target Genes of miR-21 and its Function in Acute Pancreatitis

Yong Li

UofL

RNASeq

2012

Exosome miRNA profiles as innovative biomarkers in melanoma patients

Hongying Hao

UofL

miRNASeq

2012

Gut microbiome analysis of colon cancer and IBD patients

Venkatakrishna Jala

UofL

16s

2012

To establish an RNA code regulated by hnRNPH in oligodendrocytes by mapping RNA protein interactions in vivo

Franca Cambi

UK

RIP-Seq

2012

The role of stress granule mRNA in adaptive stress responses of the murine kidney

Michael Merchant, Department of Medicine - Renal

UofL

RNASeq

2012

De Novo sequencing of Pseudomonas fluorescens

Hazel Barton

NKU

De-novo

2011

Sex specific miRNA expression profiles in mice with Left Ventricular Hypertrophy using pyrosequencing

Rebekah Waikel

EKU

miRNA Seq

2011

Next Generation Sequencing to Reveal Growth Hormone Pathways in Zebrafish Auditory Hair Cell Regeneration

Michael Smith

WKU

RNASeq

2011

Identification of axonal collateral sprouting-specific genes

Jeffrey Petruska

UofL

RNASeq

2011

Activity/stress increases acetylation of lysine 14 in histone H3 (H3K14ac) in olfactory sensory neurons

Timothy McClintock

UK

CHiPSeq

2011