TFEA calculates motif enrichment using differential and positional information.

Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of transcription factors from a single experiment

Feb. 21, 2020

Detecting differential activation of transcription factors (TFs) in response to perturbation provides insight into cellular processes. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects differential activity of hundreds of TFs given any set of perturbation data. TFEA draws inspiration from GSEA and detects positional...

Graphs and pictures from research performed by Robin Dowell and Amy Palmer

Remodeling of Zn2+ Homeostasis Upon Differentiation of Mammary Epithelial Cells

Jan. 16, 2020

Zinc is the second most abundant transition metal in humans and an essential nutrient required for growth and development of newborns. During lactation, mammary epithelial cells differentiate into a secretory phenotype, uptake zinc from blood circulation, and export it into mother’s milk. At the cellular level, many zinc-dependent cellular processes,...

Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease

Jan. 13, 2020

Flaviviruses such as dengue encode a protease that is essential for viral replication. The protease functions by cleaving well-conserved positions in the viral polyprotein. In addition to the viral polyprotein, the dengue protease cleaves at least one host protein involved in immune response. This raises the question, what other host...

The differences between stable mRNAs and other unstable nascent transcripts.

Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs

Dec. 31, 2019

Nascent transcription assays, such as global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq), have uncovered a myriad of unstable RNAs being actively produced from numerous sites genome-wide. These transcripts provide a more complete and immediate picture of the impact of regulatory events. Transcription factors recruit RNA polymerase II, effectively...

Graphical abstract

Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions

Oct. 23, 2019

Transcriptional responses to external stimuli remain poorly understood. Using global nuclear run-on followed by sequencing (GRO-seq) and precision nuclear run-on sequencing (PRO-seq), we show that CDK8 kinase activity promotes RNA polymerase II pause release in response to interferon-γ (IFN-γ), a universal cytokine involved in immunity and tumor surveillance. The Mediator...

Primary transcriptional effects of TNF and glucocorticoids determined by GRO-seq.

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression.

Oct. 23, 2019

The glucocorticoid receptor (NR3C1, also known as GR) binds to specific DNA sequences and directly induces transcription of anti-inflammatory genes that contribute to cytokine repression, frequently in cooperation with NF-kB. Whether inflammatory repression also occurs through local interactions between GR and inflammatory gene regulatory elements has been controversial. Here, using...

Experimental timeline for ex vivo macrophage stimulation. Abbreviations: FFA, free fatty acid; LPS, lipopolysaccharide

Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties

Oct. 17, 2019

Mycobacterium vaccae (NCTC 11659) is an environmental saprophytic bacterium with anti-inflammatory, immunoregulatory, and stress resilience properties. Previous studies have shown that whole, heat-killed preparations of M. vaccae prevent allergic airway inflammation in a murine model of allergic asthma. Recent studies also demonstrate that immunization with M. vaccae prevents stress-induced exaggeration...

Phil Richardson, an author on a paper recently published in Nature, developed a love for bioinformatics in BioFrontiers' Robin Dowell's lab. His next move: pursuing a graduate degree in medical genomics.

Bioinformatics answers questions

June 5, 2015

Bioinformatics answers questions of cancer and career path Phil Richardson, an author on a paper recently published in Nature, developed a love for bioinformatics in BioFrontiers' Robin Dowell's lab. His next move: pursuing a graduate degree in medical genomics. At some point in school, we were taught that humans are...

Daniel Malmer is a second-year graduate student in the IQ Biology Interdisciplinary PhD program at BioFrontiers.

IQ Biology Blog: Computing Machinery and Mouse Genomes

March 10, 2015

I recently attended the 2014 Association for Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) with fellow IQ Biology student Joey Azofeifa and our advisor Robin Dowell. The conference had many interesting talks, ranging from theory-heavy explanations of algorithm improvements to very applied talks on using...

Mary Allen is a postdoc in Robin Dowell's lab at the BioFrontiers Institute.

Sie Fellows focused on quality of life in Down syndrome

July 10, 2014

Mary Allen holds up a valentine sent to her from a childhood friend. It sits in her cubicle where she is hard at work tearing apart genomic data looking for patterns. This friend, who has Down syndrome, is part of the reason that Allen, a postdoctoral researcher in Robin Dowell’s...