Highlights

Network Publications

Diversifying the Genomic Data Science Research Community

Our first publication is now out! Preview the abstract below and find the open access paper here: https://genome.cshlp.org/content/early/2022/07/18/gr.276496.121

Abstract

Over the past 20 years, the explosion of genomic data collection and the cloud computing revolution have made computational and data science research accessible to anyone with a web browser and an internet connection. However, students at institutions with limited resources have received relatively little exposure to curricula or professional development opportunities that lead to careers in genomic data science. To broaden participation in genomics research, the scientific community needs to support these programs in local education and research at underserved institutions (UIs). These include community colleges, historically Black colleges and universities, Hispanic-serving institutions, and tribal colleges and universities that support ethnically, racially, and socioeconomically underrepresented students in the United States. We have formed the Genomic Data Science Community Network to support students, faculty, and their networks to identify opportunities and broaden access to genomic data science. These opportunities include expanding access to infrastructure and data, providing UI faculty development opportunities, strengthening collaborations among faculty, recognizing UI teaching and research excellence, fostering student awareness, developing modular and open-source resources, expanding course-based undergraduate research experiences (CUREs), building curriculum, supporting student professional development and research, and removing financial barriers through funding programs and collaborator support.

Member Highlights

Diné College School of STEM Professor Awarded NIH-NIGMS-SEPA Award to run “CONVOY: a cultural approach of Navajo youth to biomedical sciences”

GDSCN Member Shazia Tabassum Hakim, Ph.D., Diné College received a Science Education Partnership Award from the National Institute of General Medical Sciences (NIGMS) to identify complementary strategies that link traditional Navajo epistemologies with modern scientific practices to motivate Diné College, Navajo Nation’s high school and Junior high school students to study and pursue careers in Biomedical Sciences and related fields.

Students in the field to perform research. [source]

Dr. Maria Alvarez teaching students in the lab. [source]

El Paso Community College awarded Rise to the Challenge Bridge to Health and Bioinformatics

Through the efforts of GDSCN Member Maria Alvarez, Ph.D., El Paso Community College (EPCC) was awarded the Rise to the Challenge Bridge to Health and Bioinformatics through the new T34 Bridges to the Baccalaureate for a total of $1,313,900 over five years. EPCC will be providing significant matching funds.

Dr. Sourav Roy and Dr. Michael Schatz awarded contract for NIH Cloud Platforms Interoperability

GDSCN Members Sourav Roy, Ph.D. and Michael Schatz, Ph.D. were awarded a contract titled "AnVIL/Velsera-CGC interoperability project to study the genetic and transcriptomic contributions towards Hispanic colorectal cancer health disparities". This work is funded under the NIH Cloud Platform Interoperability (NCPI) effort, that will drive forward implementation of technical standards to enable scientific analysis.

Faculty Feature: Dr. Karla Fuller, Associate Professor of Biology and Program Coordinator of Science

In 2021, GDSCN Member Karla Fuller, Ph.D. was interviewed for the Guttman Community College Faculty Feature. She begins by saying: “More than anything, I want our students to know that they can succeed in science and math. They don’t have to pursue it, but I don’t want them to think that it’s not for them for any particular reason, except [if they don’t choose it.] If they want to, they can be good at it, or they can be interested in it… I just want them to feel like they belong. That it’s for them, if they want it.”

Check out the full feature here: https://guttman.cuny.edu/2021/04/19/faculty-feature-dr-karla-fuller-associate-professor-of-biology-and-program-coordinator-of-science/.

Dr. Karla Fuller teaching students in the lab. [source]

Clovis Community College celebrates Dr. Rosa Alcazar. [source]

Dr. Rosa Alcazar, corresponding author on paper to increase student access to genomics data science

GDSCN Member Rosa Alcazar, Ph.D. was recognized by Clovis Community College for her work to bring genomic data science as a field and potential career path to a greater visibility for students. She launched "Science Talks" open to the campus and teaches a course on Research in Genomics.

Read the full story here: https://www.cloviscollege.edu/news/2022/ccc-biology-instructor-dr-rosa-alcazar-corresponding-author-n-paper-to-increase-student-access-to-genomics-data-science.html.

Dr. Shazia Tabassum Hakim Publishes Article with Cold Springs Harbor Laboratory Press in Genome Research

GDSCN Member Shazia Tabassum Hakim, Ph.D. was recognized by Diné College for the publication “Diversifying the genomic data science research community” in the Cold Spring Harbor Laboratory press journal, Genome Research.

Member Publications

Direct and indirect gene repression by the ecdysone cascade during mosquito reproductive cycle

Here we highlight a recent publication by GDSCN Member Sourav Roy, Ph.D. Preview the abstract below and find the article here: https://www.pnas.org/doi/abs/10.1073/pnas.2116787119

Abstract

Hematophagous mosquitoes transmit devastating human diseases. Reproduction of these mosquitoes is cyclical, with each egg maturation period supported by a blood meal. Previously, we have shown that in the female mosquito Aedes aegypti, nearly half of all genes are differentially expressed during the postblood meal reproductive period in the fat body, an insect analog of mammalian liver and adipose tissue. This work aims to decipher how transcription networks govern these genes. Bioinformatics tools found 89 putative transcription factor binding sites (TFBSs) on the cis-regulatory regions of more than 1,400 differentially expressed genes. Putative transcription factors that may bind to these TFBSs were identified and used for the construction of temporally coordinated regulatory networks. Further molecular biology analyses have uncovered mechanisms of direct and indirect negative transcriptional regulation by the steroid hormone 20-hydroxyecdysone (20E) through the ecdysone receptor (EcR). Genes within the two groups, early genes and late mid-genes, have distinctly different expression profiles. However, both groups of genes show lower expression at the high titers of 20E and are down-regulated by the 20E/EcR cascade by different molecular mechanisms. Transcriptional repression of early genes is indirect and involves the classic 20E pathway with ecdysone-induced protein E74 functioning as a repressor. Late mid-genes are repressed directly by EcR that recognizes and binds a previously unreported DNA element, different from those utilized in the 20E-mediated gene activation, within the regulatory regions of its target genes and recruits Mi2 that acts as a corepressor, initiating chromatin condensation.