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Jason D Fernandes

Postdoctoral Scholar

Scientific Interests

My scientific interests revolve around the molecular details of evolution.

What changes - on a nucleotide and amino acid level - lead to drastic changes in phenotypes? More specifically, how does evolution create solutions to problems posed by novel selection pressures?

I am a postdoc in David Haussler's lab at UCSC. I recieved my PhD in Alan Frankel's Lab at UCSF.

Publications

Functional Segregation of Overlapping Genes in HIV.

Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. Cell. 2016; 167(7):1762-1773.e12.

Highlighted on Faculty of 1000 and GenomeWeb; In Top 5% of all articles in AltMetric

Oligomeric viral proteins: small in size, large in presence.

Jayaraman B, Smith AM, Fernandes JD, Frankel AD. Critical reviews in biochemistry and molecular biology. 2016; 51(5):379-394.

A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1.

Fernandes JD, Booth DS, Frankel AD. Wiley interdisciplinary reviews. RNA. 2016; 7(4):470-86.

The HIV-1 Rev response element: an RNA scaffold that directs the cooperative assembly of a homo-oligomeric ribonucleoprotein complex.

Fernandes J, Jayaraman B, Frankel A. RNA biology. 2012; 9(1):6-11.

Global landscape of HIV-human protein complexes

Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Nature. 2011; 481(7381):365-70.

Comment in Nat Rev Microbiol; Cited >300 times

Purification and characterization of HIV-human protein complexes.

Jäger S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ. Methods (San Diego, Calif.). 2011; 53(1):13-9.

Host cell factors in HIV replication: meta-analysis of genome-wide studies.

Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. PLoS pathogens. 2009; 5(5):e1000437.

Reduction of right medial pulvinar volume and neuron number in schizophrenia.

Byne W, Fernandes J, Haroutunian V, Huacon D, Kidkardnee S, Kim J, Tatusov A, Thakur U, Yiannoulos G. Schizophrenia research. 2007; 90(1-3):71-5.

Education

University of California, Santa Cruz & Howard Hughes Medical Institute

Postdoctoral Scholar, Genomics Institute

I am exploring how transposable elements can rewire existing gene regulatory networks to create novelty via dynamic and cell-type specific expression patterns. I am particularly interested in cases where protein regulators (a family of proteins known as KRAB Zinc Finger Proteins) of transposable elements have "domesticated" these selfish elements to perform important organismal biology.

University of California, San Francisco

PhD, Program in Pharmaceutical Science and Pharmacogenomics

I explored the ability of viruses to create novelty by creating entirely new proteins in existing ones using overlapped reading frames. I showed that HIV balances two overlapped genes by segregating protein functional motifs on the nucleotide level and that this can result in a viral population fitness advantage compared to encoding the genes separately. This work was the first study to experimentally decouple overlapped reading frames and to use deep mutational scanning techniques to comprehensively probe point-mutational space of these HIV genes.

Columbia University

BS, Chemical Engineering; Minor in Computer Science

I worked in the laboratories of Dr. Jingyue Ju (learning about Genomic Sequencing Technologies) and Dr. William Byne (learning about schizophrenia).