Author

J. D. Fernandes

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 3 Scientific Communication & Education· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:chromatin & epigenetic regulation· 2 Approach:experimental assay· 2 Research Focus:benchmarking· 1 Assay:ChIP-seq· 1 Research Focus:development & morphogenesis· 1 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

A. D. Frankel· 1 shared A. Haage· 1 shared A. J. Kozik· 1 shared A. S. Holehouse· 1 shared A. Sohota· 1 shared A. W. Bisson Filho· 1 shared B. Davis· 1 shared B. Jayaraman· 1 shared

Activity by Year

2018-2021 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 10 mutual co-author links

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1 shared paperEvolutionary Biology

A. D. Frankel

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4 papers

Recent·Most cited

Functional and Structural Segregation of Overlapping Helices in HIV-1

M. Safari, B. Jayaraman, S. Yang, C. Smith, J. D. Fernandes, A. D. Frankel

The paper investigates how overlapping genes in HIV-1 balance selective forces, finding functional segregation where each protein spaces its residues to accommodate the other's functional sites.

bioRxiv · Jul 15, 2021Evolutionary Biology

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome

M. Okhovat, K. A. Nevonen, B. Davis, P. Michener, S. Ward, M. Milhaven, L. Harshman, A. Sohota, J. D. Fernandes, S. R. Salama, R. J. O'Neill, N. Ahituv, K. R. Veeramah, L. Carbone

This study investigates the role of the lineage-specific LAVA retrotransposon in gibbon gene regulation, finding it overlaps with enhancer chromatin states and is associated with gene expression and selection.

bioRxiv · Apr 6, 2020Evolutionary Biology

Insights from a survey-based analysis of the academic job market

J. D. Fernandes, S. Sarabipour, C. T. Smith, N. M. Niemi, N. M. Jadavji, A. J. Kozik, A. S. Holehouse, V. Pejaver, O. Symmons, A. W. Bisson Filho, A. Haage

This study analyzes survey data from faculty job applicants to assess how various metrics correlate with hiring outcomes and highlights issues with the academic job application process.

bioRxiv · Dec 2, 2019Scientific Communication & Education

KRAB Zinc Finger Proteins coordinate across evolutionary time scales to battle retroelements

J. D. Fernandes, M. Haeussler, J. Armstrong, K. Tigyi, J. Gu, N. Filippi, J. Pierce, T. Thisner, P. Angulo, S. Katzman, B. Paten, D. Haussler, S. Salama

The paper examines the evolutionary arms race between KRAB Zinc Finger Proteins (KZNFs) and retrotransposable elements (RTEs), showing how KZNFs adapt to suppress RTEs over time.

bioRxiv · Sep 27, 2018 · PreprintEvolutionary Biology