Katie Rothamel

Post-Doctoral Fellow

Cellular and Molecular Medicine

 

 

Summary

Katie received her B.S. in Neuroscience at Brown University in 2010. Afterwards she became a technician at Harvard Medical School in Dr. Christophe Benoist and Dr. Diane Mathis’s lab. There she worked on and was coordinator of the Immunological Genome (ImmGen) Project, a large multidisciplinary consortium of immunologists and computational biologists who are creating comprehensive gene expression analysis of the cell differentiation and activation of the immune system. In 2014, she started graduate school at Vanderbilt University in Dr. Manuel Ascano’s lab. In the Ascano Lab, she integrated both biochemical assays and next-generation sequencing approaches to gain a comprehensive understanding of how RNA-binding proteins regulate the expression of immune-relevant mRNAs.

 

Education

Ph.D. Biochemistry, Vanderbilt University, 2020

B.S. Neuroscience, Brown University, 2010

 

Contact

krothamel@ucsd.edu

Github, Research Gate, Google Scholar, LinkedIn

Publications

  • Samantha Lisy, Katherine Rothamel, and Manuel Ascano (2021). RNA binding Proteins as Pioneer Determinants of Infection: Protective, Proviral, or Both? Viruses, doi.org/10.3390/v13112172.

  • Katherine Rothamel, Sarah Arcos, Byungil Kim, Sam Lisy, Clara Reasoner, Neelanjan Mukherjee, and Manuel Ascano (2020). ELAVL1 primarily couples mRNA Stability with the 3’UTR of Interferon Stimulated Genes. Cell Reports, doi.org/10.1101/2020.08.24.263418.

  • Byungil Kim, Sarah Arcos, Katherine Rothamel, and Manuel Ascano (2020). Viral-cross linking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes. Nature Protocols, doi:10.1038/s41596-020-00429-6.

  • Byungil Kim, Sarah Arcos, Katherine Rothamel, and Manuel Ascano (2020). Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP. Molecular Cell, doi:10.1016/j.molcel.2020.04.013.

  • Jessica Vincent, Carolina Adura, Pu Gao, Antonio Luz, Lodoe Lama, Yasutomi Asano, Rei Okamoto, Toshihiro Imaeda, Jumpei Aida, Katherine Rothamel, Tasos Gogakos, Joshua Steinberg, Seth Reasoner, Kazuyoshi Aso, Thomas Tuschl, Dinshaw J Patel, J Fraser Glickman, and Manuel Ascano (2017). Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice. Nature Communications, doi:10.1038/s41467-017-00833-92.

  • Sara Mostafavi, Hideyuki Yoshida, Devapregasan Moodley, Hugo LeBoité, Katherine Rothamel, Towfique Raj, Chun Jimmie Ye, Nicolas Chevrier, Shen-Ying Zhang, Ting Feng, Mark Lee, Jean-Laurent Casanova, James D Clark, Martin Hegen, Jean-Baptiste Telliez, Nir Hacohen, Philip L De Jager, Aviv Regev, Diane Mathis, Christophe Benoist, and the Immunological Genome Project Consortium (2016). Parsing the Interferon Transcriptional Network and Its Disease Associations. Cell, doi:10.1016/j.cell.2015.12.032.

  • Towfique Raj, Katherine Rothamel, Sara Mostafavi, Chun Ye, Mark N Lee, Joseph M Replogle, Ting Feng, Michelle Lee, Natasha Asinovski, Irene Frohlich, Selina Imboywa, Alina Von Korff, Yukinori Okada, Nikolaos A Patsopoulos, Scott Davis, Cristin McCabe, Hyun-il Paik, Gyan P Srivastava, Soumya Raychaudhuri, David A Hafler, Daphne Koller, Aviv Regev, Nir Hacohen, Diane Mathis, Christophe Benoist, Barbara E Stranger, and Philip L De Jager (2014). Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science, doi:10.1126/science.1249547.

  • Towfique Raj, Joseph M Replogle, Katie Ryan, Lori Chibnik, Jimmie Ye, Sara Mostafavi, Mark Lee, Katherine Rothamel, Cristin Mccabe, Alina Von Korff, Elizabeth M Bradshaw, Denis Evans, David Bennett, Christophe Benoist, Barbara Stranger, And Philip De Jager (2014). Expression Qtl Analysis From Primary Immune Cells Identifies Novel Regulatory Effects Underlying Alzheimer's Disease Susceptibility. Alzheimer's & Dementia, doi:10.1016/J.Jalz.2014.04.290.

  • Jeffrey A Ericson, Pierre Duffau, Kei Yasuda, Adriana Ortiz-Lopez, Katherine Rothamel, Ian R Rifkin, Paul A Monach, and ImmGen Consortium. (2014). Gene Expression during the Generation and Activation of Mouse Neutrophils: Implication of Novel Functional and Regulatory Pathways. PLoS ONE, doi:10.1371/pone.0108553.

  • Sara Mostafavi, Adriana Ortiz-Lopez, Molly A Bogue, Kimie Hattori, Cristina Pop, Daphne Koller, Diane Mathis, Christophe Benoist, and The Immunological Genome Consortium (2014). Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains. The Journal of Immunology, doi:10.4049/jimmunol.1401280.

  • Towfique Raj, Katie J Ryan, Joseph M Replogle, Lori B Chibnik, L Rosenkrantz, Katherine Rothamel, Babara E Stranger, David A Bennett, Denis A Evans, Phil De Jager, and Elizabeth M Bradshaw (2014). CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility. Human Molecular Genetics, doi:10.1093/hmg.ddt666.

  • Tal Shay, Vladimir Jojic, Or Zuk, Katherine Rothamel, David Puyraimond-Zemmour, Ting Feng, Ei Wakamatsu, Christophe Benoist, Daphne Koller, Aviv Regev, and ImmGen Consortium (2013). Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc Natl Acad Sci USA, doi:10.1073/pnas.1222738110.

  • Ayla Ergun, Graeme Doran, James C Costello, Henry H Paik, James J Collins, Diane Mathis, Christophe Benoist, and The Immunological Genome Consortium (2013). Differential splicing across immune system lineages. Proc Natl Acad Sci USA, doi: 10.1073/pnas.13118391103.

  • Vladimir Jojic, Tal Shay, Katelyn Sylvia, Or Zuk, Xin Sun, Joonsoo Kang, Aviv Regev, Daphne Koller, Immunological Genome Project Consortium: Adam J Best, Jamie Knell, Ananda Goldrath, Vladimir Joic, Nadia Cohen, Patrick Brennan, Michael Brenner, Francis Kim, Tata Nageswara Rao, Amy Wagers, Tracy Heng, Jeffrey Ericson, Katherine Rothamel, Adriana Ortiz-Lopez, Diane Mathis, Christophe Benoist, Natalie A Bezman, Joseph C Sun, Gundula Min-Oo, Charlie C Kim, Lewis L Lanier, Jennifer Miller, Brian Brown, Miriam Merad, Emmanuel L Gautier, Claudia Jakubzick, Gwendalyn J Randolph, Paul Monach, David A Blair, Michael L Dustin, Susan A Shinton, Richard R Hardy, David Laidlaw, Jim Collins, Roi Gazit, Derrick J Rossi, Nidhi Malhotra, Taras Kreslavsky, Anne Fletcher, Kutlu Elpek, Angelique Bellemarte-Pelletier, Deepali Malhotra, and Shannon Turley (2013). Identification of transcriptional regulators in the mouse immune system. Nature Immunology, doi: 10.1038/ni.2587.
    Michael Mingueneau, Taras Kreslavsky, Daniel Gray, Tracy Heng, Richard Cruse, Jeffrey Ericson, Sean Bendall, Matthew H Spitzer, Garry P Nolan, Koichi Kobayashi, Harald von Boehmer, Diane Mathis, Christophe Benoist, and The Immunological Genome Consortium (2013). The transcriptional landscape of αβ T cell differentiation. Nature Immunology doi: 10/1038/ni.2590.
    Andrew S P Lim, Anne-Marie Chang, Joshua M Shulman, Towfique Raj, Lori B Chibnik, Sean W Cain, Katherine Rothamel, Christophe Benoist, Amanda J Myers, Charles A Czeisler, Aron S Buchman, David A Bennett, Jeanne F Duffy, Clifford B Saper, and Philip L De Jager (2012). A common polymorphism near PER1and the timing of human behavioral rhythms. Annals of Neurology, doi: 10.1002/ana.23636.