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Karthik Gangavarapu, PhD

Institute Investigator

Department of Translational Medicine

Karthik Gangavarapu, PhD

Research Focus

I have a broad background in computational biology with a focus on infectious disease research. My academic journey, spanning graduate and postdoctoral experiences, has been marked by spearheading large-scale collaborative efforts. These efforts were aimed at leveraging phylogenetic and phylodynamic methodologies to unravel the transmission dynamics of viruses responsible for rapidly evolving outbreaks, including Zika, Ebola, and SARS-CoV-2. I have contributed to the field of genomic epidemiology through the development of widely used software. These tools are designed for the analysis of genomic sequencing data to assemble viral consensus genomes and facilitate expansive genomic surveillance. My work also encompasses the development of efficient computational libraries that harness the power of specialized hardware, such as graphics processing units, for statistical phylogenetics.

Select Publications

  • Gangavarapu, Karthik; Ji, Xiang; Baele, Guy; Fourment, Mathieu; Lemey, Philippe; Iv, Frederick A Matsen; Suchard, M A. Many-core algorithms for high-dimensional gradients on phylogenetic trees. ArXiv 2023.

  • Gangavarapu, Karthik; Latif, Alaa Abdel A.; Mullen, Ju L.; Alkuzweny, Manar; Hufbauer, Emory; Tsueng, Ginger; Haag, Emily; Zeller, Mark; Aceves, Christine M.; Zaiets, Karina; Cano, Marco; Zhou, Xinghua; Qian, Zhongchao; Sattler, Rachel; Matteson, Nathanie L.; Levy, Joshua I.; Lee, Raphael T C; Freitas, Lucas; Maurer-Stroh, Sebastian; Suchard, M A.; Wu, Chunlei; Su, Andrew I.; Andersen, Kristian G.; Hughes, Laura D. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. 2023, 20, 512-522.

  • Zeller, Mark; Gangavarapu, Karthik; Anderson, Catelyn; Smither, Allison R.; Vanchiere, John A.; Rose, Rebecca; Snyder, Daniel J.; Dudas, Gytis; Watts, Alexander; Matteson, Nathanie L.; Robles-Sikisaka, Refugio; Marshall, Maximilian; Feehan, Amy K.; Sabino-Santos, Gilberto; Bell-Kareem, Antoinette R.; Hughes, Laura D.; Alkuzweny, Manar; Snarski, Patricia; Garcia-Diaz, Julia; Scott, Rona S.; Melnik, L I.; Klitting, Raphaëlle; McGraw, Michelle; Belda-Ferre, Pedro; DeHoff, Peter; Sathe, Shashank; Marotz, Clarisse; Grubaugh, Nathan D.; Nolan, David J.; Drouin, Arnaud C.; Genemaras, Kaylynn J.; Chao, Karissa; Topol, Sarah; Spencer, Emily; Nicholson, Laura; Aigner, Stefan; Yeo, Gene W.; Farnaes, Lauge; Hobbs, Ch A.; Laurent, Louise C.; Knight, Rob; Hodcroft, Emma B.; Khan, Kamran; Fusco, Dahle N.; Cooper, Vaughn S.; Lemey, Phillipe; Gardner, Lauren; Lamers, Susanna L.; Kamil, Jeremy P.; Garry, Robert F.; Suchard, M A.; Andersen, Kristian G. Emergence of an early SARS-CoV-2 epidemic in the United States. 2021, 184, 4939-4952.e15.

  • Washington, Nico L.; Gangavarapu, Karthik; Zeller, Mark; Bolze, Alexandre; Cirulli, Elizabe T.; Schiabor Barrett, Kelly M.; Larsen, Brendan B B.; Anderson, Catelyn; White, Simon; Cassens, Tyler; Jacobs, Sharoni; Levan, Geraint; Nguyen, Jason; Ramirez, Ji M.; Rivera-Garcia, Charlotte; Sandoval, Efren; Wang, Xueqing; Wong, David; Spencer, Emily; Robles-Sikisaka, Refugio; Kurzban, Ezra; Hughes, Laura D.; Deng, Xianding; Wang, Candace; Servellita, Venice; Valentine, Holly; De Hoff, Peter; Seaver, Phoebe; Sathe, Shashank; Gietzen, Kimberly; Sickler, Brad; Antico, Jay; Hoon, Kelly; Liu, Jingtao; Harding, Aaron; Bakhtar, Omid; Basler, Tracy; Austin, Brett; MacCannell, Duncan; Isaksson, Magnus; Febbo, Phillip G.; Becker, David; Laurent, Marc; McDonald, Eric; Yeo, Gene W.; Knight, Rob; Laurent, Louise C.; de Feo, Eileen; Worobey, Michael; Chiu, Charles Y.; Suchard, M A.; Lu, James T.; Lee, William; Andersen, Kristian G. Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. 2021, 184, 2587-2594.e7.

  • Grubaugh, Nathan D.; Saraf, Sharada; Gangavarapu, Karthik; Watts, Alexander; Tan, Amanda L.; Oidtman, Rachel J.; Ladner, Jason T.; Oliveira, Glenn; Matteson, Nathanie L.; Kraemer, Moritz U G; Vogels, Chantal B F; Hentoff, Aaron; Bhatia, Deepit; Stanek, Danielle; Scott, Blake; Landis, Vanessa; Stryker, Ian; Cone, Ma R.; Kopp, Edgar W.; Cannons, Andrew C.; Heberlein-Larson, Lea; White, Stephen; Gillis, Leah D.; Ricciardi, Michael J.; Kwal, Jaclyn; Lichtenberger, Paola K.; Magnani, Diogo M.; Watkins, Dav I.; Palacios, Gustavo; Hamer, Davidson H.; Gardner, Lauren M.; Perkins, T A.; Baele, Guy; Khan, Kamran; Morrison, Andrea; Isern, Sharon; Michael, Scott F.; Andersen, Kristian G. Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic. 2019, 178, 1057-1071.e11.

  • Grubaugh, Nathan D.; Gangavarapu, Karthik; Quick, Joshua; Matteson, Nathanie L.; De Jesus, Jaqueline G.; Main, Bradley J.; Tan, Amanda L.; Paul, Lauren M.; Brackney, Doug E.; Grewal, Saran; Gurfield, Nikos; Van Rompay, Koen K A; Isern, Sharon; Michael, Scott F.; Coffey, Lark L L.; Loman, Nicholas J.; Andersen, Kristian G. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome biology 2019, 20, 8.
Groundbreaking Science.
Life-changing Medicine.