Research Capabilities
(1) A Computer Lab consisting of six servers, including one with four NVIDIA V100 GPUs for machine learning and high performance computing. (2) A Biosafely Level 2 Biochemistry Lab, including CRISPR/Cas9 gene editing capabilities, for the in vitro investigation of the molecular mechanisms of cancer.
Research Interests
Investigating the role of clonal hematopoitic (CH) mutation (clonally expanded mutations in immune cells) on the genesis and progression of cancer. Using Machine Learning algorithms, we have developed a genomic screening panel (“liquid biopsy”) for lung cancer based on CH mutations. We are collaborating with VT Carilion Clinic to clinically validate this screening panel. Using CRISPR/Cas9 gene editing and cDNA clones we are also investigating the molecular mechanisms by which these CH mutations may affect anti-tumor immune function and tumor growth.
Education
| Year | University | Degree |
|---|---|---|
| 2011 | Virginia Tech | PhD - Computer Science |
| 1979 | University of Maryland | MBA - Finance |
| 1977 | Indian Institute of Technology | BTech - Mechanical Engineering |
Activities
- Member, American Association for Cancer Research (AACR); Member, American Association for the Advancement of Science (AAAS)
- Member, American Association of Cancer Research
- Member, Biophysical Society
Selected Publications
| Year | Faculty | Citation | PMID |
|---|---|---|---|
| 2023 | Ramu Anandakrishnan | Anandakrishnan R, Zyvoloski IJ, Zyvoloski LR, Opoku NK, Dai A, Antony V. Potential immunosuppressive clonal hematopoietic mutations in tumor infiltrating immune cells in breast invasive carcinoma. Sci Rep. 2023 Aug 12:13(1):13131. doi: 10.1038/s41598-023-40256-9. PMID: 37573441. |
37573441 |
| 2023 | Ramu Anandakrishnan | Dash S, Monil MAH, Yin J, Anandakrishnan R, Wang F. Distributing Simplex-Shaped Nested for-Loops to Identify Carcinogenic Gene Combinations. Proceeding of 2023 IEEE International Parallel and Distributed Processing Symposium. 2023, pp. 974-984, doi: 10.1109/IPDPS54959.2023.00101. |
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| 2023 | Ramu Anandakrishnan | Montano H, Anandkrishnan R, Carruthers VB, Gaji RY. TgTKL4 Is a Novel Kinase That Plays an Important Role in Toxoplasma Morphology and Fitness. mSphere. 2023 Apr 20;8(2):e0064922. DOI: 10.1128/msphere.00649-22. PMID: 36786615. |
36786615 |
| 2022 | Ramu Anandakrishnan, A Tobey, Blaise Costa | Anandakrishnan R, Tobey H, Nguyen S, Sandoval O, Klein BG, Costa BM. Cranial manipulation affects cholinergic pathway gene expression in aged rats. J Osteopath Med. 2022 Jan 10;122(2):95-103. doi: 10.1515/jom-2021-0183. PMID: 34995434. |
34995434 |
| 2022 | Ramu Anandakrishnan | Sharp AK, Newman D, Libonate G, Borns-Stern M, Bevan AM, Anandakrishnan A. Biophysical insights into OR2T7: Investigation of a potential prognostic marker for glioblastoma. Biophys J. 2022 Oct 4;121(19):3706-3718. doi: 10.1016/j.bpj.2022.05.009. PMID: 35538663. |
35538663 |
| 2021 | Lin Kang, Ramu Anandakrishnan | Kinney N, Kang L, Bains H, Lawson E, Husain M, Husain K, Sandhu I, Shin Y, Carter JK, Anandakrishnan R, Michalak P, Garner H. Ethnically biased microsatellites contribute to differential gene expression and glutathione metabolism in Africans and Europeans. PLoS One. 2021 Mar 25;16(3):e0249148. doi: 10.1371/journal.pone.0249148. eCollection 2021. PMID: 33765058. |
33765058 |
| 2021 | Ramu Anandakrishnan | Dash S, Al-Hajri Q, Feng W-C, Garner HR, Anandakrishnan R. Scaling Out a Combinatorial Algorithm for Discovering Carcinogenic Gene Combinations to Thousands of GPUs. In 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS), pp. 837-846. IEEE, 2021. https://ieeexplore.ieee.org/abstract/document/9460537, DOI: 10.1109/IPDPS49936.2021.00093 |
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| 2020 | Ramu Anandakrishnan | Kinney N, Hickman M, Anandakrishnan R, Garner HR. Crossing complexity of space-filling curves reveals entanglement of S-phase DNA. PLoS One. 2020 Aug 31;15(8):e0238322. PMID: 32866178.
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32866178 |
| 2020 | Ramu Anandakrishnan, Tiffany Carpenetti, Lin Kang, Robin Varghese | Anandakrishnan R, Carpenetti TL, Samuel P, Wasko B, Johnson C, Smith C, Kim J, Michalak P, Kang L, Kinney N, Santo A, Anstrom J, Garner HR, Varghese RT. DNA sequencing of anatomy lab cadavers to provide hands-on precision medicine introduction to medical students. BMC Med Educ. 2020 Nov 16;20(1):437. PMID: 33198737. |
33198737 |
| 2020 | Ramu Anandakrishnan | Al Hajri Q, Dash S, Feng WC, Garner HR, Anandakrishnan R.Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU. Sci Rep. 2020 Feb 6;10(1):2002. PMID: 32029803. |
32029803 |
| 2019 | Ramu Anandakrishnan | Anandakrishnan R, Izadi S, Onufriev AV. Why computed protein folding landscapes are sensitive to the water model. Journal of chemical theory and computation. 2019 Jan 8;15(1):625-636. PMID: 30514080. |
30514080 |
| 2019 | Lin Kang, Pawel Michalak, Ramu Anandakrishnan, Robin Varghese | Kinney N, Titus-Glover K, Wren JD, Varghese RT, Michalak P, Liao H, Anandakrishnan R, Pulenthiran A, Kang L, Garner HR. CAGm: a Repository of Germline Microsatellite Variations in the 1000 Genomes Project, Nucleic Acids Res. 2019 Jan 8;47(D1):D39-D45. PMID: 30329086. |
30329086 |
| 2019 | Ramu Anandakrishnan, Robin Varghese | Dash S, Kinney N, Varghese R, Garner H, Feng W, Anandakrishnan R. Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations. Sci Rep. 2019 Jan 30;9(1):1005. PMID: 30700767. |
30700767 |
| 2019 | Ramu Anandakrishnan, Robin Varghese | Anandakrishnan R, Varghese R, Kinney N, Garner HR. Estimating the number of genetic mutations (hits) required for tumorigenesis based on the distribution of somatic mutations. PLoS Comput Biol. 2019 Mar 7;15(3):e1006881. PMID: 30845172. |
30845172 |
| 2019 | Lin Kang, Ramu Anandakrishnan, Robin Varghese | Kinney N, Kang L, Eckstrand L, Pulenthiran A, Samuel P, Anandakrishnan R, Varghese RT, Michalak P, Garner HR. Abundance of ethnically biased microsatellites in human gene regions. PLoS One. 2019 Dec 12;14(12):e0225216. PMID: 31830051. |
31830051 |
| 2019 | Ramu Anandakrishnan | Fenley A, Anandakrishnan R, Kidane Y, Adamas D, Onufriev AV. The nucleosome: from structure to function through physics. Biopolym. Cell. 2019; 35(3):171-171. |
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| 2018 | Ramu Anandakrishnan | Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV. Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core. Epigenetics & chromatin. 2018 Mar 16;11):11. PMID: 29548294. |
29548294 |
| 2017 | Ramu Anandakrishnan | Anandakrishnan R, Zuckerman DM. Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio. PloS one. 2017 Mar 20;12(3):e0173500. PMID: 28319179. |
28319179 |
| 2017 | Ramu Anandakrishnan, Robin Varghese | Kinney N, Varghese RT, Anandakrishnan R, Garner HR. ZDHHC3 as a risk and mortality marker for breast cancer in African American Women. Cancer Informatics. 2017;16:1–6. PMID: 29276372. |
29276372 |
| 2016 | Ramu Anandakrishnan | Anandakrishnan R, Zhang Z, Donovan-Maiye R, Zuckerman DM. Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process. Proceedings of the National Academy of Sciences. 2016 Oct 4;113(40):11220-11225. PMID: 27647911. |
27647911 |
| 2016 | Ramu Anandakrishnan | Izadi S, Anandakrishnan R, Onufriev AV. Implicit solvent model for million-atom atomistic simulations: Insights into the organization of 30-nm chromatin fiber. Journal of chemical theory and computation. 2016 Dec 13;12(12):5946-5959. PMID: 27748599. |
27748599 |