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Ramu Anandakrishnan, PhD

Portrait of Ramaoorthi Anandakrishnan
Ramu Anandakrishnan, PhD
Assistant Professor for Biomedical Sciences
Department/Discipline: Biomedical Affairs and Research
Campus: Virginia
Office: Knollwood
Preferred First Name: Ramu
Email: Contact
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Research Capabilities

Research Capabilities: (1) A Computer Lab for the discovery of novel cancer genes and (2) a Bio-safety Level 2 Biochemistry Lab for experimentally investigating these cancer genes.

Research Interests

  1. We are developing bioinformatics algorithms for identifying potential cancer genes. The algorithms are based on analyzing genetic mutations and gene expression levels in tumor samples. Preliminary versions of the algorithm have identified several novel cancer genes that we are currently validating, experimentally. Two papers based on this research are currently in peer review.
  2. We are using the CRISPR/Cas9 gene editing protocol to investigate the effect of mutations in the cancer genes identified above. Experimental protocols include CRISPR gene editing, cell cultures, PCR, DNA/RNA sequencing, Western Blot, cell viability and proliferation assays, etc. Overall our research includes a broad range of subjects covering genomics, genetics, bioinformatics, identifying genes responsible for cancer and other genetic disorders, biomarker discovery, algorithm design, mathematical modeling, etc.

Biological organisms represent the most complex systems imaginable. Understanding how they function requires the knowledge of biology, chemistry and physics. Our computational biology and bioinformatics group integrates knowledge across disciplines to study biological systems with the goal of understanding the mechanisms underlying diseases.

Full List of Publications

Education

Year University Degree
2011 Virginia Tech PhD - Computer Science
1979 University of Maryland MBA - Finance
1977 Indian Institute of Technology BTech - Mechanical Engineering

 

Publications

Year Faculty Citation PMID
2021 Nicholas Kinney, Lin Kang, Ramu Anandakrishnan, Pawel Michalak, Harold "Skip" Garner

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, Harold "Skip" Garner

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

2020 Ramu Anandakrishnan, Harold "Skip" Garner, Nicholas Kinney

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.

 

32866178
2020 Ramu Anandakrishnan, Tiffany Carpenetti, Pawel Michalak, Lin Kang, Nicholas Kinney, Arben Santo, John Anstrom, Harold "Skip" Garner, 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, Harold "Skip" Garner

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, Robin Varghese, Nicholas Kinney, Harold "Skip" Garner

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, Nicholas Kinney, Harold "Skip" Garner

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 Nicholas Kinney, Lin Kang, Ramu Anandakrishnan, Robin Varghese, Pawel Michalak, Harold "Skip" Garner

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.

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, Nicholas Kinney, Harold "Skip" Garner

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
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, Nicholas Kinney, Harold "Skip" Garner

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

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