Sahar Al Seesi

Visiting Assistant Professor of Computer Science

Contact & Office Hours

Ford Hall 344

413-585-1744

Education

Ph.D., University of Connecticut

M.S.A., Miami University

B.Sc., American University of Cairo

Biography

Sahar Al Seesi’s research interest is in bioinformatics. She works on developing algorithms to analyze next-generation sequencing data. Al Seesi works on various interrelated problems, including RNA transcriptome reconstruction, allele specific isoform expression estimation, gene differential expression and cancer specific mutation identification. Tackling each of these problems requires employing a combination of computational approaches such as machine learning, grammatical modeling, statistical analysis, parallel algorithms, dynamic programming and expectation maximization algorithms.


Selected Publications

Journals and Papers

Duan, J., Zhang, M., Flock, K., Al Seesi, S., Mandoiu, I., Jones, A., Johnson, E., Pillai, S., Hoffman, M., McFadden, K., Jiang, H., Reed, S., Govoni, K., Zinn, S., Jiang, Z., Tian, X. Effects of Maternal Nutrition on the Expression of Genomic Imprinted Genes in Ovine Fetuses, Epigenetics, 2018

Baumgartner, M., Olthof, A.M.,  Aquino, G.S., Hyatt, K.C., Lemoine, C., Drake, K.,  Sturrock, N., Nguyen, N., Al Seesi, S., Kanadia, R.N. Minor spliceosome inactivation causes microcephaly due to cell cycle defects and death of self-amplifying radial glial cells, Development 145(17), 2018

Mandric, I., Temate-Tiagueu, Y., Shcheglova, T., Al Seesi, S., Mathew, Zelikovsky, A., Mandoiu, I.I., Fast Bootstrapping-Based Estimation of Confidence Intervals of Expression Levels and Differential Expression from RNA-Seq Data, Bioinformatics 33(20):3302–3304, 2017.

Al Seesi, S., Mohapatra, A.D., Pawashe, A., Mandoiu, I.I., Duan, F., Finding Neoepitopes in Mouse Models of Personalized Cancer Immunotherapy, Frontiers in Biology 11:366-375, 2016.

Karunakaran, D.K.P., Al Seesi, S., Banday, A.R., Baumgartner, M., Olthof, A., Lemoine, C., Mandoiu, I.I., Kanadia, R.N., Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development , BMC Genomics 17(Suppl 5):495, 477-492, 2016

Baumgartner, M., Lemoine, C., Al Seesi, S., Karunakaran,D.K.R., Sturrok, N., Banday, A.R., Kilcollins, A.,M., Mandoiu, I., Kanadia, R.N. Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons, Developmental Neurobiology 75(9):895-907, 2015.

Banday A.R,, Baumgartner, M., Al Seesi, S., Karunakaran, D.K.P., Venkatesh, A., Congdon, S., Lemoine, C., Kilcollins, A.M., Mandoiu, I.I., Punzo, C., Kanadia, R.N., Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons, Cell Cycle 13(16), 2526-2541, 2014

Duan, F., Duitama, J., Al Seesi, S., Ayres, C.M., Corcelli, S.A., Pawashe, A.P., Blanchard, T., McMahon, D., Sidney, J., Sette, A., Baker, B.M., Mandoiu, I.I., Srivastava, P.K., Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. J Exp Med. 2014.

Al Seesi, S., Temate-Tiagueu, Y., Zelikovsky, A., Mandoiu, I., Bootstrapping-based differential gene expression analysis for RNA-Seq data with and without replicates, BMC Genomics, 15 Suppl 8:S2., 2014.