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Somaye Hashemifar
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Bio
- I am a postdoctoral researcher at Columbia University working with Yufeng Shen and Wendy K. Chung. I recieved my PhD in Computer science at TTI-Chicago, a philanthropically endowed academic institute located in the campus of the University of Chicago
under the supervision of Prof. Jinbo Xu.
My research interests are analysis of large scale data with Machine Learning/Deep Learning techniques. I am on the job market! - Predicting protein-protein interactions through sequence-based deep learning
with Behnam Neyshabur, Aly K Khan, and Jinbo Xu
Bioinformatics 34.17 (2018): i802-i810. -
Novel candidate genes in esophageal atresia/tracheoesophageal atresia identified by exome sequencing
with Jiayao Wang, Priyanka R. Ahimaz, Julie Khlevner, et al.
under review - Differential cell-intrinsic regulations of germinal center B and T cells by miR-146a and miR-146b
with Sunglim Cho, Hyang-Mi Lee, I-Shing Yu, et al.
Nature communications 9.1 (2018): 2757. -
Chemokine expression in the early response to injury in human airway epithelial cells
with Bing Xie, Bharathi Laxman, Randi Stern, et al.
PloS one 13, no. 3 (2018): e0193334. - Computational prediction and analysis of protein-protein interaction networks
PhD thesis (2017). - Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks
with Mark D'Souza, Dinanath Sulakhe, Sheng Wang, et al.
Biological Networks and Pathway Analysis. Humana Press, New York, NY (2017): 85-99. - Excessive expression of miR-27 impairs Treg-mediated immunological tolerance
with Cruz Leilani O., Cheng-Jang Wu, Sunglim Cho, et al.
The Journal of Clinical Investigation 127, no. 2 (2017): 530 - ModuleAlign: Module-based global alignment of protein-protein interaction networks
with Jianzhu Ma, Hammad Naveed, Stefan Canzar, and Jinbo Xu.
ECCB 2016 (oral presentation)
Bioinformatics 32.17 (2016): i658-i664. - Joint alignment of multiple protein-protein interaction networks via convex optimization
with Qixing Huang, and Jinbo Xu
Recomb 2016 (oral presentation)
Journal of Computational Biology 23.11 (2016): 903-911. - Pseudomonas Aeruginosa Flagellin Stimulates Broad Gene Expression In Human Airway Epithelial Cells That Is Mitigated By Concurrent Treatment With Azithromycin
with White, Steven R., Bharathi Laxman, Bingqing Xie, et al.
In A40. EPITHELIAL REGULATION OF INFLAMMATION, pp. A1482-A1482. American Thoracic Society (2016)
- Excessive miR-27 expression impairs regulatory T cell-mediated immunological tolerance
with Cruz Leilani O., Sunglim Cho, Cheng-Jang Wu, et al.
The Journal of Immunology 196, no. 1 Supplement (2016): 127-5 - Joint inference of tissue-specific networks with a scale free topology
with Behnam Neyshabur, and Jinbo Xu
Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on. IEEE (2015)
- Lynx: A Knowledge Base and an Analytical Workbench for Integrative Medicine
with Dinanath Sulakhe, Bingqing Xie, Andrew Taylor, et al.
Nucleic acids research (2015): gkv1257.
- HubAlign: An accurate and efficient method for global alignment of protein-protein interaction networks
with Jinbo Xu
ECCB 2014 (oral presentation)
Bioinformatics 30.17 (2014): i438-i444
Also accepted as a poster by NetBio SIG 2014.
- Analysis of tissue-specific co-expression networks
with Daniela Boernigen, Natalia Maltsev and Jinbo Xu
NetBio SIG 2014 (Poster).
- NETAL: a new graph-based method for global alignment of protein-protein interaction networks
with Behnam Neyshabur, Ahmadreza Khadem, and Seyed Shahriar Arab
Bioinformatics 29.13 (2013): 1654-1662
- Genetic algorithm for dyad pattern finding in DNA sequences
with Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdi Sadeghi, et al.
Genes & Genetic Systems, 84: 81-93 (2009)
- PSOMF: An algorithm for pattern discovery using PSO
with Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdi Sadeghi, et al.
Proceedings of the Third IAPR International Conferences on Pattern Recognition in Bioinformatics, Melbourne Australia, 61-72, (2008).
Publication
Software
- DPPI: It uses a convolutional neural network to predict PPI interactions by using only the protein sequences.
- ConvexAlign: It finds a global alignment between multiple input PPI networks by convex optimization of a scoring function composed of sequence similarity, topological score, and interaction conservation score.
- HubAlign: A software for the alignment of protein-protein interaction networks that is based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information.
- NETAL: It uses a greedy method, based on the alignment scoring matrix, which is derived from both biological and topological information of input networks to find the best global network alignment. The running time of NETAL is much less than other available methods.
- Research at university of Chicago's hospital (2015-2016)
Project: Using different pre-designed tools such as WGCNA and Affymetrix Expression Console for analysis of RNA expression data of colon cancer patients
with Prof. Nikolai Khodarev , and Dr. Natalia Maltsev - Research at Computational Institute at university of Chicago (2012-2014)
Project: Applying a Gaussian model for reconstructing tissue specific network, Using R packages for analysis of gene expression data of Asthma patients
with Prof. Steve White, and Dr. Natalia Maltsev - Research at Institute of Biochemistry and Biophysics (IBB), University of Tehran (2010-2011)
Project: Developing a computational method for alignment of protein-protein Interaction networks
with Prof. Bahram Goliaei - Reviewer for IEEE/ACM Transactions on Computational Biology and Bioinformatics
- Reviewer for BMC Bioinformatics
- Reviewer for RECOMB conference 2016
- Reviewer for Engineering in Medicine and Biology Conference
- I like running. Sometimes, I run half marathon ;)
- I enjoy backpacking and mountain climbing. I've done off-trail backpacking in Alaska and stood on top of Damavand, the tallest mountain of Iran (about 18,400 ft).