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<span>about me</span>
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I will be joining Fred Hutchinson Cancer Research Center as an Assitant Professor in the Basic Sciences Division and Translation Data Sciences IRC in January 2021. Please see <b><a href="https://research.fhcrc.org/setty/en.html">setty-lab.org</a></b> for more information and updates.
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I am a post-doctoral fellow in the <a href="https://www.mskcc.org/research/ski/labs/dana-pe-er">Dana Pe'er lab</a> in <a href="https://www.mskcc.org/research/ski/programs/computational-biology">Computational & Systems Biology</a> at <a href="https://www.mskcc.org/research/ski">Sloan Kettering Institute</a>. I am fascinated by the complex mechanisms that drive lineage decisions in development and differentiation. In a quest to understand these mechanisms, I have developed computational methods for modeling trajectory detection using single-cell data and regulatory networks using large scale -omics datasets. As a post-doctoral researcher, I developed methods for <a href="https://www.nature.com/articles/nbt.3569">detecting bifurcations</a> in differentiation, <a href="https://www.nature.com/articles/s41587-019-0068-4">modeling continuities</a> in cell fate choices and <a href="https://www.nature.com/articles/s41586-019-1127-1">harmonizing</a> developmental datasets measured at discrete time points. In an extensive and gratifying collaboration with the <a href="https://www.mskcc.org/research/ski/labs/anna-katerina-hadjantonakis">Dr. Kat Hadjantonakis lab</a>, I helped contributed to a deep characterization of <a href="https://www.nature.com/articles/s41586-019-1127-1">spatio-temporal trajectories</a> underlying endoderm emergence during mouse development (<a href="http://endoderm-explorer.com">Data explorer</a>).
</p>
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<p align="justify">
I received my PhD in Systems Biology under the supervision of <a href="https://www.mskcc.org/research/ski/labs/christina-leslie">Dr. Christina Leslie</a> at <a href="http://pbsb.med.cornell.edu">Weill Cornell Graduate School</a>. My doctoral research focused on building methods to integrate diverse genomic datasets to infer regulatory changes in differentiation and disease. As part of my graduate work, I developed <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004271">k-mer models</a> for determining TF sequence preferences and developed regression models to identify regulatory drivers in <a href="https://www.nature.com/ng/journal/v47/n11/abs/ng.3402.html">differentiation</a> and <a href="http://msb.embopress.org/cgi/pmidlookup?view=long&pmid=22929615">disease</a>.
</p>
<br/>
<p align="justify">
I received a Masters degree in <a href="http://www.cs.columbia.edu/education/ms/">Computer Science </a> from Columbia University specializing in Computational Biology and an undergraduate degree in Computer Science from <a href="https://www.nitk.ac.in">National Institute of Technology Karnataka</a>. I have worked at Celsius Therapeutics as a Senior Scientist in Computational Biology.
</p>
<br/>
<p align="justify">
Over the course of my training, I have developed a fascination for understanding biology at a molecular level using high dimensional, high throughput data and I have worked on a variety of biological systems spanning embryonic development, differentiation, immunology and cancer biology.
</p>
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<h2>
Publications
</h2>
<span>publications</span>
</div>
<ol>
<li><i>The emergent landscape of the mouse gut endoderm at single-cell resolution</i>.<br/>Nowotschin S*, <b>Setty M*</b>, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Katerina-Hadjantonakis A, Pe'er D.
<a href="https://www.nature.com/articles/s41586-019-1127-1">Nature</a>. April 2019.
</li>
<br/>
<li><i>Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States.</i><br/>Wei SC, Sharma R, Anang NAS, Levine JH, Zhao Y, <b>Setty M</b>, Manusco JJ, Sharma P,Wang J, Pe'er D, Allison JP. <a href="https://www.cell.com/immunity/fulltext/S1074-7613(19)30094-9">Cell Immunity</a>. March 2019.
</li>
<br/>
<li><i>Characterization of cell fate probabilities in single-cell data with Palantir</i>.<br/><b>Setty M</b>, Kiseliovas V, Levine J, Gayoso A, Mazutis L, Pe'er D. <a href="https://www.nature.com/articles/s41587-019-0068-4">Nature Biotechnology</a>. March 2019.
</li>
<br/>
<li><i>Single-cell Map of Diverse Immune Phenotypes Driven by the Tumor Microenvironment.</i><br/>Azizi E, Carr AJ, Plitas G, Cornish AE, Konopacki C, Prabhakaran S, Nainys J, Wu K, Kiseliovas V, <b>Setty M</b>, Choi K, Fromme RM, Dao P, McKenney PT, Wasti RC, Kadaveru K, Mazutis L, Rudensky AY, Pe'er D. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(18)30723-2">Cell</a>. June 2018.
</li>
<br/>
<li><i>Epigenomic-guided mass cytometry profiling reveals disease-specific features of exhausted CD8 T cells.</i><br/>Bengsch B, Ohtani T, Khan O, <b>Setty M</b>, Manne1 M, O’Brien S, Gherardini PF, Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen AN, Pe’er D, Albelda SM, Wherry EJ. <a href="https://www.cell.com/immunity/fulltext/S1074-7613(18)30195-X">Cell Immunity</a>. May 2018.
</li>
<br/>
<li><i>Wishbone identifies bifurcating developmental trajectories from single-cell data.</i><br/><b>Setty M*</b>, Tadmor MD*, Reich-Zeliger S, Angel O, Salame TM, Kathail P, Choi K, Bendall S, Friedman N, Pe'er D. <a href="http://www.nature.com/nbt/journal/v34/n6/full/nbt.3569.html">Nature Biotechnology</a>. June 2016.
</li>
<br/>
<li><i>Integrated genomic profiling identifies microRNA-92a regulation of IQGAP2 in locally advanced rectal cancer.</i><br/> Pelossof R, Chow OS, Fairchild L, Smith JJ, <b>Setty M</b>, Chen CT, Chen Z, Egawa F, Avila K, Leslie CS, Garcia-Aguilar J. <a href="http://onlinelibrary.wiley.com/doi/10.1002/gcc.22329/abstract;jsessionid=F8398303A9A7CEA57A733F09E3D222CA.f04t01">Genes, Chromosomes & Cancer</a>. Apr 2016.
</li>
<br/>
<li><i>Enhancer poising and regulatory locus complexity shape gene expression changes in hematopoietic differentiation</i>. <br/> Gonzalez JA*, <b>Setty M*</b>, Leslie CS. <a href="http://www.nature.com/ng/journal/v47/n11/full/ng.3402.html">Nature Genetics</a>. Aug 2015.
</li>
<br/>
<li><i>SeqGL identifies binding profiles from genome-wide regulatory maps.</i><br/><b>Setty M,</b> Leslie CS. <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004271">PLoS Computational Biology</a>. May 2015.
</li>
<br/>
<li><i>MiR-28 controls cell proliferation and is down-regulated in B cell lymphomas.</i><br/>Schneider C, <b>Setty M,</b> Holmes A, Maute RL, Leslie CS, Mussolin L, Rosolen A, Dalla-Favera R, Basso K. <a href="http://www.pnas.org/content/111/22/8185.long">Proceedings of the National Academy of Sciences</a>. June 2014.
</li>
<br/>
<li>
<i>A Novel Mutation in Bruton Tyrosine Kinase Confers Resistance to Ibrutinib (PCI-32765) in CLL.</i><br/>Furman RR, Cheng S, Lu P, <b>Setty M,</b> Perez A, Guo A, Racchumi J, Xu G, Ma J, Coleman M, Chen W, James D, Chang BY, Buggy J, Leslie CS, Wang YL.<a href="http://www.nejm.org/doi/full/10.1056/NEJMc1402716">New England Journal of Medicine</a>. May 2014.
</li>
<br/>
<li><i>CSF-1R inhibition alters macrophage polarization and blocks gliomagenesis.</i><br/>Pyonteck S, Schumacher A, Bowman R, Akkari L, Sevenich L, Olson O, Teijeiro V, <b>Setty M,</b> Leslie CS, Huse J, Oei Y, Holland EC, Daniel D, Joyce J. <a href="http://www.nature.com/nm/journal/v19/n10/full/nm.3337.html">Nature Medicine</a>. Oct 2013.
</li>
<br/>
<li><i>BCL6 positively regulates AID and germinal center gene expression via repression of miR-155.</i><br/>Basso K, Schneider C, Shen Q, Holmes A, <b>Setty M,</b> Leslie CS, Dalla-Favera R. <a href="http://jem.rupress.org/content/209/13/2455.full">Journal of Experimental Medicine</a>. Dec 2012.
</li>
<br/>
<li><i>Identification of global alterations of translational regulation in glioma in vivo.</i><br/>Helmy K, Halliday J, Fomchenko E, <b>Setty M,</b> Pitter K, Hafemeister C, Holland EC. <a href="http://www.plosone.org/article/authors/info\%3Adoi\%2F10.1371\%2Fjournal.pone.0046965;jsessionid=6F76D22C712EF0B94DEF2B5587B094AF">PLoS One.</a> Oct 2012.
</li>
<br/>
<li><i>Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma.</i><br/><b>Setty M,</b> Helmy K, Khan AA, Arvey A, Agius P, Holland EC, Leslie CS. <a href="http://msb.embopress.org/content/8/1/605">Nature/EMBO Molecular Systems Biology</a>. Aug 2012.
</li>
<br/>
<li><i>A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL) </i><br/>Mavrakis KJ, Van Der Meulen J, Wolfe AL, Liu X, Mets E, Taghon T, Khan AA, <b>Setty M,</b> Rondou P, Vandenberghe P, Delabesse E, Benoit Y, Socci NB, Leslie CS, Van Vlierberghe P, Speleman F, Wendel HG. <a href="http://www.nature.com/ng/journal/v43/n7/full/ng.858.html">Nature Genetics</a>. Jul 2011.
</li>
<br/>
<li><i>Genomic safe harbors permit high $\beta$-globin transgene expression in thalassemia induced pluripotent stem cells.</i><br/> Papapetrou E, Lee G, Malani N, <b>Setty M,</b> Riviere I, Tirunagari L, Kadota K, Roth S, Giardina P, Viale A, Leslie C, Bushman F, Studer L, Sadelain M. <a href="http://www.nature.com/nbt/journal/v29/n1/full/nbt.1717.html">Nature Biotechnology</a>. Jan 2011.
</li>
<br/>
<li><i>HLA type inference via haplotypes identical by descent.</i><br/><b>Setty M,</b> Gusev A, Pe'er I. <a href="http://online.liebertpub.com/doi/abs/10.1089/cmb.2010.0258">Journal of Computational Biology</a>. Aug 2010.
</li>
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<h2>
Computational Methods
</h2>
<span>Computational Methods</span>
</div>
<!-- /.Section-title -->
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<ol>
<li><i>Harmony</i>. Harmonize single cell data measured at discrete developmental time points. <br/><a href="https://github.com/dpeerlab/Harmony">Link</a>.
<a href="https://www.nature.com/articles/s41586-019-1127-1">Reference</a>.
</li>
<br/>
<li><i>Palantir</i>. Modeling continuities in cell fate choices. <br/><a href="https://github.com/dpeerlab/Palantir">Link</a>.
<a href="https://www.nature.com/articles/s41587-019-0068-4">Reference</a>.
</li>
<br/>
<li><i>Wishbone</i>. Identifying bifurcations in single cell data. <br/><a href="https://github.com/dpeerlab/wishbone">Link</a>.
<a href="http://www.nature.com/nbt/journal/v34/n6/full/nbt.3569.html">Reference</a>.
</li>
<br/>
<li><i>SeqGL</i>. k-mer models for TF sequence specificity. <br/><a href="https://bitbucket.org/leslielab/seqgl">Link</a>.
<a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004271">Reference</a>.
</li>
<br/>
<li><i>RegulatorInference</i>. Regression models for identify dysregulated regulators in disease. <br/><a href="https://bitbucket.org/leslielab/regulatorinference">Link</a>.
<a href="http://msb.embopress.org/content/8/1/605">Reference</a>.
</li>
<br/>
<li><i>HLA-IBD</i>. HLA type inference using SNP data. <br/><a href="http://www.cs.columbia.edu/~itsik/software/HLA-IBD.html">Link</a>.
<a href="http://online.liebertpub.com/doi/abs/10.1089/cmb.2010.0258">Reference</a>.
</li>
</ol>
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manu.n.setty @gmail.com
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</footer>
<!-- /.footer-section -->
<!-- ==================== footer-section end ==================== -->
</div>
<!-- ========== ========== right side body end ========== ========== -->
<!-- jquery and bootstrap.js -->
<script src="assets/js/jquery-3.1.1.min.js"></script>
<script src="assets/js/materialize.min.js"></script>
<script src="assets/js/owl.carousel.min.js"></script>
<script src="assets/js/isotope.pkgd.min.js"></script>
<script src="assets/js/circle-progress.js"></script>
<!-- my custom js -->
<script src="assets/js/custom.js"></script>
</body>
</html>