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Tri-Institutional PhD Program in Computational Biology and Medicine. A program @Cornell @WeillCornell @sloan_kettering @RockefellerUniv Instagram: cbm_student

New York
Joined August 2014
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Tri-i CBM held our annual retreat 10/27-28. We welcomed the new first years, had wonderful talks and discussions, and enjoyed rejuvenating group bonding time⭐️! Application portals are now open for perspective applicants, and we invite you to join our CBM family!
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feel free to reach out to us about application-related questions via email at [email protected] and [email protected]!
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Hi all, I am currently on the academic job market. I am a postdoctoral researcher in Dr. Christina Leslie's lab at the Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center. My research focuses on deciphering causal and dynamic gene regulation mechanisms by integrating observational data—genomics, epigenomics, transcriptomics, and 3D chromatin conformation like Hi-C—with perturbational data from CRISPRi/a screens and Perturb-seq in single-cell multiomics. I employ techniques from statistical machine learning, causal inference, dynamical modeling, and artificial intelligence (AI) to achieve this goal. The models that I have developed include GraphReg, ENCODE-rE2G, and DynaVelo (to be submitted soon). Why is this important? Designing any effective and off-target-free therapeutic intervention for diseases, including cancer, first requires a complete understanding of the underlying wildtype system and then identifying the components that malfunction in disease states. With the ever-growing role of AI in synthetic biology and drug design, it is crucial to ensure that the models are causal and comprehend the basic biology of all cells. This is a challenging problem, but I am very hopeful that with the increasing scale of perturbational and multiomic data across cell types, we will achieve significant outcomes. If you believe I could be a good fit for your department, please reach out to me. Sincerely, Alireza
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💥💥💥New preprint 💥💥💥on the EuPRI resource. Where we reconstruct the motifs for 34,736 RBPs and study their function and evolution. Joint work with @ProfTimHughes (Toronto), Matt Weirauch, @LXandR_, Deb Ray, Kaitlin Laverty and many more. More details to come
Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes biorxiv.org/cgi/content/shor… #biorxiv_genomic
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Happy to announce that PERT is now published in @NatureComms ! With PERT, we explore replication timing variability (Fig 3-4), chrXi reactivation (Fig 5), and how S-phase fractions struggle to approximate clone fitness (Fig 6). nature.com/articles/s41467-0… 1/n
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Excited to publish my book chapter with @mason_lab @Springernomics and edited by @sonivijay07 and Dr. Akhade on Role and Relation of Microbiome to address AMR.
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AutoFocus, a project YEARS in the making, is finally out in @CommsBio! When clustering multi-omic data, systemic correlation bias focuses on intra-omic clusters and excludes multi-omic interactions - so we designed an algorithm to help change the focus: nature.com/articles/s42003-0…
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We are humbled to have our lab's work featured this week on the cover of @Nature (below), with many, many people to thank. First, the stellar crew of @inspiration4x, @rookisaacman, @ArceneauxHayley, @ChrisSembroski, @DrSianProctor, who donated time, blood, fluids, and sweat for the mission. These data were the foundation of the Space Omics and Medical Atlas (SOMA), expanding upon the findings from @StationCDRKelly & @CaptMarkKelly in the NASA Twins Study and enabling an unprecedented look the human body (and its microbes) in space. Second, thanks to many science teams , especially co-leaders for the SOMA effort @AfshinBeheshti, @EliahOverbey, @cemmeydan, Chris Jones, @mathiasbasner, @KeithSiew, Stephen Walsh, @joseph_borg_ , & Susan Bailey, the I4 mission science leads Frederic Zenhausern, Mark Shelhamer, Eric Bershad, @aesargsyan, @7irz, @DoritPhD, @EUrquietaMD, Ashot Sargsyan, Doug Ebert, Mathias Basner, and leadership from @IwijnDeVlaminck, @Astro_Kate7, @trialx, @LabMelnick, @nebula_rd, @FathiKarouia, @giacomello_lab, Scott Smith, Sara Zwart, @SpaceLuisZea, and many more. Third, the amazing med-ops and mission teams at @spaceX and @NASA, especially @jmat_, @astro_anil (now at NASA), Sean Mullane, Seth Stravers Tigchelaar, Steven Levitte, & Marissa Rosenberg, plus all the support teams in the planning and logistics stages before, during, and after the missions. Fourth, the labs at @WeillCornell who worked for several years on the papers and data portals, especially @EliahOverbey, @KJangkeun @BradenTierney @krista_ryon @JIWOONPARK_ @mjdmackay @asierra93, @ChrisRChin, & Dan Butler, Sebastian Garcia Medina, Namita Damle, Deena Najjar, Kirill Grigorev, Karolina Sienkiewicz, Laura Patras, Remi Klotz, Veronica Ortiz, Annalise Schweickart, Theodore M. Nelson, Gabriel Deards, Jonathan Foox, Craig Westover, Chandrima Bhattacharya, Serena Lucotti, Jacqueline Proszynski, Marissa Burke, Ashley S. Kleinman, Daniel J. Butler, Conor Loy, Omary Mzava, and Jeremy Hirschberg, which also led the creation of the Cornell Aerospace Medicine Biobank (CAMBank). Fifth, the superb @NASAGeneLab teams, @CostesSylvain, @RyanTScott, Sam Gebre, Egle Cekanaviciute, Lauren Sanders, and others for enabling controlled and long-term data access, ensuring these data as a resource for the field for the decades of spaceflight ahead. Finally, thanks to the vision of @elonmusk and Jared Issacman to enable such ambitious studies, including the upcoming @PolarisProgram missions with Jared, @KiddPoteet, @annawmenon, @Gillis_SarahE. Also, we have the upcoming @framonauts mission led by @satofishi which will greatly expand upon this work and launch humanity into The Second Space Age. More details here: nature.com/collections/soma/ If you want a fun ride that highlights the results and shows ideas for future missions, grab a cup of coffee or a glass of wine (or both) and head here: nature.com/immersive/d42859-…
This week in Nature: Space Omics – Biomedical atlas captures health effects of spaceflight. Browse the full issue: nature.com/nature/volumes/63…
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During National Postdoc Appreciation Week, we post social cards and profiles to celebrate our remarkable #MSKPostdocs (@MSKPDA). A week is not enough, so we dedicate ALL of September to our outstanding scientists! Stay tuned to learn more about them. @MSKCancerCenter #NPAW2024🎉
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We are at #ISMB24 in Montreal ! Come listen to @cbm_student Marjorie Roskes talk at #HitSeq on Sun at 5:20 pm, visit Weiling's poster A-133. Or shoot me a message if you would like to chat about opportunities in the lab.
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Paper out!📢 @AnupriyaSingha9 and #HannahStyers from the lab find acute resistance to targeting KRAS in pancreas cancer is surprisingly driven by a classical epithelial state. Co-targeting classical cells and KRAS augments response - clinically important! aacrjournals.org/cancerdisco…
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Metient reconstructs the migration histories of metastatic cancers by scoring a Pareto front of parsimonious histories. It can be auto-calibrated to different cohorts. Superstar PhD student @divyakoyy will present at #ISMB2024 in MLCSB Check it out: biorxiv.org/content/10.1101/…
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Thrilled to announce that my PhD thesis work has been published in Nature Genetics! 🎉 Huge thanks to my advisors, @SohrabShah and @EdReznik, for their guidance and support throughout the years!
I thought my 2 year old was going through a sleep regression at 5 am, but no, he just wanted to let me know that our lab's newest work with @SohrabShah and led by Minsoo Kim was finally online @NatureGenet nature.com/articles/s41588-0…
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✨New paper alert @CD_AACR✨ - GDD-ENS distinguishes 38 cancer types (>96% of patients) w/ high accuracy using routinely collected DNA sequencing data #MSKIMPACT and generalizes well to other gene panels w/o retraining - CNAs (arm/gene level) are key features for classification
Now online in @CD_AACR: #DeepLearning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data @mmdarmofal @MFBerger1 @quaidmorris doi.org/10.1158/2159-8290.CD… @MSKCancerCenter
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So proud to see the defense of Mar (Mohith) who worked in our lab on new algorithms for detecting and phasing 8-oxo-guanosine and other base modifications from @nanopore data from Earth and in space @cbm_student #defense @WeillCornell
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1/ Not every #oncogene acts like an oncogene – context is key. Here, with the Varmus Lab @WCM @WCM_MeyerCancer, we demonstrate an ‘oncogene’ in the wrong cell type doesn’t act like an oncogene anymore. science.org/doi/epdf/10.1126…
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🎙️ Alon Millet's talk is on YouTube! "An exhausted-like #microglial population accumulates in aged and #APOE4 genotype Alzheimer’s brains" (Ref: Immunity 2023) @AlonMillet @Jhledo @SohailTavazoie @RockefellerUniv @cbm_student youtu.be/IiQK_NrjN7o #Openscience
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