Sourya Bhattacharyya
@SouryaBhattach5
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Lead Data Scientist, Empirico, San Diego, USA Postdoc + Instructor at La Jolla Institute for Immunology Ph.D. Computer Science at IIT Kharagpur
San Diego
Joined September 2018
RT @pkoo562: Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZq….
genomebiology.biomedcentral.com
Background The emergence of genomic language models (gLMs) offers an unsupervised approach to learning a wide diversity of cis-regulatory patterns in the non-coding genome without requiring labels of...
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RT @KatieEYost: Our work on 3D genome organization in human cancer is out! In collaboration with @ZYanding @HowardYChang @WJGreenleaf and T….
www.nature.com
Nature Genetics - This study characterizes the three-dimensional (3D) genome architecture of 15 primary human cancer types from The Cancer Genome Atlas. The analyses identify different archetypes...
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RT @BiologyAIDaily: Variant effect predictor correlation with functional assays is reflective of clinical classification performance. 1. Th….
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RT @ferhatay: Happy to share Dante Bolzan’s delicious new preprint-Soffritto. He developed a deep learning model that accurately predicts h….
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Incredibly thankful to my post doc supervisor Dr. @ferhatay for all his guidance and comments in shaping up this paper, which should serve as a great tool to the community.
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It was wonderful to mentor Daniela Salgado Figueroa, Ph.D. student in UCSD, who did an incredible work on validating DiffHiChIP.
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We have tested with various HiChIP datasets between two conditions, with small (=2) or large (=6) number of replicates, confirming the utility of DiffHiChIP as a go-to model for calling differential HiChIP (and other 3C) loops.
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DiffHiChIP is also benchmarked with compatible Hi-C loops, and various experimentally validated reference chromatin contacts from validation experiments.
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DiffHiChIP shows that generalized linear models (GLM) in edgeR employing either likelihood ratio test (LRT) or quasi-likelihood F test, coupled with distance stratification via independent hypothesis weighting (IHW), shows better detection of differential long-range HiChIP loops.
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Extremely happy to share that our work DiffHiChIP: a method to identify differential chromatin interactions from HiChIP (and any other chromatin interaction data such as Hi-C, ChIA-PET), is now online. Preprint in:
www.biorxiv.org
High-resolution conformation capture assays such as HiChIP are commonly used for profiling chromatin loops among cis -regulatory elements including enhancers and promoters. Detection of differential...
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@Empirico Looking forward to see you all at ASHG @GeneticsSociety 2024 (.
www.ashg.org
Attracting over 8,000 scientific attendees, the ASHG Annual Meeting is the world’s largest gathering of human genetics and genomics professionals.
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I will be @ASHG2024, Denver, CO, Nov 5-9 along with my colleagues at @Empirico (. Looking forward to discuss latest research in computational and ML models for Human Genetics. Let me know if anybody wants to catch up.
www.empiri.co
Empirico combines human genetics-driven target discovery with siRNA drug discovery, across a range of common diseases with unmet medical need.
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RT @pkoo562: Excited that CREME (Cis-Regulatory Element Model Explanations) is published in @NatureGenet! Work led by @ToneyanSh!. tl;dr CR….
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RT @ferhatay: Forgot a little detail, the link itself :) let us know if you have any feedback:
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RT @ferhatay: Our multi-year effort on putting together a comprehensive database of loop calls from 1000+ HiChIP samples plus enabling visu….
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Looking forward to attend the CSHL Genome Organization & Nuclear Function meeting @cshlmeetings from April 30 - May 4. Hope to listen great lectures, meet and discuss with the stalwarts of 3D genome research.
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RT @jsantoyo: VarChat: the generative AI assistant for the interpretation of human genomic variations. #GenomicVariants #LiteratureSearch #….
academic.oup.com
AbstractMotivation. In the modern era of genomic research, the scientific community is witnessing an explosive growth in the volume of published findings.
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RT @biorxiv_bioinfo: A deep profile of gene expression across 18 human cancers #biorxiv_bioinfo.
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RT @LB_Barreiro: Finally, our data indicates that epigenetic QTLs provide a means to markedly increase the number of QTLs that colocalize (….
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