Research in Computational Molecular Biology

Discovery of Genetic Relatives across Large Scale and Distributed Genomic Datasets.
.- GFETM Genome Foundation based Embedded Topic Model for scATAC seq Modeling.
.- SEM sized based expectation maximization for characterizing nucleosome positions and subtypes.
.- Centrifuger lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
.- BONOBO Bayesian Optimized sample specific Networks Obtained By Omics data.
.- regLM Designing realistic regulatory DNA with autoregressive language models.
.- DexDesign A new OSPREY based algorithm for designing de novo D peptide inhibitors.
.- Memory bound and taxonomy aware kmer selection for ultra large reference libraries.
.- SpaCeNet Spatial Cellular Networks from omics data.
.- Discovering and overcoming the bias in neoantigen identification by unified machine learning models.
.- MaSk LMM A Matrix Sketching Framework for Linear Mixed Models in Association Studies.
.- Community structure and temporal dynamics of viral epistatic networks allow for early detection of emerging variants with altered phenotypes.
.- Maximum Likelihood Inference of Time scaled Cell Lineage Trees with Mixed type Missing Data.
.- TRIBAL Tree Inference of B cell Clonal Lineages.
.- Mapping the topography of spatial gene expression with interpretable deep learning.
.- GraSSRep Graph Based Self Supervised Learning for Repeat Detection in Metagenomic Assembly.
.- PRS Net Interpretable polygenic risk scores via geometric learning.
.- Haplotype aware sequence alignment to pangenome graphs.
.- Disease Risk Predictions with Differentiable Mendelian Randomization.
.- DIISCO A Bayesian framework for inferring dynamic intercellular interactions from time series single cell data.
.- Protein domain embeddings for fast and accurate similarity search.
.- Processing bias correction with DEBIAS M improves cross study generalization of microbiome based prediction models.
.- VICTree a Variational Inference method for Clonal Tree reconstruction.
.- DeST OT Alignment of Spatiotemporal Transcriptomics Data.
.- Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History.
.- Accurate Assembly of Circular RNAs with TERRACE.
.- Semi Supervised Learning While Controlling the FDR With an Application to Tandem Mass Spectrometry Analysis.
.- CoRAL accurately resolves extrachromosomal DNA genome structures with long read sequencing.
.- A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex Traits.
.- Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation.
.- Inferring allele specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics.
.- Contrastive Fitness Learning Reprogramming Protein Language Models for Low N Learning of Protein Fitness Landscape.
.- Scalable summary statistics based heritability estimation method with individual genotype level accuracy.
.- scMulan a multitask generative pre trained language model for single cell analysis.