Research in Computational Molecular Biology

.- Enhancing gene set analysis in embedding spaces a novel best match approach.

.- Prompt based Learning on Large Protein Language Models Improves Signal Peptide Prediction.

.- Decoil Reconstructing extrachromosomal DNA structural heterogeneity from longread sequencing data.

.- Privacy Preserving Epigenetic PaceMaker Stronger Privacy and Improved Efficiency.

.- Mapping Cell Fate Transition in Space and Time.

.- Approximate IsoRank for Scalable Global Alignment of Biological Networks.

.- Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors.

.- Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts.

.- Secure federated Boolean count queries using fully homomorphic cryptography.

.- FragXsiteDTI Revealing Responsible Segments in Drug Target Interaction with Transformer Driven Interpretation.

.- An integer programming framework for identifying stable components in asynchronous Boolean networks.

.- ImputeCC enhances integrative Hi C based metagenomic binning through constrained random walk based imputation.

.- Graph based genome inference from Hi C data.

.- Meta colored de Bruijn graphs.

.- Color Coding for the Fragment Based Docking Design and Equilibrium Statistics of Protein Binding ssRNAs.

.- Automated design of efficient search schemes for lossless approximate pattern matching.

.- CELL E A Text To Image Transformer for Protein Localization Prediction.

.- A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements.

.- Overcoming Observation Bias for Cancer Progression Modeling.

.- Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning.

.- Computing robust optimal factories in metabolic reaction networks.

.- Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition.

.- Structure and Function Aware Substitution Matrices via Learnable Graph Matching.

.- Secure 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.