Sayan Mukherjee

Social and environmental predictors of gut microbiome age in wild baboons

The paper develops a microbiome-based age predictor for wild baboons using 13,563 gut microbial profiles and finds that microbiome age reflects current social and environmental conditions but not developmental milestones or lifespan.

The accuracy of absolute differential abundance analysis from relative count data

This study evaluates the accuracy of differential abundance analysis using renormalized relative count data compared to absolute abundances, finding high consistency but potential for increased false positives under widespread abundance changes.

A Statistical Pipeline for Identifying Physical Features that Differentiate Classes of 3D Shapes

This paper introduces SINATRA, a statistical pipeline for identifying physical features differentiating 3D shape classes without requiring correspondences, and demonstrates its application to primate mandibular molars.

Naught all zeros in sequence count data are the same

The paper evaluates zero-handling models in genomic and microbiome data, showing significant disagreement in identifying differentially expressed sequences and finding simple count models sufficient across processes.

Estimating Rates of Progression and Predicting Future Visual Fields in Glaucoma Using a Deep Variational Autoencoder

This paper develops a deep variational autoencoder to estimate glaucoma progression rates and predict future visual field loss, showing improved performance compared to traditional methods.

Label propagation defines signaling networks associated with recurrently mutated cancer genes

The paper uses label propagation to analyze gene expression signatures from cancer mutations, identifying signaling networks and drug response markers across multiple tumor types.

Measuring and Mitigating PCR Bias in Microbiome Data

The paper measures and mitigates PCR bias in microbiome data using experimental validation and Bayesian models.

Unifying mutualism diversity for interpretation and prediction

The paper develops a general rule for predicting mutualistic system outcomes and introduces a calibration method to apply it without full mechanistic understanding.

Evolution of DNA methylation in Papio baboons

The paper profiles DNA methylation in Papio baboons to study evolutionary changes and finds that methylation divergence mirrors genetic structure and is influenced by selection in functionally relevant regions.

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts

The paper develops a modeling framework to analyze microbiota dynamics in artificial human guts, revealing technical noise as a major source of variation and identifying sub-daily fluctuations and replicable trajectories.

Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals in Drosophila

The paper shows that DIPs and Dprs control the organization of olfactory receptor neuron terminals in Drosophila by mediating class-specific self-adhesion and axon sorting.

HOMINID: A framework for identifying associations between host genetic variation and microbiome composition

HOMINID identifies host SNPs correlated with microbiome taxa abundances using Lasso regression, showing improved accuracy over existing methods and identifying 13 SNPs across body sites.

Development and assessment of fully automated and globally transitive geometric morphometric methods, with application to a biological comparative dataset with high interspecific variation

The paper evaluates and improves automated geometric morphometric methods for shape analysis, showing enhanced accuracy and taxonomic distinctiveness compared to existing approaches.

Detecting Epistasis with the Marginal Epistasis Test in Genetic Mapping Studies of Quantitative Traits

The paper introduces MAPIT, a method to detect epistasis by testing marginal epistatic effects instead of direct pairwise interactions, improving computational efficiency and statistical power.

Differential Expression Analysis for RNAseq using Poisson Mixed Models

This paper introduces a Poisson mixed model for differential expression analysis in RNAseq, accounting for over-dispersion and sample non-independence, showing improved power in real data.

Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples

The paper develops an optimized lab protocol and computational method to analyze non-invasively collected samples for genome-wide sequencing and low-coverage pedigree reconstruction, validated on baboon fecal samples.