Benjamin P. Kellman

Neurodegeneration risk variants promote lysosomal TMEM106B fibrilaccumulation

The paper identifies TMEM106B fibril accumulation as a shared mechanism in neurodegeneration linked to genetic variants in TMEM106B and GRN.

mRNA-Protein Coordination is Contextualized by Metastatic Biological Phenotypes

The paper shows that integrating mRNA and protein data improves understanding of metastasis by leveraging complementary and reinforcing signals between modalities.

Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network

The paper trains a hybrid neural network to predict N-glycosylation events and structures from protein sequences using glycosite-flanking data, demonstrating its ability to predict glycan composition and abundance.

Protein structure, a genetic encoding for glycosylation

The paper identifies a relationship between protein structure and glycan structure, introducing a glycoimpact matrix to predict glycosylation patterns and validate it through disease variants and engineered antibodies.

Preparing glycomics data for robust statistical analysis with GlyCompareCT

GlyCompareCT preprocesses glycomics data to address sparsity and non-independence, improving statistical power for downstream analysis.

Inferring a cell's capabilities from omics data with ImmCellFie

ImmCellFie infers cell metabolic capabilities from transcriptomic or proteomic data using genome-scale models and provides interactive analysis tools.

Simple and practical sialoglycan encoding system reveals vast diversity in nature and identifies a universal sialoglycan-recognizing probe derived from AB5 toxin B subunits

The paper introduces a 9-digit code system for sialyltrisaccharides, revealing vast sialoglycan diversity and identifying a universal probe from AB5 toxin B subunits.

Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration

The paper constructs an HMO biosynthesis network using multi-omics integration to predict glycosyltransferases and propose candidate genes for HMO synthesis pathways.

What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data

The paper introduces a framework to predict how changes in omics data affect metabolic functions in mammalian cells using curated metabolic tasks and genome-scale networks.

Optimal balancing of clinical factors in large scale clinical RNA-Seq studies

This paper introduces BalanceIT, a method using genetic algorithms to balance clinical factors in RNA-Seq studies, improving differential gene expression and pathway analysis in autism research.

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing

This study quantifies how repeated freeze-thaw cycles affect RNA-Seq reliability, showing that poly(A)-enriched samples lose reproducibility after three cycles.

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

This paper extends Linear Code to represent reaction rules in glycobiology, aiming to improve consistency and interoperability in glycan synthesis models.

A perturbed gene network containing PI3K/AKT, RAS/ERK, WNT/β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity

The paper identifies a perturbed gene network in leukocytes linked to ASD genetics and symptom severity through analysis of transcriptomics data from toddlers.

Correcting for sparsity and non-independence in glycomic data through a systems biology framework

The paper introduces GlyCompare, a glycomic analysis method that addresses sparsity and non-independence by leveraging biosynthetic pathways, revealing biological insights in glycoprofiles and human milk oligosaccharides.