Martin Hemberg

scRepresenter provides a workflow to compute, integrate, and benchmark cellular representations from scRNA-seq data using different methods for complex disease analysis.

The paper presents a cross-species single-cell atlas of the entorhinal cortex across mammals, identifying conserved and species-specific cellular innovations related to spatial navigation.

SpatialQuery identifies multicellular spatial patterns and characterizes their molecular programs in spatial omics data, revealing cross-germ-layer signaling and disease-specific niches.

Harmony2 integrates large single-cell RNA-seq datasets efficiently and accurately, preventing overintegration in biologically diverse data.

This study identifies distinct malignant cell states and myeloid glutamate signaling in aggressive pancreatic neuroendocrine tumors, linking them to poor clinical outcomes and therapeutic vulnerabilities.

scCausalVI disentangles intrinsic cellular states from treatment effects using a causality-aware generative model, outperforming existing methods in causal inference and multi-source data integration.

This study identifies Pdgfd-Pdgfrb signaling as a driver of perineural invasion in pancreatic cancer by promoting cancer cell invasiveness and nerve engagement.

The paper identifies TL1A-driven cellular and transcriptomic changes in rectal mucosa of Crohn's disease patients with perianal fistulizing disease, revealing a novel TL1A-LT1{beta}2/IL-22 axis independent of TNF signaling.

The paper maps G-quadruplexes across the human genome and haplotypes, showing their enrichment in repetitive regions and association with genomic instability and PRDM9 binding.

The paper finds that ApoE ε4-dependent changes in CXCR3+CD127+ CD4+ T cells in peripheral blood correlate with elevated neurofilament light chain in Alzheimer's disease.

MEA-NAP analyzes microscale functional connectivity and network dynamics from MEA recordings in neuronal cultures, revealing differences in topology and network development.

scASfind identifies cell type-specific alternative splicing patterns in scRNA-seq data, revealing splicing events missed by gene-level analysis.

Demuxafy improves droplet assignment and doublet removal in scRNA-seq by combining multiple demultiplexing and doublet detection methods.

The paper uses a pangenomic approach to analyze Lake Malawi cichlid genomes, revealing extensive structural variation driven by transposable elements.

The paper uses a convolutional neural network to identify regulatory motifs and their cell type-specific importance from single-cell data, explaining 29% of gene expression variance in mouse tissues.

This study uses single-cell sequencing to identify cellular and molecular differences in the kidneys and pancreases of insectivorous and frugivorous bats, linking them to diabetes-related mechanisms.

SC3s provides an efficient k-means clustering method for large single-cell RNA-seq datasets, scaling linearly with cell count.

The paper integrates single-cell RNA and ATAC-seq data from mouse and human hypothalamus to identify sex-specific genes and obesity-associated regulatory elements.

scHumanNet identifies cell-type-specific gene functions by analyzing single-cell transcriptomes, revealing disease-related gene effects in specific cell types.

The paper identifies G-quadruplex motifs enriched near splice junctions and shows their involvement in alternative splicing in neuronal cells.

TransposonUltimate is a software package for transposon classification, annotation, and detection, outperforming existing methods and providing a unified framework.

The paper identifies nullomers and nullpeptides across species, showing they are under negative selection and could serve as DNA fingerprints or for phylogenetic analysis.

The paper shows acute paternal Dexamethasone exposure alters sperm RNA and offspring metabolism, identifying circRNAs as novel RNA-mediated inheritance candidates.

This paper introduces a new spatial transcriptomic technology, WTA, and applies it to map the cellular architecture of the developing human neocortex, showing spatial enrichment of autism-related genes.

scfind enables efficient querying of single-cell data to evaluate marker genes, perform in silico gating, and support multi-omics analyses.

MicroExonator identifies and quantifies microexons across mouse embryonic development, revealing 332 differentially spliced microexons and cell-type specific inclusion in neuronal subpopulations.

The paper evaluates batch correction methods for single-cell RNA-seq using BatchBench, showing their performance across datasets.

The paper constructs a single-cell atlas of the frontal cortex in early-onset monogenic Alzheimer's disease to identify cellular and molecular changes in disease mechanisms.

The paper analyzes indel distribution relative to transcription to show strand asymmetry and links it to DNA repair mechanisms in human cancers.