Bin Zhang

Exploring transcriptomic and genomic latent variable correction approaches in differential expression analysis.

This paper evaluates combining expression-based surrogate variables and genotype-based principal components in differential expression analysis, finding the combined approach improves replicability and biological recall in ALS datasets.

A Multi-Omics Study of Cognitive Resilience to Alzheimer's Disease

The paper develops a multi-omics cohort of prefrontal cortex data from cognitively normal older adults to identify molecular signatures of cognitive resilience to Alzheimer's disease.

Repositioning of polyubiquitin alters the pathologic tau filament structure

This study shows that polyubiquitin repositioning affects tau filament structure in tauopathies, altering their seeding activity in mice.

Normalizing LZ+ MYPT1 Expression Prevents the Development of HFpEF

This study shows that maintaining normal LZ+ MYPT1 expression prevents HFpEF development in mice by improving vascular reactivity and diastolic function.

Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics

The paper develops a pipeline for protein-level cell annotation in human PBMCs using mass spectrometry-based single-cell proteomics and validates it on unsorted samples.

Multiomic State-Transitions Reveal Post-Treatment Transcriptome Desynchronization in Acute Myeloid Leukemia

The paper uses a state-transition model to study transcriptome dynamics in AML, finding delayed miRNA responses and linking the Dlk1-Dio3 locus to treatment-induced desynchronization.

Endogenously generated Dutch-type Aβ nonfibrillar aggregates dysregulate presynaptic neurotransmission in the absence of detectable inflammation

This study shows that nonfibrillar Aβ aggregates in APPE693Q mice disrupt presynaptic function without causing inflammation.

Single-Nuclei Transcriptomic Characterization of APOE4-Associated Alzheimer's Disease

This study characterizes cell-type-specific transcriptomes across APOE genotypes in Alzheimer's disease using single-nuclei RNA sequencing, revealing APOE4-associated changes in excitatory neurons and microglia.

Genome-Wide Variations of End Motif in Cell-Free DNA Fragments Distinguish Immunotherapy Responders from Non-Responders in Head and Neck Cancer: A Multi-Institute Prospective Study

This study identifies a novel cfDNA fragmentomic metric, rMDS, that distinguishes immunotherapy responders from non-responders in HNSCC with high accuracy.

Endogenous retroviral elements LTR8B and MER65 rewire PSG9regulation to control trophoblast syncytialization and pre-eclampsia risk

The paper identifies retroviral elements LTR8B and MER65 that regulate PSG9 expression, influencing trophoblast syncytialization and pre-eclampsia risk.

A shared transcriptional network in the nucleus accumbens supports resilience to chronic stress across sex.

The paper identifies a shared transcriptional network in the nucleus accumbens that supports stress resilience in both sexes and shows causal effects of hub genes.

A systems approach uncovers drivers of the multifocal emergence of an astrocyte state contributing to cognitive decline in Alzheimer's disease

The paper identifies a novel astrocyte state linked to cognitive decline in Alzheimer's disease and validates its regulators through multi-modal analysis and mechanistic experiments.

Transcriptional activation of Bmal1 drives the inflammatory activity of monocytes by modulating mitochondrial unfolded protein response during hypobaric hypoxic stress

This study identifies Bmal1 activation as a driver of mitochondrial stress and inflammation in monocytes under hypobaric hypoxia, mediated by BHLHE40 and Fis1-mediated mitochondrial fission.

A global atlas of substrate specificities for the human serine/threonine kinome

Positional scanning peptide arrays profile substrate sequence specificities across 303 human serine/threonine kinases, enabling computational kinase-substrate annotation and signaling pathway inference across the human phosphoproteome.

Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer's disease risk in humans

The paper identifies an epigenomic factor linked to reduced activated microglia that mitigates the risk of Alzheimer's disease in APOE ε4 carriers.

Zfp189 Mediates Stress Resilience Through a CREB-Regulated Transcriptional Network in Prefrontal Cortex

The paper identifies Zfp189 as a key driver of a transcriptional network promoting stress resilience in prefrontal cortex neurons through CREB regulation.

Genome-wide identification of CDC34 that stabilizes EGFR and promotes lung carcinogenesis

This study identifies CDC34 as a critical E2 ubiquitin conjugase that stabilizes EGFR and promotes lung carcinogenesis by inhibiting its degradation.

A Transferable Model For Chromosome Architecture

The paper introduces a theoretical model that explains and accurately reproduces the three-dimensional structure of interphase chromosomes using experimental data.

Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia

The paper uses gene expression data from schizophrenia cases and controls to show that common variants at 20% of schizophrenia risk loci regulate brain gene expression, with functional impacts on neural progenitor cells and zebrafish neuroanatomy.

An alternative class of targets for microRNAs containing CG dinucleotide

The paper identifies a class of microRNA targets involving bulge structures and shows they can be recognized by miRNAs, improving computational target prediction when combined with conservation.

Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome

The paper derives an energy landscape for mitotic chromosomes that exhibits chiral symmetry breaking and helical twisting, similar to interphase TAD structures.