DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype–phenotype prediction

scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning

(2022) Yingxin Lin et al.   NATURE BIOTECHNOLOGY

MoGCN: A Multi-Omics Integration Method Based on Graph Convolutional Network for Cancer Subtype Analysis

(2022) Xiao Li et al.   Frontiers in Genetics

Microbiome-based disease prediction with multimodal variational information bottlenecks

(2022) Filippo Grazioli et al.   PLoS Computational Biology

Robust probabilistic modeling for single-cell multimodal mosaic integration and imputation via scVAEIT

(2022) Jin-Hong Du et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multimodal deep learning models for early detection of Alzheimer’s disease stage

(2021) Janani Venugopalan et al.   Scientific Reports

Sex differences in the human brain transcriptome of cases with schizophrenia

(2021) Gabriel E. Hoffman et al.   BIOLOGICAL PSYCHIATRY

Bayesian estimation of cell type-specific gene expression with prior derived from single-cell data

(2021) Jiebiao Wang et al.   GENOME RESEARCH

Fibroblast Growth Factor Signalling in the Diseased Nervous System

(2021) Lars Klimaschewski et al.   MOLECULAR NEUROBIOLOGY

BABEL enables cross-modality translation between multiomic profiles at single-cell resolution

(2021) Kevin E. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults

(2021) Binglan Li et al.   PLoS Genetics

Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer’s dementia

(2021) Shizhen Tang et al.   PLoS Genetics

Prioritization of schizophrenia risk genes from GWAS results by integrating multi-omics data

(2021) Dan He et al.   Translational Psychiatry

The Role of G Protein-Coupled Receptors (GPCRs) and Calcium Signaling in Schizophrenia. Focus on GPCRs Activated by Neurotransmitters and Chemokines

(2021) Tomasz Boczek et al.   Cells

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

(2021) Urmo Võsa et al.   NATURE GENETICS

MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification

(2021) Tongxin Wang et al.   Nature Communications

scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks

(2021) Ting Jin et al.   Genome Medicine

Polygenic scores: prediction versus explanation

(2021) Robert Plomin et al.   MOLECULAR PSYCHIATRY

Deep supervised learning using self-adaptive auxiliary loss for COVID-19 diagnosis from imbalanced CT images

(2021) Kai Hu et al.   NEUROCOMPUTING

Peripheral Blood-Based Gene Expression Studies in Schizophrenia: A Systematic Review

(2021) Vipul Vilas Wagh et al.   Frontiers in Genetics

Manifold learning analysis suggests strategies to align single-cell multimodal data of neuronal electrophysiology and transcriptomics

(2021) Jiawei Huang et al.   Communications Biology

Chromatin accessibility dynamics in a model of human forebrain development

(2020) Alexandro E. Trevino et al.   SCIENCE

Prediction of Alzheimer’s disease using blood gene expression data

(2020) Taesic Lee et al.   Scientific Reports

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

(2020) Janine Arloth et al.   PLoS Computational Biology

G-Protein-Coupled Receptors in CNS: A Potential Therapeutic Target for Intervention in Neurodegenerative Disorders and Associated Cognitive Deficits

(2020) Shofiul Azam et al.   Cells

Aberrant glycosylation in schizophrenia: a review of 25 years of post-mortem brain studies

(2020) Sarah E. Williams et al.   MOLECULAR PSYCHIATRY

Polygenic risk scores: from research tools to clinical instruments

(2020) Cathryn M. Lewis et al.   Genome Medicine

Integrating Multi-Omics Data by Learning Modality Invariant Representations for Improved Prediction of Overall Survival of Cancer

(2020) Li Tong et al.   METHODS

Diverse proteins aggregate in mild cognitive impairment and Alzheimer’s disease brain

(2020) Devin Kepchia et al.   Alzheimers Research & Therapy

Varmole: A biologically drop-connect deep neural network model for prioritizing disease risk variants and genes

(2020) Nam D Nguyen et al.   BIOINFORMATICS

Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network

(2020) Akram Yazdani et al.   BMC BIOINFORMATICS

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions

(2020) Solveig K. Sieberts et al.   Scientific Data

Rho GTPases in the Amygdala—A Switch for Fears?

(2020) Tasnuva Sarowar et al.   Cells

Association of Sensory Impairments With Cognitive Decline and Depression Among Older Adults in China

(2020) Hongguo Rong et al.   JAMA Network Open

Brain transcriptome wide association study (TWAS) implicates 8 genes across 6 loci in Alzheimer’s disease

(2020) Jake Gockley et al.   Alzheimers & Dementia

LDpred2: better, faster, stronger

(2020) Florian Privé et al.   BIOINFORMATICS

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

Predicting Alzheimer’s disease progression using multi-modal deep learning approach

(2019) Garam Lee et al.   Scientific Reports

Opportunities and challenges for transcriptome-wide association studies

(2019) Michael Wainberg et al.   NATURE GENETICS

Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

(2019) Brian W. Kunkle et al.   NATURE GENETICS

Exploring the use of molecular dynamics in assessing protein variants for phenotypic alterations

(2019) Aditi Garg et al.   HUMAN MUTATION

The role of inflammation and endoplasmic reticulum stress in obesity-related cognitive impairment

(2019) Yilan Liu et al.   LIFE SCIENCES

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

PRSice-2: Polygenic Risk Score software for biobank-scale data

(2019) Shing Wan Choi et al.   GigaScience

Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas

(2019) Federico Scala et al.   Nature Communications

Multimodal Integration of Brain Images for MRI-Based Diagnosis in Schizophrenia

(2019) Raymond Salvador et al.   Frontiers in Neuroscience

Making multi-omics data accessible to researchers

(2019) Ana Conesa et al.   Scientific Data

OUP accepted manuscript

(2018)   BIOINFORMATICS

HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues

(2018) Gen Li et al.   BMC BIOINFORMATICS

Functional analysis of schizophrenia genes using GeneAnalytics program and integrated databases

(2018) Tharani Sundararajan et al.   GENE

A multimodal deep neural network for human breast cancer prognosis prediction by integrating multi-dimensional data

(2018) Dongdong Sun et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights

(2018) Alexander Gusev et al.   NATURE GENETICS

The personal and clinical utility of polygenic risk scores

(2018) Ali Torkamani et al.   NATURE REVIEWS GENETICS

(Micro)Glia as Effectors of Cortical Volume Loss in Schizophrenia

(2018) Allyson P Mallya et al.   SCHIZOPHRENIA BULLETIN

Classification of First-Episode Schizophrenia Using Multimodal Brain Features: A Combined Structural and Diffusion Imaging Study

(2018) Sugai Liang et al.   SCHIZOPHRENIA BULLETIN

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

(2018) Alvaro N. Barbeira et al.   Nature Communications

GWAS on family history of Alzheimer’s disease

(2018) Riccardo E. Marioni et al.   Translational Psychiatry

Implications of Newly Identified Brain eQTL Genes and Their Interactors in Schizophrenia

(2018) Lei Cai et al.   Molecular Therapy-Nucleic Acids

OUP accepted manuscript

(2018)   SCHIZOPHRENIA BULLETIN

A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research

(2018) Philip L. De Jager et al.   Scientific Data

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma

(2018) Li Zhang et al.   Frontiers in Genetics

Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data

(2017) Shweta Bagewadi Kawalia et al.   JOURNAL OF ALZHEIMERS DISEASE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

The genomic landscape of tuberous sclerosis complex

(2017) Katie R. Martin et al.   Nature Communications

Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization

(2017) Xiaoquan Wen et al.   PLoS Genetics

Endoplasmic Reticulum Stress and Disrupted Neurogenesis in the Brain Are Associated with Cognitive Impairment and Depressive-Like Behavior after Spinal Cord Injury

(2016) Junfang Wu et al.   JOURNAL OF NEUROTRAUMA

Age-Related Sensory Impairments and Risk of Cognitive Impairment

(2016) Mary E. Fischer et al.   JOURNAL OF THE AMERICAN GERIATRICS SOCIETY

Classifying Schizophrenia Using Multimodal Multivariate Pattern Recognition Analysis: Evaluating the Impact of Individual Clinical Profiles on the Neurodiagnostic Performance

(2016) Carlos Cabral et al.   SCHIZOPHRENIA BULLETIN

G Protein-Coupled Receptors (GPCRs) in Alzheimer’s Disease: A Focus on BACE1 Related GPCRs

(2016) Juan Zhao et al.   Frontiers in Aging Neuroscience

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

A molecular pathway analysis informs the genetic background at risk for schizophrenia

(2015) Concetta Crisafulli et al.   PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Cross-validation pitfalls when selecting and assessing regression and classification models

(2014) Damjan Krstajic et al.   Journal of Cheminformatics

Genotype to phenotype: lessons from model organisms for human genetics

(2013) Ben Lehner   NATURE REVIEWS GENETICS

N-Glycosylation of GABAA Receptor Subunits is Altered in Schizophrenia

(2013) Toni Marie Mueller et al.   NEUROPSYCHOPHARMACOLOGY

Role of endoplasmic reticulum Ca2+ signaling in the pathogenesis of Alzheimer disease

(2013) Elena Popugaeva et al.   Frontiers in Molecular Neuroscience

From phenotype to genotype: an association study of longitudinal phenotypic markers to Alzheimer's disease relevant SNPs

(2012) H. Wang et al.   BIOINFORMATICS

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Gene expression analysis reveals schizophrenia-associated dysregulation of immune pathways in peripheral blood mononuclear cells

(2012) Erin J. Gardiner et al.   JOURNAL OF PSYCHIATRIC RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them)

(2011) D. Berrar et al.   BRIEFINGS IN BIOINFORMATICS

Dysregulated phosphorylation of Ca2+/calmodulin-dependent protein kinase II-α in the hippocampus of subjects with mild cognitive impairment and Alzheimer’s disease

(2011) Lindsay C. Reese et al.   JOURNAL OF NEUROCHEMISTRY

Hypothesis review: are clathrin-mediated endocytosis and clathrin-dependent membrane and protein trafficking core pathophysiological processes in schizophrenia and bipolar disorder?

(2011) K O Schubert et al.   MOLECULAR PSYCHIATRY

Abnormal Activity of the MAPK- and cAMP-Associated Signaling Pathways in Frontal Cortical Areas in Postmortem Brain in Schizophrenia

(2011) Adam J Funk et al.   NEUROPSYCHOPHARMACOLOGY

Genome-wide association studies: the key to unlocking neurodegeneration?

(2010) Sonia Gandhi et al.   NATURE NEUROSCIENCE

Identifying gene regulatory networks in schizophrenia

(2010) Steven G. Potkin et al.   NEUROIMAGE

Relative Contribution of Feedforward Excitatory Connections to Expression of Ocular Dominance Plasticity in Layer 4 of Visual Cortex

(2010) Lena A. Khibnik et al.   NEURON

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

(2010) C. Zhang et al.   SCIENCE

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

A systematic analysis of performance measures for classification tasks

(2009) Marina Sokolova et al.   INFORMATION PROCESSING & MANAGEMENT

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

The 844ins68 polymorphism of the cystathionine beta-synthase gene is associated with schizophrenia

(2009) Vera Golimbet et al.   PSYCHIATRY RESEARCH

Fibroblast Growth Factors in Schizophrenia

(2009) A. F. T. van Scheltinga et al.   SCHIZOPHRENIA BULLETIN

The determination of projection neuron identity in the developing cerebral cortex

(2008) Dino P Leone et al.   CURRENT OPINION IN NEUROBIOLOGY

Sizing up human height variation

(2008) Peter M Visscher   NATURE GENETICS

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS