List of works by Michael P. Snyder

A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data ⬇️

scientific article (publication date: 17 October 2003)

A Customizable Analysis Flow in Integrative Multi-Omics

scientific article published on 27 November 2020

A Droplet Microfluidics Based Platform for Mining Metagenomic Libraries for Natural Compounds

scientific article published on 25 July 2017

A Quantitative Proteome Map of the Human Body

scientific article published on 05 September 2020

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

scientific article

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

A dynamic approach to mapping coordinates between microplates and microarrays

scientific article

A genome-scale resource for in vivo tag-based protein function exploration in C. elegans

scientific article

A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth

scientific article published on 9 January 2018

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation

scientific article

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

scientific article published on 2 April 2018

A high throughput embryonic stem cell screen identifies Oct-2 as a bifunctional regulator of neuronal differentiation

scientific article published on March 2009

A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster

scientific article

A high-stringency blueprint of the human proteome

scientific article published on 16 October 2020

A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells

scientific article published on September 2012

A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1.

scientific article

A limited set of transcriptional programs define major cell types

scientific article published on 29 July 2020

A longitudinal big data approach for precision health

scientific article published on 08 May 2019

A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity

scientific article published on 12 April 2022

A machine-compiled database of genome-wide association studies

scientific article published on 26 July 2019

A major epigenetic programming mechanism guided by piRNAs

scientific article published on 21 February 2013

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

scientific article

A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA.

scientific article

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

scientific article published in September 2005

A plethora of sites

scientific article

A procedure for highly specific, sensitive, and unbiased whole-genome amplification

scholarly article

A proposal for validation of antibodies.

scientific article published on 5 September 2016

A question of size: the eukaryotic proteome and the problems in defining it.

scientific article published on March 2002

A scalable, secure, and interoperable platform for deep data-driven health management

scientific article published on 01 October 2021

A single-molecule long-read survey of the human transcriptome

scientific article

A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.

scientific article published in February 2002

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge

scientific article

AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae.

scientific article published on 17 March 2015

Abstract B38: Splice variants in aggressive human breast cancer subtypes

Accurate identification and analysis of human mRNA isoforms using deep long read sequencing

scientific article

Achieving high-sensitivity for clinical applications using augmented exome sequencing

scientific article

Advances in functional protein microarray technology

scientific article

AlleleSeq: analysis of allele-specific expression and binding in a network framework

scientific article published on 2 August 2011

An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans.

scientific article

An encyclopedia of mouse DNA elements (Mouse ENCODE).

scientific article

An exercise-inducible metabolite that suppresses feeding and obesity ⬇️

scientific article published on 15 June 2022

An integrated approach for finding overlooked genes in yeast.

scientific article published in January 2002

An integrated global regulatory network of hematopoietic precursor cell self-renewal and differentiation.

scientific article

An integrative ENCODE resource for cancer genomics

scientific article published on 29 July 2020

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

scientific article published on 08 October 2008

Analysis of the Complete Genome Sequence of a Novel, Pseudorabies Virus Strain Isolated in Southeast Europe

scientific article published on 04 April 2019

Analyzing antibody specificity with whole proteome microarrays

scientific article published on 09 November 2003

Annotating non-coding regions of the genome

scientific article

Annotation of functional variation in personal genomes using RegulomeDB

scientific article (publication date: September 2012)

Annotation of spatially resolved single-cell data with STELLAR

scientific article published on 24 October 2022

Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery

scientific article

Architecture of the human regulatory network derived from ENCODE data

scientific article (publication date: 6 September 2012)

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

scientific article published on 21 November 2006

Association of AHSG with alopecia and mental retardation (APMR) syndrome

scientific article published on 4 January 2017

Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma.

scientific article published on 13 November 2017

Author Correction: Novel mutations in PIEZO1 cause an autosomal recessive generalized lymphatic dysplasia with non-immune hydrops fetalis

scientific article published on 26 April 2019

Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder

scientific article published on 16 February 2018

BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments

scientific article published on January 2006

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

scientific article

CREB binds to multiple loci on human chromosome 22.

scientific article published on May 2004

Can Metabolic Profiles Be Used as a Phenotypic Readout of the Genome to Enhance Precision Medicine?

scientific article published on 9 March 2016

Candidate variants in TUB are associated with familial tremor

scientific article published on 21 September 2020

Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers

scientific article published on 25 November 2020

Centromere-like regions in the budding yeast genome

scientific article

ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites

scientific article

ChIP-Seq: a method for global identification of regulatory elements in the genome.

scientific article published in July 2010

ChIP-chip: a genomic approach for identifying transcription factor binding sites

scientific article

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

Challenges and recommendations for epigenomics in precision health.

scientific article published in December 2017

Characterization of enhancer function from genome-wide analyses

scientific article published on 11 June 2012

Characterization of novel transcripts in pseudorabies virus.

scientific article published on 22 May 2015

Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing

scientific article

Charging it up: global analysis of protein phosphorylation

scientific article published on 5 September 2006

Chromatin Remodeling in Response to BRCA2-Crisis

scientific article published on 01 August 2019

Chromatin accessibility associates with protein-RNA correlation in human cancer

scientific article published on 30 September 2021

Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans

scientific article published on January 2014

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

scientific article published on 01 July 2020

Circular DNA elements of chromosomal origin are common in healthy human somatic tissue.

scientific article published on 14 March 2018

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

scientific article

Classifying non-small cell lung cancer types and transcriptomic subtypes using convolutional neural networks

scientific article published on 01 May 2020

CliniDigest: A Case Study in Large Language Model Based Large-Scale Summarization of Clinical Trial Descriptions

scientific article published on 15 August 2023

Clinical interpretation and implications of whole-genome sequencing

scientific article published in March 2014

Close association of RNA polymerase II and many transcription factors with Pol III genes

scientific article

Cloud-based Interactive Analytics for Terabytes of Genomic Variants Data

scientific article published on 26 July 2017

Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association

scientific article

Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'

scientific article published on 27 June 2019

Comparative analysis of regulatory information and circuits across distant species

scientific article

Comparative annotation of functional regions in the human genome using epigenomic data

scientific article

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae

scientific article

Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes

scientific article

Computational Methods and Bioinformatic Tools

Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis

scientific article published on 25 April 2016

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data

scientific article

Cooperative transcription factor associations discovered using regulatory variation

scientific article

Correction: AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae.

scientific article published on 27 May 2015

Corrigendum: Long-read sequencing of the human cytomegalovirus transcriptome with the pacific biosciences RSII platform.

scientific article published on 6 March 2018

Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution

scientific article published in Nature

Corrigendum: Secure cloud computing for genomic data

scientific article

Cross-Platform Comparison of Untargeted and Targeted Lipidomics Approaches on Aging Mouse Plasma

scientific article published in Scientific Reports

Cumulative Lifetime Burden of Cardiovascular Disease From Early Exposure to Air Pollution

scientific article published on 15 March 2020

Cytoskeletal Activation of a Checkpoint Kinase ⬇️

scientific article published on September 1, 2003

DNA gyrase on the bacterial chromosome: DNA cleavage induced by oxolinic acid ⬇️

scientific article published on June 25, 1979

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states

scientific article

De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease.

scientific article published on 26 January 2017

Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs

scientific article

Decoding the Genomics of Abdominal Aortic Aneurysm

scientific article published on 01 September 2018

Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing

scientific article published on 25 November 2019

Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California

scientific article published on 01 October 2020

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

scientific article

Defining functional DNA elements in the human genome

scientific article

Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research

Design optimization methods for genomic DNA tiling arrays

scientific article

Detecting and annotating genetic variations using the HugeSeq pipeline

scientific article

Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays

scholarly article

Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis

scientific article

Discovery of stress responsive DNA regulatory motifs in Arabidopsis

scientific article

Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis.

scientific article published in December 2016

Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing

scientific article

Dissecting phosphorylation networks: lessons learned from yeast

scientific article

Distinct genomic aberrations associated with ERG rearranged prostate cancer

scientific article published on April 2009

Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes

scientific article

Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells.

scientific article published on 4 April 2018

Distribution of NF-kappaB-binding sites across human chromosome 22

scientific article

Divergence of transcription factor binding sites across related yeast species

scientific article

Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes

scientific article

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches

scientific article

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

scientific article

Dual Platform Long-Read RNA-Sequencing Dataset of the Human Cytomegalovirus Lytic Transcriptome

scientific article published on 27 September 2018

Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring

scientific article published on 01 September 2018

Dynamic Transcriptome Profiling Dataset of Vaccinia Virus Obtained from Long-read Sequencing Techniques

scientific article published on 01 December 2018

Dynamic and complex transcription factor binding during an inducible response in yeast

scientific article published on June 2009

Dynamic trans-acting factor colocalization in human cells

scientific article published on 24 October 2013

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

scientific article

EBNA1 regulates cellular gene expression by binding cellular promoters

scientific article

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

scientific article

Erratum: Corrigendum: Performance comparison of whole-genome sequencing platforms

scholarly article by Hugo Y K Lam et al published June 2012 in Nature Biotechnology

Evaluation of the impact of ul54 gene-deletion on the global transcription and DNA replication of pseudorabies virus

scientific article published on 2 June 2017

Evaluation of whole exome sequencing as an alternative to BeadChip and whole genome sequencing in human population genetic analysis

scientific article published on 29 October 2018

Exome Sequencing of Neonatal Blood Spots and the Identification of Genes Implicated in Bronchopulmonary Dysplasia

scientific article

Exome sequencing by targeted enrichment

scientific article published on 01 January 2013

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Exploring successful community pharmacist-physician collaborative working relationships using mixed methods ⬇️

scientific article published on February 11, 2010

ExpressYourself: A modular platform for processing and visualizing microarray data

scientific article

Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses

scientific article

Extensive transcript diversity and novel upstream open reading frame regulation in yeast

scientific article published on February 2013

Extensive variation in chromatin states across humans

scientific article

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies

scientific article published on January 2006

Fast Metagenomic Binning via Hashing and Bayesian Clustering

scientific article published on 16 April 2018

Fast optimal genome tiling with applications to microarray design and homology search.

scientific article published in January 2004

Fetal de novo mutations and preterm birth

scientific article

Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips

scientific article

Full Genome Sequence of the Western Reserve Strain of Vaccinia Virus Determined by Third-Generation Sequencing.

scientific article published on 15 March 2018

Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus

scientific article

Functional profiling of the Saccharomyces cerevisiae genome

scientific article (publication date: 25 July 2002)

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis

scientific article

Gene-Environment Interaction in the Era of Precision Medicine

scientific article published on 01 March 2019

Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci

scientific article published on 20 February 2014

Genetic Adaptation of Porcine Circovirus Type 1 to Cultured Porcine Kidney Cells Revealed by Single-Molecule Long-Read Sequencing Technology.

scientific article published on 2 February 2017

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

scientific article

Genetic analysis of variation in transcription factor binding in yeast

scientific article published on 17 March 2010

Genome interpretation and assembly-recent progress and next steps

scientific article published on November 2012

Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer

scientific article

Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations

scientific article

Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. ⬇️

scientific article

Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni

scientific article published on 11 September 2019

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response

scientific article

Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms

scientific article

Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes

scientific article

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

scientific article (publication date: August 2007)

Genome-wide profiling of human cap-independent translation-enhancing elements

scientific article

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

scientific article published on 11 September 2008

Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae

scientific article

Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2.

scientific article published on 10 August 2015

Genomic analysis of regulatory network dynamics reveals large topological changes

scientific article

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

scientific article published on 25 April 2010

Genomics. Defining genes in the genomics era.

scientific article published in April 2003

Getting connected: analysis and principles of biological networks

scientific article published on May 2007

Global analysis of gene expression in yeast

scientific article

Global analysis of protein function using protein microarrays

scientific article

Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes

scientific article published on 15 September 2009

Global analysis of transcription factor-binding sites in yeast using ChIP-Seq.

scientific article

Global changes in STAT target selection and transcription regulation upon interferon treatments

scientific article

Global identification of human transcribed sequences with genome tiling arrays

scientific article (publication date: 24 December 2004)

Global identification of protein kinase substrates by protein microarray analysis

scientific article published on January 2009

Global metabolic profiling to model biological processes of aging in twins

scientific article published on 19 November 2019

Glucotypes reveal new patterns of glucose dysregulation

scientific article published on 24 July 2018

Gpr124 is essential for blood-brain barrier integrity in central nervous system disease

scientific article published on 13 March 2017

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

scientific article published on 19 November 2015

H3K4me3 breadth is linked to cell identity and transcriptional consistency.

scientific article published on July 2014

HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS.

scientific article

HAT1 Coordinates Histone Production and Acetylation via H4 Promoter Binding

scientific article published on 02 July 2019

HTRA1 promoter polymorphism in wet age-related macular degeneration

scientific article

Heterogeneity in old fibroblasts is linked to variability in reprogramming and wound healing

scientific article published on 23 October 2019

High Throughput Sequencing and Assessing Disease Risk

scientific article published on 02 January 2019

High-Coverage Whole-Exome Sequencing Identifies Candidate Genes for Suicide in Victims with Major Depressive Disorder.

scientific article published on 2 August 2017

High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients

scientific article published on 07 June 2019

High-frequency actionable pathogenic exome variants in an average-risk cohort

scientific article published on 17 December 2018

High-quality binary protein interaction map of the yeast interactome network

scientific article

High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution

scientific article

High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays

scientific article

How many human proteoforms are there?

scientific article published in February 2018

Human-engineered Treg-like cells suppress FOXP3-deficient T cells but preserve adaptive immune responses <i>in vivo</i>

scientific article published on 25 November 2020

Humans Are Selectively Exposed to Pneumocystis jirovecii

scientific article published on 10 March 2020

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders

scientific article published on November 2015

Identification of STAT5A and STAT5B target genes in human T cells

scientific article published on 30 January 2014

Identification of a novel mutation in the APTX gene associated with ataxia-oculomotor apraxia.

scientific article published on 26 June 2017

Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays

scholarly article

Identification of end‐stage renal disease metabolic signatures from human perspiration

scientific article published on 9 January 2023

Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis

scientific article

Identification of genomic indels and structural variations using split reads

scientific article

Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens

scientific article published on 05 November 2018

Identification of potential glycan cancer markers with sialic acid attached to sialic acid and up-regulated fucosylated galactose structures in epidermal growth factor receptor secreted from A431 cell line

scientific article published on 31 January 2013

Immunologic effects of forest fire exposure show increases in IL-1β and CRP

scientific article published on 28 February 2020

Impact of chromatin structures on DNA processing for genomic analyses

scientific article

Insertional mutagenesis: transposon-insertion libraries as mutagens in yeast

scientific article

Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance

scientific article published on 21 June 2016

Integrated analysis of co-expressed MAP kinase substrates in Arabidopsis thaliana

scientific article published on 25 June 2009

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

scientific article

Integrated systems analysis reveals a molecular network underlying autism spectrum disorders

scientific article published on 30 December 2014

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants

scientific article

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

scientific article published on 16 January 2018

Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile

scientific article

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

Integrative omics for health and disease.

scientific article published on 26 February 2018

Interpretome: a freely available, modular, and secure personal genome interpretation engine

scientific article published on January 2012

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

scientific article published on August 2005

Kinase substrate interactions.

scientific article published in January 2011

Landscape of cohesin-mediated chromatin loops in the human genome

scientific article published on 29 July 2020

Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon

scientific article

Leptin affects endocardial cushion formation by modulating EMT and migration via Akt signaling cascades

scientific article published on 14 April 2008

Lifelong physical activity is associated with promoter hypomethylation of genes involved in metabolism, myogenesis, contractile properties and oxidative stress resistance in aged human skeletal muscle

article

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

scientific article published on 15 August 2016

Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.

scientific article published on 14 August 2017

Linking DNA-binding proteins to their recognition sequences by using protein microarrays

scientific article

Linking disease associations with regulatory information in the human genome

scientific article

Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1.

scientific article

Long-Read Sequencing - A Powerful Tool in Viral Transcriptome Research

scientific article published on 26 February 2019

Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses

scientific article published on 17 July 2018

Long-Read Sequencing Reveals a GC Pressure during the Evolution of Porcine Endogenous Retrovirus

scientific article published on 5 October 2017

Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials.

scientific article

Long-read sequencing of the human cytomegalovirus transcriptome with the Pacific Biosciences RSII platform.

scientific article published on 19 December 2017

Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 with Clostridia and Insulin Sensitivity in Humans

scientific article published on 04 May 2020

Longitudinal multi-omics of host-microbe dynamics in prediabetes

scientific article published on 29 May 2019

Longitudinal personal DNA methylome dynamics in a human with a chronic condition

scientific article published on 05 November 2018

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays

scientific article published on 18 December 2008

MISTERMINATE Mechanistically Links Mitochondrial Dysfunction with Proteostasis Failure

scientific article published on 01 August 2019

MITI minimum information guidelines for highly multiplexed tissue images

scientific article published on 01 March 2022

MOTIPS: automated motif analysis for predicting targets of modular protein domains

scientific article

MSB: a mean-shift-based approach for the analysis of structural variation in the genome

scientific article published on 26 November 2008

Macrophage de novo NAD+ synthesis specifies immune function in aging and inflammation

scientific article published on 26 November 2018

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function

scientific article published in June 2004

Mapping accessible chromatin regions using Sono-Seq

scientific article

Mapping copy number variation by population-scale genome sequencing

scientific article

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies

scientific article

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).

scientific article published on June 2007

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

scientific article published in 2021

Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility

scientific article published on 08 July 2019

Measuring the evolutionary rewiring of biological networks

scientific article

Meta-analytic approach for transcriptome profiling of herpes simplex virus type 1

scientific article published on 09 July 2020

Metabolites as global regulators: a new view of protein regulation: systematic investigation of metabolite-protein interactions may help bridge the gap between genome-wide association studies and small molecule screening studies

scientific article published on 14 April 2011

Metabolome progression during early gut microbial colonization of gnotobiotic mice

scientific article published on 29 June 2015

Metadata Checklist for the Integrated Personal Omics Study: Proteomics and Metabolomics Experiments

scientific article published on December 2013

Metadata checklist for the integrated personal OMICS study: proteomics and metabolomics experiments

scientific article (publication date: 2014)

Metformin Affects Heme Function as a Possible Mechanism of Action

scientific article published on 07 February 2019

Microarrays to characterize protein interactions on a whole‐proteome scale ⬇️

scientific article published on November 1, 2003

Microbial synergy via an ethanol-triggered pathway

scientific article

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

scientific article published in December 2017

Minimum information about a protein affinity reagent (MIAPAR)

scientific article published on 01 July 2010

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

scientific article

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

scientific article published on 06 September 2019

Modeling ChIP sequencing in silico with applications

scientific article

Molecular Choreography of Acute Exercise

scientific article published on 01 May 2020

Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing

scientific article

Much ado about nothing: A qualitative study of the experiences of an average-risk population receiving results of exome sequencing

scientific article published on 05 March 2019

Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus.

scientific article published in January 2017

Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma

scientific article published on 22 July 2020

Multi-platform analysis reveals a complex transcriptome architecture of a circovirus

scientific article published on 23 May 2017

Multiplatform next-generation sequencing identifies novel RNA molecules and transcript isoforms of the endogenous retrovirus isolated from cultured cells.

scientific article published on 18 January 2018

Multiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome

scientific article published on 24 September 2019

Multiple Pairwise Analysis of Non-homologous Centromere Coupling Reveals Preferential Chromosome Size-Dependent Interactions and a Role for Bouquet Formation in Establishing the Interaction Pattern

scientific article

Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway

scientific journal article

Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body

scientific article published on 24 January 2008

NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells.

scientific article

Nat1 Deficiency Is Associated with Mitochondrial Dysfunction and Exercise Intolerance in Mice

scientific article published on October 2016

Natural Selection Has Differentiated the Progesterone Receptor among Human Populations

scientific article published on 21 June 2018

Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I

scientific article

Network analyses identify liver-specific targets for treating liver diseases

scientific article published on 21 August 2017

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis

scientific article published on March 2007

Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem-cell self-renewal

scientific article

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

scientific article

Omics AnalySIs System for PRecision Oncology (OASISPRO): A Web-based Omics Analysis Tool for Clinical Phenotype Prediction.

scientific article published on 12 September 2017

Omics Profiling in Precision Oncology

scientific article published on 20 April 2016

Optimized Analytical Procedures for the Untargeted Metabolomic Profiling of Human Urine and Plasma by Combining Hydrophilic Interaction (HILIC) and Reverse-Phase Liquid Chromatography (RPLC)-Mass Spectrometry

scientific article published on 18 March 2015

PATH-SCAN: a reporting tool for identifying clinically actionable variants

scientific article

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

scientific article (publication date: 23 February 2009)

PPARγ-p53-Mediated Vasculoregenerative Program to Reverse Pulmonary Hypertension

scientific article published on 16 December 2020

Paired-end mapping reveals extensive structural variation in the human genome

scientific article

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

scientific article

Performance comparison of exome DNA sequencing technologies

scientific article

Performance comparison of whole-genome sequencing platforms

scientific article

Personal Omics for Precision Health

scientific article published on 01 April 2018

Personal aging markers and ageotypes revealed by deep longitudinal profiling

scientific article published on 13 January 2020

Personal genome sequencing: current approaches and challenges

scientific article

Personal genomes, quantitative dynamic omics and personalized medicine

scientific article

Personal omics profiling reveals dynamic molecular and medical phenotypes

scientific article (publication date: 16 March 2012)

Personal phenotypes to go with personal genomes

scientific article published on 19 May 2009

Perspectives on ENCODE

scientific article published on 29 July 2020

Phased whole-genome genetic risk in a family quartet using a major allele reference sequence

scientific article

Phenotypically Silent Bone Morphogenetic Protein Receptor 2 Mutations Predispose Rats to Inflammation-Induced Pulmonary Arterial Hypertension by Enhancing the Risk for Neointimal Transformation

scientific article published on 29 August 2019

Physiological blood-brain transport is impaired with age by a shift in transcytosis

scientific article published on 01 July 2020

Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool

scientific article published on 7 December 2006

Pre-symptomatic detection of COVID-19 from smartwatch data

scientific article published on 18 November 2020

Precision medicine: role of proteomic in changing clinical management and care

scientific article published on 22 October 2018

Predicting Ovarian Cancer Patients' Clinical Response to Platinum-Based Chemotherapy by Their Tumor Proteomic Signatures

scientific article published on 17 June 2016

Predicting essential genes in fungal genomes

scientific article published on 9 August 2006

Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features

scientific article published on 16 August 2016

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

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ProCAT: a data analysis approach for protein microarrays

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Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

scientific article published on 2 August 2015

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project

scientific article published on 23 August 2018

Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

scientific article published on 13 September 2019

Prospects and challenges in proteomics.

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Protein analysis on a proteomic scale

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Protein complexes take the bait

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Protein microarrays

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Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405.

scientific article published on 13 March 2013

Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1

scientific article published on February 2016

Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects

scientific journal article

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

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Quantifying environmental adaptation of metabolic pathways in metagenomics

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RNA polymerase II stalling: loading at the start prepares genes for a sprint

scientific article published on 2 May 2008

RNA sequencing

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RNA-Seq: a method for comprehensive transcriptome analysis

scientific article published on January 2010

RNA-Seq: a revolutionary tool for transcriptomics

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RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

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Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

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Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene

scientific article published on 01 December 2020

Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.

scientific article published on March 2015

Recurrent somatic mutations in regulatory regions of human cancer genomes

scientific article published on 8 June 2015

Regulation of gene expression by a metabolic enzyme

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Regulatory analysis of the C. elegans genome with spatiotemporal resolution

scientific article published on August 2014

Regulatory variation within and between species.

scientific article published on January 2011

Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension

scientific article published on 03 April 2020

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

Reproducibility: In praise of open research measures

scientific article published in June 2013

Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, according to the HUPO Human Proteome Project

scientific article published on 15 September 2020

RobNorm: Model-Based Robust Normalization Method for Labeled Quantitative Mass Spectrometry Proteomics Data

scientific article published on 24 October 2020

STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma

scientific article published on 09 December 2013

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud

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Secure cloud computing for genomic data

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Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

scientific article published on September 2012

Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data

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Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females

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Serum profiling using protein microarrays to identify disease related antigens

scientific article published on January 2014

Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray

scholarly article

Sexual dimorphism in mammalian gene expression

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Smooth Muscle Contact Drives Endothelial Regeneration by BMPR2-Notch1-Mediated Metabolic and Epigenetic Changes

scientific article published on 01 January 2019

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

scientific article published in 2021

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

scientific article published in September 2017

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

scientific article published in June 2007

Strain Kaplan of Pseudorabies Virus Genome Sequenced by PacBio Single-Molecule Real-Time Sequencing Technology

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Structured RNAs in the ENCODE selected regions of the human genome

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Studies concerning the temporal and genetic control of cell polarity in Saccharomyces cerevisiae ⬇️

scientific article published on August 1, 1991

Succinate and its G-protein-coupled receptor stimulates osteoclastogenesis.

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Superhelical Escherichia coli DNA: Relaxation by coumermycin ⬇️

scientific article published on April 5, 1978

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

scientific article published on 5 June 2014

Swarm: A federated cloud framework for large-scale variant analysis

scientific article published on 12 May 2021

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

scientific article (publication date: 2016)

Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen

scientific article published on 17 September 2019

Systematic Identification of Regulators of Oxidative Stress Reveals Non-canonical Roles for Peroxisomal Import and the Pentose Phosphate Pathway

scientific article published on 01 February 2020

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

scientific article published on 3 January 2008

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

scientific article published on 7 February 2008

Systematic functional regulatory assessment of disease-associated variants.

scientific article published on 20 May 2013

Systematic identification of silencers in human cells

scientific article published on 24 February 2020

Systematic investigation of protein-small molecule interactions.

scientific article published on 07 December 2012

Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome

scholarly article

Systems biology approaches to disease marker discovery

scientific article published on January 2010

TOS9 regulates white-opaque switching in Candida albicans

scientific article published on September 2006

Target hub proteins serve as master regulators of development in yeast

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Template-switching artifacts resemble alternative polyadenylation

scientific article published on 08 November 2019

Tet enzymes are essential for early embryogenesis and completion of embryonic genome activation

scientific article published on 06 December 2021

The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics

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The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.

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The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

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The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

scientific article published on 01 April 2020

The MEK5-ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer

scientific article published on 22 January 2020

The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight

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The TRIPLES database: a community resource for yeast molecular biology

scientific article published on January 2002

The X chromosome from telomere to telomere: key achievements and future opportunities

scientific article published in 2021

The current excitement about copy-number variation: how it relates to gene duplications and protein families

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The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors.

scientific article published on 23 October 2007

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies

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The genetic predisposition to bronchopulmonary dysplasia

scientific article published on 8 March 2016

The human proteome project: Current state and future direction.

scientific article published on 29 April 2011

The transcriptional activity of human Chromosome 22

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The transcriptional landscape of the yeast genome defined by RNA sequencing

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The variable somatic genome

scientific article published on 19 December 2012

Tilescope: online analysis pipeline for high-density tiling microarray data

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Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs

scientific article published on 23 January 2013

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation

scientific article published on 20 September 2017

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

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Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

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Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms

scientific article published on 19 July 2007

Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture

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Transcriptome-wide survey of pseudorabies virus using next- and third-generation sequencing platforms.

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Transcriptomic study of Herpes simplex virus type-1 using full-length sequencing techniques

scientific article published on 27 November 2018

Transformation of Candida albicans with a synthetic hygromycin B resistance gene ⬇️

scientific article published on 24 August 2010

Transglutaminase 4 as a prostate autoantigen in male subfertility

scientific article published on June 2015

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

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Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

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Unlocking the secrets of the genome

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VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

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Value of Circulating Cytokine Profiling During Submaximal Exercise Testing in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

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Variation and genetic control of protein abundance in humans

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Variation in transcription factor binding among humans

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WISP3 mutation associated with Pseudorheumatoid Dysplasia

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Where Next for Genetics and Genomics?

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Whole-Exome Enrichment with the Agilent SureSelect Human All Exon Platform

scientific article published on 11 March 2015

Whole-Exome Enrichment with the Illumina TruSeq Exome Enrichment Platform

scientific article published on 11 March 2015

Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform

scientific article published on 11 March 2015

Whole-exome sequencing data of suicide victims who had suffered from major depressive disorder

scientific article published on 05 February 2019

Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias.

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Whole-genome haplotyping using long reads and statistical methods

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Windows Into Human Health Through Wearables Data Analytics

scientific article published on 28 January 2019

X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils

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YMD: a microarray database for large-scale gene expression analysis.

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Yeast genomics: past, present, and future promise

scientific article published on 01 September 2002

mTOR-mediated dedifferentiation of the retinal pigment epithelium initiates photoreceptor degeneration in mice.

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