List of works by John Quackenbush

A Gene Map of the Human Genome

scientific article

A concise guide to cDNA microarray analysis

scientific article

A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution

scientific article

A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers

scientific article

A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets

scientific article published on 27 November 2013

A guide to microarray experiments-an open letter to the scientific journals

scientific article published in The Lancet

A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study

scientific article

A network model for angiogenesis in ovarian cancer

scientific article published on 11 April 2015

A network-based approach to eQTL interpretation and SNP functional characterization

A nucleotide substitution in the promoter of human angiotensinogen is associated with essential hypertension and affects basal transcription in vitro

scientific article published on April 1997

A robust method for the amplification of RNA in the sense orientation

scientific article

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

scientific article

A three-gene model to robustly identify breast cancer molecular subtypes

scientific article published on 18 January 2012

A tiered hidden Markov model characterizes multi-scale chromatin states

scientific article (publication date: July 2013)

Abstract 4922:KRASandBRAFmutations influence correlation structure of locus-specific CpG island methylation and CIMP in colorectal cancer

Accelerating genomic data publishing and sharing

scientific article

An STS content map of human chromosome 11: localization of 910 YAC clones and 109 islands

scientific article published on September 1995

An STS-based radiation hybrid map of the human genome

scientific article published on May 1997

An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

scientific article

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).

scientific article

An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks

scientific article published in 2022

An open letter on microarray data from the MGED Society

scientific article published on November 2004

An optimized predictive strategy for interactome mapping

scientific article published on 22 July 2008

An optimized protocol for analysis of EST sequences

scientific article published on September 2000

Analysis of Array Data and Clinical Validation of Array-Based Assays

Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index

scientific article

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD

scientific article

Anchoring of rice BAC clones to the rice genetic map in silico

scientific article

Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer

scientific article (publication date: 2012)

Artificial intelligence in radiology

scientific article published on 01 August 2018

Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays

scientific article

Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data

scientific article

Assessment of pharmacogenomic agreement

scientific article

AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum

scientific article

BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52

scientific article published on 03 February 2021

BatchQC: interactive software for evaluating sample and batch effects in genomic data

scientific article

Bioinformatics for next generation sequencing.

scientific article

Biomarker correlation network in colorectal carcinoma by tumor anatomic location

scientific article

Bipartite Community Structure of eQTLs ⬇️

scientific article

BmiGI: a database of cDNAs expressed in Boophilus microplus, the tropical/southern cattle tick

scientific article published on 27 March 2005

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data

scientific article

COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing

scientific article

CRX is a diagnostic marker of retinal and pineal lineage tumors

scientific article

CXCR4 pathway associated with family history of melanoma

scientific article

Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research

scientific article published in November 2017

Cancer subtype identification using somatic mutation data

Cancer subtype identification using somatic mutation data.

scientific article published on 16 May 2018

Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation

scientific article published on 4 May 2011

Cardiac transcriptional response to acute and chronic angiotensin II treatments

scientific article published on 08 July 2004

Career Issues

scientific article published in Science

Challenges and emerging directions in single-cell analysis

scientific article published on 8 May 2017

Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment

scientific article published on 10 January 2012

Characterization of a Vibrio vulnificus LysR homologue, HupR, which regulates expression of the haem uptake outer membrane protein, HupA.

scientific article published in December 2001

Characterizing The Lung Disease Transcriptome With Next Generation Rna-Sequencing

Characterizing The Small RNA Transcriptome Associated With COPD And ILD Using Next Generation Sequencing

scholarly article published May 2012

Characterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencing

scholarly article by Joshua D Campbell et al published October 2012 in BMC Proceedings

Chiral anomalies in two-dimensional quantum field theory

scientific article published on 01 November 1989

Comparative analyses of potato expressed sequence tag libraries

scientific article

Comparative gene expression analysis in mouse models for multiple sclerosis, Alzheimer's disease and stroke for identifying commonly regulated and disease-specific gene changes

scientific article

Comparative genome-wide transcriptional analysis of human left and right internal mammary arteries

scientific article

Comparison and validation of genomic predictors for anticancer drug sensitivity

scientific article published on 26 January 2013

Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-Seq

scholarly article published May 2012

Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample

scientific article

Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq

scientific article published in October 2012

Computational analysis of microarray data

scientific article (publication date: June 2001)

Computational approaches to analysis of DNA microarray data.

scientific article

Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".

scientific article published on September 2009

Connectivity of variants in eQTL networks dictates reproducibility and functionality

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage

scientific article published in June 2003

Corrigendum: Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach

scientific article published on 7 August 2014

Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA)

scientific article

DNA methylation profiling in human lung tissue identifies genes associated with COPD.

scientific article published on 26 August 2016

Data Analysis Strategies in Medical Imaging

scholarly article by Chintan Parmar et al published 1 August 2018 in Clinical Cancer Research

Data reporting standards: making the things we use better

scientific article

Data standards for 'omic' science

scientific article

Data standards for Omics data: the basis of data sharing and reuse

scientific article (publication date: 2011)

Data standards: a call to action

scientific article

Data-driven normalization strategies for high-throughput quantitative RT-PCR.

scientific article

Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach

scientific article

Decomposition of gene expression state space trajectories

scientific article

Defining an informativeness metric for clustering gene expression data

scientific article

Detecting phenotype-driven transitions in regulatory network structure.

scientific article

Development and evaluation of an automated annotation pipeline and cDNA annotation system

scientific article

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

scientific article published on January 2006

Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa

scientific article

Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma

scientific article published on 20 July 2017

Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens

scientific article published on 18 September 2013

Discrimination of non-protein-coding transcripts from protein-coding mRNA.

scientific article published on January 2006

E(mu)-TCL1 mice represent a model for immunotherapeutic reversal of chronic lymphocytic leukemia-induced T-cell dysfunction

scholarly article

Effects of Ischemia on Gene Expression

article

Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus).

scientific article published on 24 February 2009

Enhancing reproducibility in cancer drug screening: how do we move forward?

scientific article

Enrichment of gene-coding sequences in maize by genome filtration

scientific article

Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease

scientific article published on 15 January 2018

Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors

scientific article published on August 2016

Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome

scientific article

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth

scientific article

Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines

scientific article

Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.

scientific article published on 28 October 2013

Erratum: The complete genome sequence of the gastric pathogen Helicobacter pylori

scientific article published in Nature

Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

scientific article published in Nature

Estimating Gene Regulatory Networks with pandaR.

scientific article published on 11 March 2017

Estimating Sample-Specific Regulatory Networks

article

Estimating drivers of cell state transitions using gene regulatory network models

scientific article published on 13 December 2017

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

scientific article

Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology

scientific article published on 30 March 2016

Exploring regulation in tissues with eQTL networks

scientific article published on 29 August 2017

Exploring the transcriptome of the malaria sporozoite stage

scientific article

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue

scientific article

Expression profiling of archival tumors for long-term health studies

scientific article

Extracting biology from high-dimensional biological data

scientific article

Extracting meaning from functional genomics experiments

scientific article

From 'omes to biology.

scientific article

Functional annotation of a full-length mouse cDNA collection

scientific article (publication date: 8 February 2001)

Functional classification analysis of somatically mutated genes in human breast and colorectal cancers

scientific article published on 22 April 2008

Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue

scientific article published on 13 March 2017

GCOD - GeneChip Oncology Database

scientific article

GRAND: a database of gene regulatory network models across human conditions

scientific article published on 08 September 2021

Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma

scientific article

Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism

article

Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages

scientific article

Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray

scientific article

Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells

scientific article published on March 2013

Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes

scientific article

Gene expression signature of normal cell-of-origin predicts ovarian tumor outcomes

scientific article

Gene expression variability as a unifying element of the pluripotency network

scientific article

Gene index analysis of the human genome estimates approximately 120,000 genes.

scientific article published in June 2000

Gene-environment interactions reveal a homeostatic role for cholesterol metabolism during dietary folate perturbation in mice

scientific article published on 12 August 2008

GeneSigDB--a curated database of gene expression signatures

scientific article

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

scientific article published on 21 November 2011

Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva

scientific article

Genesis: cluster analysis of microarray data

scientific article (publication date: 2002)

Genetic basis of murine antibacterial defense to streptococcal lung infection

article

Genetic control of gene expression at novel and established chronic obstructive pulmonary disease loci

scientific article published on 14 October 2014

Genetic regulation of endotoxin-induced airway disease

scientific article published in June 2004

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

scientific article

Genome-wide siRNA screen for mediators of NF-κB activation

scientific article published on 17 January 2012

Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi

article in Nature, 1997

Genomics and proteomics of lung disease: conference summary

scientific article

Genomics of Theileria Parva

Genomics. Microarrays--guilt by association

scientific article published in October 2003

Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis

scientific article published on 25 February 2005

Grape-seed derived procyanidins interfere with adipogenesis of 3T3-L1 cells at the onset of differentiation

scientific article published on August 2005

HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition

scientific article

Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring

scientific article

High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report

scientific article published on 01 January 2019

Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction

scientific article

Histopathological Image QTL Discovery of Immune Infiltration Variants

Histopathological image QTL discovery of immune infiltration variants

Human Lung DNA Methylation Quantitative Trait Loci Colocalize with COPD Genome-wide Association Loci

scientific article

Identification Of Lung Disease-Associated Novel Transcripts And Alternative Splicing By RNA-Sequencing

Identification of Src transformation fingerprint in human colon cancer

scientific article published on October 2002

Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors

scientific article published in January 2007

Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer

scientific article published on 06 October 2009

Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray

scholarly article

Identifying Novel Transcripts And Alternative Splicing Associated With The ILD And COPD Lung Transcriptome Using MRNA-Seq

scholarly article published May 2011

Inconsistency in large pharmacogenomic studies

scientific article

Independence and reproducibility across microarray platforms

scientific article

Inference and validation of predictive gene networks from biomedical literature and gene expression data

scientific article

Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples

scientific article

Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer

scientific article

Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database

scientific article

Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators

scientific article published on 14 November 2015

Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old

scientific article

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

scientific journal article

It is time to end the patenting of software

scientific article published on June 2006

John Quackenbush talks about the clinical promise of genetic microarrays. Interviewed by Brian Vastag

scientific article published in January 2003

Large-scale screening of yeast artificial chromosome libraries using PCR

scientific article published on 01 September 1994

Learning to share

scientific article published on July 2014

Left ventricular global transcriptional profiling in human end-stage dilated cardiomyopathy

scientific article

Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities.

scientific article published on 17 November 2006

MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.

scientific article published on 26 May 2005

Merkel Cell Polyomavirus Small T Antigen Promotes Pro-Glycolytic Metabolic Perturbations Required for Transformation

scientific article

MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32.

scientific article published on 22 January 2013

MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma

scientific article published on 10 March 2020

Microarray analysis and tumor classification

scientific article

Microarray analysis of the in vivo effects of hypophysectomy and growth hormone treatment on gene expression in the rat.

scientific article published in July 2001

Microarray blob-defect removal improves array analysis

scientific article published in March 2007

Microarray data normalization and transformation

scientific article (publication date: December 2002)

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

scientific article (publication date: December 2001)

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

scientific article

Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice

scientific article published on 11 January 2016

Molecular networks in Network Medicine: Development and applications

scientific article published on 19 April 2020

Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

scientific article

Molecular staging for survival prediction of colorectal cancer patients

scientific article

Monitoring of representational difference analysis subtraction procedures by global microarrays.

scientific article published on June 2002

Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing.

scientific article published in October 2012

Multi-platform, multi-site, microarray-based human tumor classification

scientific article

Multiple-input multiple-output causal strategies for gene selection

scientific article

Multiple-laboratory comparison of microarray platforms

article

Multistrain genetic comparisons reveal CCR5 as a receptor involved in airway hyperresponsiveness

scientific article published on 10 February 2006

Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface.

scientific article published on 6 March 2018

Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication

scientific article published on February 2005

Mutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting

scientific article

NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML

scientific article

Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation

scientific article published on 27 January 2016

Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance

scientific article

Nongenic cancer-risk SNPs affect oncogenes, tumor suppressor genes, and immune function

article

Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function

scientific article published on 06 December 2019

Novel application of structural equation modeling to correlation structure analysis of CpG island methylation in colorectal cancer

scientific article

Open source software for the analysis of microarray data.

scientific article

Open-source software accelerates bioinformatics

scientific article

Optimized growth conditions for direct amplification of cDNA clone inserts from culture

article

Orthologous gene-expression profiling in multi-species models: search for candidate genes

scientific article

Osteopontin identified as colon cancer tumor progression marker

scientific article published on 01 October 2003

Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling

scientific article

Ovarian reserve status in young women is associated with altered gene expression in membrana granulosa cells

scientific article

PAX8 and lineage dependence in high grade serous ovarian cancer

scholarly article by Kevin M. Elias et al published December 2015 in Gynecologic Oncology

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

scientific article

Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants

scientific article published on 01 September 2020

Passing messages between biological networks to refine predicted interactions

scientific article

Perspective: Learning to share

scientific article published on May 2014

Physical mapping of complex genomes by sampled sequencing: a theoretical analysis.

scientific article published in May 1995

Physiogenomic resources for rat models of heart, lung and blood disorders

scientific article

Plant database resources at The Institute for Genomic Research

scientific article published in January 2007

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach

scientific article

Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes.

scientific article published on 23 March 2018

Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly

scientific article

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks

scientific article published on 16 November 2011

Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome

scientific article

Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue

scientific article published on 06 March 2009

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

PyPanda: a Python package for gene regulatory network reconstruction ⬇️

scientific article

RESOURCERER: a database for annotating and linking microarray resources within and across species

scientific article

RNA-Seq analysis in MeV.

scientific article

RamiGO: an R/Bioconductor package providing an AmiGO visualize interface

scientific article published on 6 January 2013

Regulation of caspase expression and apoptosis by adenomatous polyposis coli.

scientific article

Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme

scientific article published on 07 September 2021

Regulatory network changes between cell lines and their tissues of origin

scientific article published on 12 September 2017

Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis

scientific article

Relevance of different prior knowledge sources for inferring gene interaction networks

scientific article published on 24 June 2014

Report and abstracts of the Sixth International Workshop on Human Chromosome 21 Mapping 1996. Cold Spring Harbor, New York, USA. May 6-8,1996.

scientific article

Response to Shields: ‘MIAME, we have a problem’

article

Revisiting inconsistency in large pharmacogenomic studies

scientific article published on 16 September 2016

Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species

scientific article

Safikhani et al. reply

scientific article published in Nature

Safikhani et al. reply

Safikhani et al. reply.

scientific article

Search for antiproton decay at the Fermilab antiproton accumulator

scientific article published in Physical Review Letters

Seeded Bayesian Networks: constructing genetic networks from microarray data

scientific article

Sequence analysis of a rainbow trout cDNA library and creation of a gene index

scientific article

Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle

scientific article

Sequential binary gene ratio tests define a novel molecular diagnostic strategy for malignant pleural mesothelioma

scientific article published on 14 March 2013

Serotonin receptor 2B signaling with interstitial cell activation and leaflet remodeling in degenerative mitral regurgitation

scientific article published on 29 December 2017

Sexual dimorphism in gene expression and regulatory networks across human tissues

article

Sexually-dimorphic targeting of functionally-related genes in COPD

scientific article

Shear-induced cyclooxygenase-2 via a JNK2/c-Jun-dependent pathway regulates prostaglandin receptor expression in chondrocytic cells

scientific article

Significance analysis of prognostic signatures

scientific article

Smooth quantile normalization

scientific article published on 10 July 2017

Somatic Mutations Drive Distinct Imaging Phenotypes in Lung Cancer.

scientific article published on 31 May 2017

Sonic hedgehog promotes CD4+ T lymphocyte proliferation and modulates the expression of a subset of CD28-targeted genes

article

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

scientific article

Standardizing the standards

scientific article

Standards for microarray data

scientific article

Standards for microarray data: an open letter

scientific article

Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis

scientific article

Submission of microarray data to public repositories

scientific article

Symposium on Genomic Medicine, University of Maryland, Shady Grove Campus, Rockville, Maryland, March 17-18, 1997.

scientific article

Synchronous global assessment of gene and protein expression in colorectal cancer progression

article

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets

scientific article (publication date: 22 March 2003)

TM4 microarray software suite

scientific article (publication date: 2006)

TM4: a free, open-source system for microarray data management and analysis

scientific article (publication date: February 2003)

TNF receptor I sensitizes neurons to erythropoietin- and VEGF-mediated neuroprotection after ischemic and excitotoxic injury

scholarly article

Technical improvement in permanent seed implantation: a two-stage brachytherapy system. Description and comparison with current technique.

scientific article published in January 2004

Testing CP and CPT violation in the neutral kaon system at a phi factory

scientific article published in June 1992

The African trypanosome genome

scientific article

The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer

scientific article published on 23 December 2019

The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

scientific article published in 2023

The Schistosoma mansoni gene index: gene discovery and biology by reconstruction and analysis of expressed gene sequences

scientific article

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species

scientific article

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes

scientific article

The TIGR Maize Database

scientific article

The TIGR gene indices: reconstruction and representation of expressed gene sequences

scientific article

The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists

scientific article

The complete genome sequence of the gastric pathogen Helicobacter pylori

scientific article

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

scientific article

The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis

scientific article

The death of a pet. How it can affect owners

scientific article published in March 1985

The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

scientific article published on 30 October 2003

The genetics of innate immunity in the lung

scientific article

The impact of stroma on the discovery of molecular subtypes and prognostic gene signatures in serous ovarian cancer:

article

The limits of log-ratios

scientific article

The power of public access: the human genome project and the scientific process

scientific article

The quest for the mechanisms of life

scientific article published in December 2003

The transcriptional landscape of the mammalian genome

scientific article

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

The underlying principles of scientific publication.

scientific article published in November 2002

Time-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures

scientific article published on January 2009

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

scientific article published on 3 October 2017

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

scholarly article published 20 October 2016

Top-down standards will not serve systems biology

scientific article published in Nature

Toward clinical genomics in everyday medicine: perspectives and recommendations

scientific article published on 25 January 2016

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs

scientific article

Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome

article

Transcriptional landscape of cell lines and their tissues of origin

Transparency and reproducibility in artificial intelligence

scientific article published on 14 October 2020

Tumor associated seizures in glioblastomas are influenced by survival gene expression in a region-specific manner: a gene expression imaging study

scientific article

Understanding Tissue-Specific Gene Regulation

scientific article published in October 2017

Understanding Tissue-specific Gene Regulation

article

Uneven chromosome contraction and expansion in the maize genome.

scientific article

Universal RNA reference materials for gene expression.

scientific article

Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses

Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis

scientific article

Using a single daytime performance test to identify most individuals at high-risk for performance impairment during extended wake

journal article published in 2019

Using shRNA experiments to validate gene regulatory networks

scientific article

Using the DFCI gene index databases for biological discovery

scientific article

Using the TIGR gene index databases for biological discovery

scientific article

Variance of gene expression identifies altered network constraints in neurological disease

scientific article

Viral perturbations of host networks reflect disease etiology

scientific article

Viva la revolution! A report from the FANTOM Meeting

WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data

scientific article published on November 2017

Weighing our measures of gene expression

scientific article published on 14 November 2006

What would you do if you could sequence everything?

scientific article

Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples

scientific article

Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data

scientific article

Within the fold: assessing differential expression measures and reproducibility in microarray assays.

scientific article

Wrestling with SUMO and bio-ontologies.

scientific article

Yeast artificial chromosome cloning of 3.2 megabases within chromosomal band 11q24 closely linking c-ets 1 and Fli-1 and encompassing the Ewing sarcoma breakpoint

scientific article published on July 1994

attract: A method for identifying core pathways that define cellular phenotypes

scientific article

iBBiG: iterative binary bi-clustering of gene sets

scientific article

lionessR: single-sample network reconstruction in R

nEASE: a method for gene ontology subclassification of high-throughput gene expression data.

scientific article

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models

scientific article published on 7 September 2011

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