List of works - Lincoln Stein

35th Annual Meeting of the European Association for the Study of Diabetes

article

35th Annual Meeting of the European Association for the Study of Diabetes : Brussels, Belgium, 28 September-2 October 1999

article

A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set.

scientific article

A Metastatic Mouse Model Identifies Genes That Regulate Neuroblastoma Metastasis

scientific article published on 29 November 2016

A cancer cell-line titration series for evaluating somatic classification

scientific article published on 26 December 2015

A cloned ATP:guanidino kinase in the trematode Schistosoma mansoni has a novel duplicated structure

scientific article

A comprehensive map of insulator elements for the Drosophila genome

scientific article

A genome-wide association search for type 2 diabetes genes in African Americans

scientific article published on 4 January 2012

A human functional protein interaction network and its application to cancer data analysis

scientific article

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

scientific article (publication date: 15 February 2001)

A network module-based method for identifying cancer prognostic signatures ⬇️

scientific article published on December 10, 2012

A physical map of 30,000 human genes

scientific article published on October 1998

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

scientific article

A second generation human haplotype map of over 3.1 million SNPs

scientific article

A standard variation file format for human genome sequences

scientific article (publication date: 2010)

ATIDB: Arabidopsis thaliana insertion database

scientific article

Abstract 3184: Whole genome sequencing of low-input fresh frozen prostate cancer biopsies

Abstract A9: The pancreatic ductal adenocarcinoma project at the Ontario Institute for Cancer Research

Abstracts

article by L. Bie et al published 1 April 2013 in Neuro-Oncology

Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells

scientific article

Alternative splicing of the Schistosoma mansoni gene encoding a homologue of epidermal growth factor receptor

scientific article published on July 1, 1992

An Introduction to the Informatics of “Next‐Generation” Sequencing ⬇️

scientific article published on December 1, 2011

An STS-based map of the human genome

scientific article published on December 1995

Annotating cancer variants and anti-cancer therapeutics in reactome

scientific article

Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt

article by Phillip Lord et al published 2004 in The Semantic Web – ISWC 2004: Third International Semantic Web Conference, Hiroshima, Japan, November 7-11, 2004. Proceedings

Arabidopsis reactome: a foundation knowledgebase for plant systems biology

article

Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma

scientific article

Bioinformatics: alive and kicking

scientific article published on 17 December 2008

CMap 1.01: a comparative mapping application for the Internet

scientific article published on 30 July 2009

Cancer genomics: technology, discovery, and translation

scientific article published on 23 January 2012

Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer

scientific article

Candidate cancer driver mutations in super-enhancers and long-range chromatin interaction networks

Chromosome evolution in eukaryotes: a multi-kingdom perspective

scientific article

Clinical significance of specific autoantibodies in juvenile dermatomyositis

scientific article published in October 1996

Cloning of a developmentally regulated tegument antigen of Schistosoma mansoni

scientific article

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE ⬇️

scientific article (publication date: 22 July 2013)

Comparison of genes among cereals

scientific article

Computational approaches to identify functional genetic variants in cancer genomes

scientific article published on August 2013

Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans

scientific article published on 10 April 2006

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

scientific article published on 28 February 2008

Corrigendum: Insights into cancer severity from biomolecular interaction mechanisms

scientific article

Corrigendum: Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

scholarly article published in Nature Genetics

Creating Databases for Biological Information: An Introduction ⬇️

scientific article published on June 1, 2013

Creating databases for biological information: an introduction

scientific article

Cross-organism analysis using InterMine

scientific article

Data analysis: Create a cloud commons

scientific article

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.).

scientific article

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Distinct regulatory elements mediate similar expression patterns in the excretory cell of Caenorhabditis elegans

scientific article published on 13 September 2005

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

scientific article

Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

scientific article published on 6 February 2016

Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents

Epstein-Barr virus-induced IgE production in limiting dilution cultures of normal human B cells

scientific article

Erratum: A comprehensive genetic map of the mouse genome

scientific article published in Nature

Erratum: CORRIGENDUM: InterMOD: integrated data and tools for the unification of model organism research

scientific article published in Scientific Reports

Evidence-based gene predictions in plant genomes

scientific article published on 18 June 2009

Evolution of Arabidopsis microRNA families through duplication events

scientific article

Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer

scientific article published on 5 April 2013

Exome-Wide Association Study of Pancreatic Cancer Risk

scientific article published on 23 October 2017

Expression of IgE from a nonrearranged epsilon locus in cloned B-lymphoblastoid cells that also express IgM.

scientific article published on May 1990

Expression of Schistosoma mansoni genes involved in anaerobic and oxidative glucose metabolism during the cercaria to adult transformation

scientific article published on July 1993

Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial

scientific article

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

scientific article published on 17 March 2015

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

Gallus GBrowse: a unified genomic database for the chicken

scientific article

Genome-wide detection and characterization of positive selection in human populations

scientific article

Global optimization of somatic variant identification in cancer genomes with a global community challenge

scientific article

Glucocorticoid-induced reversal of interleukin-1β-stimulated inflammatory gene expression in human oviductal cells

scientific article

Gramene 2013: comparative plant genomics resources.

scientific article

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

scientific article published on 10 November 2020

Gramene Database: Navigating Plant Comparative Genomics Resources

scientific article

Gramene QTL database: development, content and applications

scientific article published on 08 May 2009

Gramene, a tool for grass genomics

scientific article

Gramene: a bird's eye view of cereal genomes

scientific article

Gramene: a growing plant comparative genomics resource

scientific article

Gramene: a resource for comparative grass genomics ⬇️

scientific article published on January 1, 2002

Gramene: development and integration of trait and gene ontologies for rice

scientific article published on January 2002

Heterogeneity of the human phosphocholine-specific B cell repertoire ⬇️

scientific article published on March 1, 1984

ISOWN: accurate somatic mutation identification in the absence of normal tissue controls

scientific article

Identification of a Therapeutic Strategy Targeting Amplified FGF19 in Liver Cancer by Oncogenomic Screening ⬇️

scientific article published on March 8, 2011

Identification of a nematode chemosensory gene family

scientific article

Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics

scientific article

Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer

scientific article

Identification of functional elements and regulatory circuits by Drosophila modENCODE

scientific article (publication date: 24 December 2010)

Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants

scientific article

Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia

scientific article

Idiopathic periosteal hyperostosis with dysproteinemia (Goldbloom's syndrome): case report and review of the literature

scientific article published on November 1987

IgE-enhancing activity directly and selectively affects activated B cells: evidence for a human IgE differentiation factor

scientific article published in June 1987

Impact of knowledge accumulation on pathway enrichment analysis

Impact of outdated gene annotations on pathway enrichment analysis

scientific article

Inferring clonal evolution of tumors from single nucleotide somatic mutations

scientific article published on February 2014

Inhibition of leucocyte migration by stimulated mononuclear cell supernatants from patients with ischaemic heart disease

scientific article published on April 1983

Insights into cancer severity from biomolecular interaction mechanisms

scientific article

Integrating biological databases ⬇️

scientific article published on May 1, 2003

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

InterMOD: integrated data and tools for the unification of model organism research

scientific article (publication date: 2013)

Interleukins and their signaling pathways in the Reactome biological pathway database

scientific article published on 25 January 2018

International network of cancer genome projects

scientific article

Internet access to the C. elegans genome

scientific article published in October 1999

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

scientific article

Intravenous immunoglobulin therapy

scientific article published on June 1995

JADE: an approach for interconnecting bioinformatics databases

scientific article

JBrowse: a dynamic web platform for genome visualization and analysis

scientific article published on 12 April 2016

JBrowse: a next-generation genome browser

scientific article

Large scale sequencing

scientific article published on August 2003

Linkage disequilibrium mapping of the replicated type 2 diabetes linkage signal on chromosome 1q

scientific article (publication date: July 2009)

Localizing triplet periodicity in DNA and cDNA sequences

scientific article

Maize-targeted mutagenesis: A knockout resource for maize

scientific article

Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process

scientific article published on 28 February 2013

Modulation of chronic lymphocytic leukemia cells by phorbol ester: increase in Ia expression, IgM secretion and MLR stimulatory capacity.

scientific article published in May 1982

Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress

scientific article published on 25 January 2018

Next-generation sequencing identifies rare variants associated with Noonan syndrome

scientific article

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals

scientific article

Of Mice and Men: Navigating Public Physical Mapping Databases ⬇️

scientific article published on January 1, 1998

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

scientific article

Panzea: a database and resource for molecular and functional diversity in the maize genome

scientific article

Panzea: an update on new content and features

scientific article

Pathprinting: An integrative approach to understand the functional basis of disease

scientific article published on 26 July 2013

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

Patterns of isotype commitment in human B cells: limiting dilution analysis of Epstein Barr virus-infected cells

scientific article published in April 1983

PeakRanger: a cloud-enabled peak caller for ChIP-seq data

scientific article

PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

scientific article published on 13 February 2015

Phylogenomic Analysis of BAC-end Sequence Libraries in Oryza (Poaceae)

scholarly article by Karen Cranston et al published 1 September 2010 in Systematic Botany

Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages

scientific article

Plant Reactome: a resource for plant pathways and comparative analysis

scientific article published on 30 October 2016

Quantifying Immune-Based Counterselection of Somatic Mutations

RNASequel: accurate and repeat tolerant realignment of RNA-seq reads

scientific article

Reactome pathway analysis to enrich biological discovery in proteomics data sets

scientific article

Reactome – a knowledgebase of human biological pathways

Reactome: a database of reactions, pathways and biological processes

scientific article

Reactome: a knowledge base of biologic pathways and processes

scientific article

ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis

scientific article

Recommendations of the 2006 Human Variome Project meeting

scientific article published in April 2007

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma

scientific article published on 8 May 2017

Redefining genomic privacy: trust and empowerment

scientific article

Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza

scientific article

Schistosoma mansoni: increasing saline concentration signals cercariae to transform to schistosomula

scientific article

Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing

scientific article

Site preferences of insertional mutagenesis agents in Arabidopsis

scientific article

Spatial genomic heterogeneity within localized, multifocal prostate cancer

scientific article published on 25 May 2015

Species trees from highly incongruent gene trees in rice

scientific article published on 21 September 2009

SynBrowse: a synteny browser for comparative sequence analysis

scientific article

TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA.

scientific article

The Bioperl toolkit: Perl modules for the life sciences

scientific article

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

scientific article

The International HapMap Project Web site

scientific article

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

scientific article

The Reactome BioMart

scientific article (publication date: 2011)

The Reactome pathway knowledgebase

scientific article from 2014

The Reactome pathway knowledgebase

scientific article published on 01 January 2020

The SNP Consortium website: past, present and future

scientific article published on January 2003

The Sequence Ontology: a tool for the unification of genome annotations

scientific article published in 2005

The camptodactyly-arthropathy-pericarditis syndrome: case report and literature review

scientific article

The case for cloud computing in genome informatics

scientific article (publication date: 2010)

The generic genome browser: a building block for a model organism system database

scientific article

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

scientific article published in November 2003

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

scientific article published in 2011

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details

scientific article (publication date: 2011)

The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species

scientific article published in September 2005

The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant

scientific article

The reactome pathway knowledgebase 2022

scientific article published on 14 October 2021

The systematic annotation of the three main GPCR families in Reactome

scientific article

Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

scientific article

Towards patient-based cancer therapeutics

scientific article

Training pediatricians for the evolving generalist-specialist interface in the managed care era ⬇️

scientific article published on April 1, 1998

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

scientific article

Unix Survival Guide

scientific article

Unix survival guide

scientific article published on January 2007

Unlocking the secrets of the genome

scientific article

Using GBrowse 2.0 to visualize and share next-generation sequence data ⬇️

scientific article published on February 1, 2013

Using Reactome to build an autophagy mechanism knowledgebase

scientific article published on 02 June 2020

Using the reactome database

scientific article

Web Apollo: a web-based genomic annotation editing platform

scientific article (publication date: 30 August 2013)

Whole-plant growth stage ontology for angiosperms and its application in plant biology

scientific article

WormBase 2007

scientific article

WormBase 2012: more genomes, more data, new website

scientific article

WormBase as an integrated platform for the C. elegans ORFeome

scientific article published on October 2004

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics

scientific article

WormBase: a comprehensive resource for nematode research

scientific article

WormBase: a cross-species database for comparative genomics

scientific article

WormBase: a multi-species resource for nematode biology and genomics

scientific article

WormBase: better software, richer content

scientific article

WormBase: methods for data mining and comparative genomics

scientific article

WormBase: new content and better access

scientific article

WormBook: the online review of Caenorhabditis elegans biology

scientific article

X Window System survival guide

scientific article published on March 2007

modMine: flexible access to modENCODE data

scientific article

nGASP--the nematode genome annotation assessment project

scientific article

List of works by Lincoln Stein

35th Annual Meeting of the European Association for the Study of Diabetes

35th Annual Meeting of the European Association for the Study of Diabetes : Brussels, Belgium, 28 September-2 October 1999

A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set.

A Metastatic Mouse Model Identifies Genes That Regulate Neuroblastoma Metastasis

A cancer cell-line titration series for evaluating somatic classification

A cloned ATP:guanidino kinase in the trematode Schistosoma mansoni has a novel duplicated structure

A comprehensive map of insulator elements for the Drosophila genome

A genome-wide association search for type 2 diabetes genes in African Americans

A human functional protein interaction network and its application to cancer data analysis

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

A network module-based method for identifying cancer prognostic signatures ⬇️

A physical map of 30,000 human genes

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

A second generation human haplotype map of over 3.1 million SNPs

A standard variation file format for human genome sequences

ATIDB: Arabidopsis thaliana insertion database

Abstract 3184: Whole genome sequencing of low-input fresh frozen prostate cancer biopsies

Abstract A9: The pancreatic ductal adenocarcinoma project at the Ontario Institute for Cancer Research

Abstracts

Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells

Alternative splicing of the Schistosoma mansoni gene encoding a homologue of epidermal growth factor receptor

An Introduction to the Informatics of “Next‐Generation” Sequencing ⬇️

An STS-based map of the human genome

Annotating cancer variants and anti-cancer therapeutics in reactome

Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt

Arabidopsis reactome: a foundation knowledgebase for plant systems biology

Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma

Bioinformatics: alive and kicking

CMap 1.01: a comparative mapping application for the Internet

Cancer genomics: technology, discovery, and translation

Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer

Candidate cancer driver mutations in super-enhancers and long-range chromatin interaction networks

Chromosome evolution in eukaryotes: a multi-kingdom perspective

Clinical significance of specific autoantibodies in juvenile dermatomyositis

Cloning of a developmentally regulated tegument antigen of Schistosoma mansoni

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE ⬇️

Comparison of genes among cereals

Computational approaches to identify functional genetic variants in cancer genomes

Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

Corrigendum: Insights into cancer severity from biomolecular interaction mechanisms

Corrigendum: Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

Creating Databases for Biological Information: An Introduction ⬇️

Creating databases for biological information: an introduction

Cross-organism analysis using InterMine

Data analysis: Create a cloud commons

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.).

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Distinct regulatory elements mediate similar expression patterns in the excretory cell of Caenorhabditis elegans

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents

Epstein-Barr virus-induced IgE production in limiting dilution cultures of normal human B cells

Erratum: A comprehensive genetic map of the mouse genome

Erratum: CORRIGENDUM: InterMOD: integrated data and tools for the unification of model organism research

Evidence-based gene predictions in plant genomes

Evolution of Arabidopsis microRNA families through duplication events

Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer

Exome-Wide Association Study of Pancreatic Cancer Risk

Expression of IgE from a nonrearranged epsilon locus in cloned B-lymphoblastoid cells that also express IgM.

Expression of Schistosoma mansoni genes involved in anaerobic and oxidative glucose metabolism during the cercaria to adult transformation

Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Gallus GBrowse: a unified genomic database for the chicken

Genome-wide detection and characterization of positive selection in human populations

Global optimization of somatic variant identification in cancer genomes with a global community challenge

Glucocorticoid-induced reversal of interleukin-1β-stimulated inflammatory gene expression in human oviductal cells

Gramene 2013: comparative plant genomics resources.

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Gramene Database: Navigating Plant Comparative Genomics Resources

Gramene QTL database: development, content and applications

Gramene, a tool for grass genomics

Gramene: a bird's eye view of cereal genomes

Gramene: a growing plant comparative genomics resource

Gramene: a resource for comparative grass genomics ⬇️

Gramene: development and integration of trait and gene ontologies for rice

Heterogeneity of the human phosphocholine-specific B cell repertoire ⬇️

ISOWN: accurate somatic mutation identification in the absence of normal tissue controls