Lincoln Stein
#34,772
Most Influential Person Now
American scientist
Lincoln Stein's AcademicInfluence.com Rankings
Lincoln Steinbiology Degrees
Biology
#1608
World Rank
#2646
Historical Rank
#782
USA Rank
Bioinformatics
#27
World Rank
#27
Historical Rank
#10
USA Rank
Computational Biology
#49
World Rank
#49
Historical Rank
#16
USA Rank
Genetics
#607
World Rank
#690
Historical Rank
#220
USA Rank
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Biology
Lincoln Stein's Degrees
- PhD Genetics Cornell University
Why Is Lincoln Stein Influential?
(Suggest an Edit or Addition)According to Wikipedia, Lincoln David Stein is a scientist and Professor in bioinformatics and computational biology at the Ontario Institute for Cancer Research. Education Stein completed a Doctor of Medicine at Harvard Medical School and a PhD in Cell Biology at Harvard University both in 1989 via the MD-PhD program. His thesis investigated gene cloning in Schistosoma mansoni.
Lincoln Stein's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- A second generation human haplotype map of over 3.1 million SNPs (2007) (4567)
- The Reactome pathway knowledgebase (2013) (3833)
- A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms (2001) (2879)
- Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. (1998) (2194)
- The Reactome pathway Knowledgebase (2015) (1905)
- International network of cancer genome projects (2010) (1839)
- Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis (2010) (1801)
- Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes (2012) (1752)
- The Bioperl toolkit: Perl modules for the life sciences. (2002) (1700)
- The Gene Ontology resource: enriching a GOld mine (2020) (1508)
- Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). (2002) (1501)
- The Reactome Pathway Knowledgebase (2017) (1475)
- The Gene Ontology Resource: 20 years and still GOing strong (2019) (1467)
- Reactome: a database of reactions, pathways and biological processes (2010) (1462)
- Reactome: a knowledgebase of biological pathways (2004) (1353)
- The International HapMap Project Web site. (2005) (1226)
- The generic genome browser: a building block for a model organism system database. (2002) (1223)
- Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE (2010) (1211)
- A Gene Map of the Human Genome (1996) (1080)
- Pan-cancer analysis of whole genomes (2017) (1073)
- Reactome knowledgebase of human biological pathways and processes (2008) (981)
- The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003) (972)
- Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project (2010) (931)
- Unlocking the secrets of the genome (2009) (832)
- Reactome pathway analysis: a high-performance in-memory approach (2017) (791)
- The Sequence Ontology: a tool for the unification of genome annotations (2005) (788)
- Identification of pre-leukemic hematopoietic stem cells in acute leukemia (2014) (701)
- A physical map of 30,000 human genes. (1998) (670)
- Reactome: a knowledge base of biologic pathways and processes (2007) (667)
- WormBase: a multi-species resource for nematode biology and genomics (2004) (644)
- A human functional protein interaction network and its application to cancer data analysis (2010) (634)
- JBrowse: a next-generation genome browser. (2009) (621)
- Corrigendum: Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia (2014) (620)
- A comprehensive genetic map of the mouse genome (1996) (615)
- Distinct routes of lineage development reshape the human blood hierarchy across ontogeny (2016) (603)
- The case for cloud computing in genome informatics (2010) (573)
- A genetic map of the mouse with 4,006 simple sequence length polymorphisms (1994) (571)
- The reactome pathway knowledgebase (2019) (555)
- JBrowse: a dynamic web platform for genome visualization and analysis (2016) (540)
- A comprehensive genetic map of the mouse genome (1996) (497)
- Reactome graph database: Efficient access to complex pathway data (2018) (487)
- The Distributed Annotation System (2001) (483)
- The iPlant Collaborative: Cyberinfrastructure for Plant Biology (2011) (448)
- Spatial genomic heterogeneity within localized, multifocal prostate cancer (2015) (401)
- A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns (2016) (399)
- Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening. (2011) (391)
- Genome annotation: from sequence to biology (2001) (388)
- WormBase: a comprehensive resource for nematode research (2009) (383)
- Patterns of somatic structural variation in human cancer genomes (2020) (377)
- Creating a bioinformatics nation (2002) (355)
- WormBase: network access to the genome and biology of Caenorhabditis elegans (2001) (350)
- The reactome pathway knowledgebase 2022 (2021) (335)
- A Comprehensive Map of Insulator Elements for the Drosophila Genome (2010) (331)
- Genomewide scan of multiple sclerosis in Finnish multiplex families. (1997) (321)
- Human genome: End of the beginning (2004) (321)
- PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors (2014) (321)
- Web Apollo: a web-based genomic annotation editing platform (2013) (319)
- Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome (2012) (296)
- Evolution of Arabidopsis microRNA families through duplication events. (2006) (293)
- Pathway and network analysis of cancer genomes (2015) (285)
- WormBase 2016: expanding to enable helminth genomic research (2015) (284)
- Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution (2020) (258)
- Gramene: a resource for comparative grass genomics (2002) (245)
- Chromosome evolution in eukaryotes: a multi-kingdom perspective. (2005) (241)
- Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome (1999) (234)
- Childhood Cerebellar Tumors Mirror Conserved Fetal Transcriptional Programs (2018) (232)
- Inferring clonal evolution of tumors from single nucleotide somatic mutations (2012) (225)
- RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans (2000) (225)
- Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (2020) (220)
- WormBase: a comprehensive data resource for Caenorhabditis biology and genomics (2004) (209)
- The International Cancer Genome Consortium Data Portal (2019) (209)
- Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma (2017) (205)
- WormBase 2012: more genomes, more data, new website (2011) (198)
- Comprehensive molecular characterization of mitochondrial genomes in human cancers (2017) (197)
- Gramene: a bird's eye view of cereal genomes (2005) (196)
- WormBase: a modern Model Organism Information Resource (2019) (195)
- ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis (2014) (189)
- Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) (supplement). (2002) (188)
- Gramene: a growing plant comparative genomics resource (2007) (184)
- The SNP Consortium website: past, present and future (2003) (183)
- Gramene, a Tool for Grass Genomics (2002) (182)
- WormBook: the online review of Caenorhabditis elegans biology (2006) (182)
- Cancer genomics: technology, discovery, and translation. (2012) (181)
- Reactome enhanced pathway visualization (2017) (179)
- Integrating biological databases (2003) (178)
- Building human genome maps with radiation hybrids (1997) (177)
- Gramene 2013: comparative plant genomics resources (2013) (177)
- PeakRanger: A cloud-enabled peak caller for ChIP-seq data (2011) (169)
- WormBase 2014: new views of curated biology (2013) (168)
- Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes (2020) (166)
- Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges (2008) (165)
- A network module-based method for identifying cancer prognostic signatures (2012) (161)
- Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages (2005) (161)
- Computational approaches to identify functional genetic variants in cancer genomes (2013) (161)
- Next-generation sequencing identifies rare variants associated with Noonan syndrome (2014) (156)
- The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations (2008) (154)
- WormBase 2017: molting into a new stage (2017) (154)
- The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species (2005) (150)
- modMine: flexible access to modENCODE data (2011) (144)
- Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt (2004) (131)
- WormBase: a cross-species database for comparative genomics (2003) (129)
- Gramene 2016: comparative plant genomics and pathway resources (2015) (124)
- Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms (2014) (120)
- A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. (2003) (120)
- Gramene 2018: unifying comparative genomics and pathway resources for plant research (2017) (120)
- Maize-targeted mutagenesis: A knockout resource for maize (2003) (115)
- Interoperability with Moby 1.0 - It's better than sharing your toothbrush! (2008) (114)
- A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns (2020) (113)
- A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns (2020) (113)
- Using GBrowse 2.0 to visualize and share next-generation sequence data (2013) (112)
- The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant1[W][OA] (2006) (106)
- Impact of outdated gene annotations on pathway enrichment analysis (2016) (104)
- Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing (2016) (103)
- WormBase: new content and better access (2006) (102)
- Gramene: Development and Integration of Trait and Gene Ontologies for Rice (2002) (100)
- WormBase: better software, richer content (2005) (100)
- Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics (2006) (99)
- Species trees from highly incongruent gene trees in rice. (2009) (99)
- Reactome pathway analysis to enrich biological discovery in proteomics data sets (2011) (98)
- The U1 spliceosomal RNA is recurrently mutated in multiple cancers (2019) (98)
- Integrative pathway enrichment analysis of multivariate omics data (2018) (96)
- Data analysis: Create a cloud commons (2015) (94)
- Panzea: a database and resource for molecular and functional diversity in the maize genome (2005) (94)
- A standard variation file format for human genome sequences (2010) (94)
- Redefining Genomic Privacy: Trust and Empowerment (2014) (91)
- A YAC-based physical map of the mouse genome (1999) (88)
- Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza (2008) (87)
- Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial (2013) (86)
- The Plant Ontology (TM) Consortium and plant ontologies (2002) (83)
- Reactome diagram viewer: data structures and strategies to boost performance (2017) (83)
- Gramene QTL database: development, content and applications (2009) (81)
- Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis (2020) (80)
- Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing (2017) (79)
- Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis (2014) (79)
- Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. (1998) (78)
- CMap 1.01: a comparative mapping application for the Internet (2009) (77)
- Identification of Differentially Expressed Proteins in Direct Expressed Prostatic Secretions of Men with Organ-confined Versus Extracapsular Prostate Cancer* (2012) (77)
- SynBrowse: a synteny browser for comparative sequence analysis (2005) (74)
- Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. (2001) (74)
- The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows (2017) (72)
- Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma (2019) (71)
- nGASP – the nematode genome annotation assessment project (2008) (70)
- Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma (2020) (66)
- Towards patient-based cancer therapeutics (2010) (65)
- Web Security: A Step-by-Step Reference Guide (1998) (65)
- Using the Reactome Database (2012) (63)
- The Genome Knowledgebase: a resource for biologists and bioinformaticists. (2003) (63)
- GA4GH: International policies and standards for data sharing across genomic research and healthcare (2021) (62)
- Identification of a nematode chemosensory gene family. (2005) (61)
- Plant Reactome: a resource for plant pathways and comparative analysis (2016) (60)
- scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy (2019) (59)
- TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA (2014) (59)
- Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology[W] (2008) (58)
- modENCODE Project Genome by the Caenorhabditis elegans Integrative Analysis of the (2011) (57)
- Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology1[OA] (2006) (56)
- Site Preferences of Insertional Mutagenesis Agents in Arabidopsis (2005) (53)
- Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma (2017) (51)
- Early G1 Cyclin-Dependent Kinases as Prognostic Markers and Potential Therapeutic Targets in Esophageal Adenocarcinoma (2011) (50)
- Evidence-based gene predictions in plant genomes. (2009) (50)
- Recurrent non-coding U1-snRNA mutations drive cryptic splicing in Shh medulloblastoma (2019) (49)
- Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. (2020) (49)
- Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. (2006) (48)
- Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. (2010) (48)
- ATIDB: Arabidopsis thaliana insertion database. (2003) (48)
- Gramene 2021: harnessing the power of comparative genomics and pathways for plant research (2020) (47)
- Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer. (2016) (47)
- Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer (2017) (47)
- Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes (2017) (46)
- Genome maps 7. The human transcript map. Wall chart. (1996) (45)
- Distinct Regulatory Elements Mediate Similar Expression Patterns in the Excretory Cell of Caenorhabditis elegans* (2005) (45)
- GMODWeb: a web framework for the generic model organism database (2008) (45)
- Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells (2012) (43)
- Global optimization of somatic variant identification in cancer genomes with a global community challenge (2014) (43)
- Gramene Database: Navigating Plant Comparative Genomics Resources. (2016) (41)
- Plant Reactome: a knowledgebase and resource for comparative pathway analysis (2019) (41)
- Sex differences in oncogenic mutational processes (2019) (41)
- Writing Apache Modules with PERL and C (1999) (40)
- WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans (2022) (40)
- Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants (2013) (40)
- Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival (2020) (38)
- Comparison of genes among cereals. (2003) (37)
- Exome-Wide Association Study of Pancreatic Cancer Risk. (2017) (37)
- The Reactome BioMart (2011) (35)
- The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details (2011) (34)
- Official guide to programming with CGI.pm (1998) (33)
- ISOWN: accurate somatic mutation identification in the absence of normal tissue controls (2017) (33)
- Localizing triplet periodicity in DNA and cDNA sequences (2010) (33)
- The NCI Genomic Data Commons (2021) (33)
- Surveillance in Patients With Barrett's Esophagus for Early Detection of Esophageal Adenocarcinoma: A Systematic Review and Meta-Analysis (2015) (32)
- Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer (2013) (32)
- Combined burden and functional impact tests for cancer driver discovery using DriverPower (2020) (31)
- PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors (2014) (31)
- Combined burden and functional impact tests for cancer driver discovery using DriverPower (2020) (31)
- The LabBase system for data management in large scale biology research laboratories (1998) (31)
- InterMOD: integrated data and tools for the unification of model organism research (2013) (31)
- Using the Reactome Database (2004) (30)
- Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig (2020) (30)
- Cross‐organism analysis using InterMine (2015) (30)
- AceDB: a genome database management system (1999) (30)
- Detection of Circulating Tumor DNA in Plasma: A Potential Biomarker for Esophageal Adenocarcinoma. (2019) (30)
- Panzea: an update on new content and features (2007) (29)
- Linkage Disequilibrium Mapping of the Replicated Type 2 Diabetes Linkage Signal on Chromosome 1q (2009) (28)
- Building a Laboratory Information System Around a C++-Based Object-Oriented DBMS (1994) (27)
- A Metastatic Mouse Model Identifies Genes That Regulate Neuroblastoma Metastasis. (2017) (27)
- Inferring structural variant cancer cell fraction (2020) (27)
- Correction: A comprehensive genetic map of the mouse genome (Nature (1996) 380 (149-152)) (1996) (27)
- Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments (2017) (26)
- The transcriptional landscape of Shh medulloblastoma (2021) (26)
- Requirements for a Deductive Query Language in the MapBase Genome-Mapping Database (1993) (25)
- COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms (2021) (24)
- Harmonizing model organism data in the Alliance of Genome Resources (2022) (24)
- Bioinformatics: alive and kicking (2008) (24)
- Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (2020) (22)
- The systematic annotation of the three main GPCR families in Reactome (2010) (21)
- Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer (2016) (21)
- An Introduction to the Informatics of “Next‐Generation” Sequencing (2011) (21)
- WormBase as an integrated platform for the C. elegans ORFeome. (2004) (21)
- ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis. (2014) (20)
- Tumor mutational landscape is a record of the pre-malignant state (2019) (20)
- How to Set-Up and Maintain a Web Site (1996) (19)
- Identifyng microRNAs in plant genomes (2004) (19)
- The Green Commerce Model (1995) (18)
- Splicing UNIX into a Genome Mapping Laboratory (1994) (18)
- Splicing arrays reveal novel RBM10 targets, including SMN2 pre-mRNA (2017) (17)
- Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress. (2018) (17)
- Aberrant PRDM9 expression impacts the pan-cancer genomic landscape (2018) (17)
- Plasma circulating tumor DNA as a potential tool for disease monitoring in head and neck cancer (2018) (17)
- Insights into cancer severity from biomolecular interaction mechanisms (2016) (16)
- Failure of human rhombic lip differentiation underlies medulloblastoma formation (2022) (16)
- Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents (2010) (16)
- Bile Exposure Inhibits Expression of Squamous Differentiation Genes in Human Esophageal Epithelial Cells (2012) (16)
- Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz (2019) (16)
- Exosomes transmit retroelement RNAs to drive inflammation and immunosuppression in Ewing Sarcoma (2019) (15)
- WormBase: methods for data mining and comparative genomics. (2006) (15)
- Correction: Reactome: a knowledge base of biologic pathways and processes (2009) (15)
- Constructing a Domain-Specific DBMS using a Persistent Object System (1994) (15)
- Corrigendum: Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis (2011) (15)
- Pathprinting: An integrative approach to understand the functional basis of disease (2013) (14)
- The electronic medical record: promises and threats (1997) (14)
- The Oryza Map Alignment Project (OMAP): A New Resource for Comparative Genome Studies within Oryza (2007) (14)
- SBOX: Put CGI Scripts in a Box (1999) (14)
- An Introduction to the Reactome Knowledgebase of Human Biological Pathways and Processes (2007) (14)
- Combined EsophaCap cytology and MUC2 immunohistochemistry for screening of intestinal metaplasia, dysplasia and carcinoma (2019) (13)
- How to Set Up and Maintain a World Wide Web Site: The Guide for Information Providers (1995) (13)
- Clinical genomics information management software linking cancer genome sequence and clinical decisions. (2013) (13)
- Network Programming with Perl (1999) (13)
- Candidate cancer driver mutations in superenhancers and long-range chromatin interaction networks (2017) (12)
- LabBase: A Database to Manage Laboratory Data in a Large-Scale Genome-Mapping Project (1995) (12)
- Large Scale Sequencing (2003) (12)
- LabBase: managing lab data in a large-scale genome-mapping project (1995) (12)
- JBrowse 2: A modular genome browser with views of synteny and structural variation (2022) (11)
- Using Perl to facilitate biological analysis. (2001) (11)
- Interleukins and their signaling pathways in the Reactome biological pathway database (2018) (11)
- How Perl Saved the Human Genome Project (2011) (11)
- Web applets: Java, JavaScript and ActiveX. (1996) (11)
- COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms (2020) (11)
- Creating Databases for Biological Information: An Introduction (2013) (11)
- Official guide to programming with CGI.pm: the standard for building Web scripts (1998) (10)
- Internet access to the C. elegans genome. (1999) (10)
- Erratum: WormBase: Network access to the genome and biology of Caenorhabditis elegans (Nucleic Acids Research (2001) vol. 29 (82-86)) (2001) (10)
- Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support (2006) (10)
- Ewing Sarcoma-Derived Extracellular Vesicles Impair Dendritic Cell Maturation and Function (2021) (10)
- Glucocorticoid-Induced Reversal of Interleukin-1β-Stimulated Inflammatory Gene Expression in Human Oviductal Cells (2014) (10)
- Childhood cerebellar tumours mirror conserved fetal transcriptional programs (2019) (10)
- Reactome and ORCID—fine-grained credit attribution for community curation (2019) (9)
- Impact of knowledge accumulation on pathway enrichment analysis (2016) (9)
- A cancer cell-line titration series for evaluating somatic classification (2015) (9)
- Gallus GBrowse: a unified genomic database for the chicken (2007) (9)
- How to set up and maintain a World Wide Web site (1995) (9)
- Quantifying immune-based counterselection of somatic mutations (2017) (9)
- A genetic linkage map of the mouse: current applications and future prospects [see comments] (1993) (9)
- RNASequel: accurate and repeat tolerant realignment of RNA-seq reads (2015) (9)
- Unix Survival Guide (2006) (9)
- Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process (2013) (9)
- JBrowseR: an R interface to the JBrowse 2 genome browser (2021) (9)
- ACEDB: The Ace Database Manager (2002) (9)
- The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols (2021) (8)
- A Glimpse at the DBMS Challenges Posed by the Human Genome Project (1994) (8)
- The LabFlow System for Workflow Management in Large Scale Biology Research Laboratories (1998) (8)
- How to set up and maintain a Web site (2nd ed.) (1996) (8)
- Butler enables rapid cloud-based analysis of thousands of human genomes (2020) (8)
- GENOMIC SIGNAL PROCESSING AND STATISTICS (GENSIPS) (2010) (8)
- A deep learning system can accurately classify primary and metastatic cancers based on patterns of passenger mutations (2019) (8)
- Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer (2019) (7)
- Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE (2013) (7)
- Phylogenomic Analysis of BAC-end Sequence Libraries in Oryza (Poaceae) (2010) (6)
- A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours (2022) (6)
- Writing Apache modules with Perl and C - the Apache API and mod Perl (1999) (6)
- Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution (2020) (6)
- A genome‐wide association study platform built on iPlant cyber‐infrastructure (2015) (6)
- DriverPower: Combined burden and functional impact tests for cancer driver discovery (2017) (6)
- Reactome - a knowledgebase of human biological pathways (2007) (6)
- Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages: Research Articles (2005) (5)
- Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree (2022) (5)
- Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns (2016) (5)
- What's next for bioinformatics? (2005) (5)
- The relationships among GC content, nucleosome occupancy, and exon size (2014) (4)
- The Oryza Map Alignment Project (2008) (4)
- DNMT3a Mutations Define a Pre-Leukemic Stem Cell Reservoir In Human Acute Myeloid Leukemia (2013) (4)
- Requirements for a Deductive Query Language in a Genome-Mapping Database (1993) (4)
- Reactome: An integrated expert model of human molecular processes and access toolkit (2007) (3)
- Caenorhabditis elegans Databases (2002) (3)
- JBrowse Jupyter: a Python interface to JBrowse 2 (2022) (3)
- Creating Databases for Biological Information: An Introduction (2003) (3)
- Using Reactome to build an autophagy mechanism knowledgebase (2020) (3)
- Abstract B48: Feasibility study of molecular profiling (MP) in patients (Pts) with advanced solid cancers using targeted mutation analysis and targeted exome sequencing. (2011) (3)
- Genome-Wide shRNA Screen for DNA Damage Response Regulators in Human Hematopoietic Stem and Progenitor Cells (2011) (2)
- The Oryza map alignment project (OMAP): a new resource for comparative genomics studies within Oryza (2009) (2)
- Unix Survival Guide (2015) (2)
- Abstract 378: The Cancer Genome Collaboratory (2017) (2)
- Database-and Workflow-Management Challenges Posed by the Human Genome Project (1995) (2)
- Vennter – An interactive analysis tool for WormBase interaction data using Venn diagrams (2020) (2)
- A high-resolution human SNP linkage map (2002) (2)
- Genetic Analyses on DNA Microarrays (2000) (2)
- Original article The Reactome BioMart (2011) (2)
- A User ' s Guide to the International HapMap Project Web Site (2)
- Author Correction: Pan-cancer analysis of whole genomes (2023) (1)
- Accelerating cancer omics and precision oncology in health care and research: a Lancet Oncology Commission. (2023) (1)
- PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2 (2022) (1)
- MEDU-40. MATCHING OF SINGLE CELL TRANSCRIPTOMICS FROM CEREBELLAR DEVELOPMENT IDENTIFIES PUTATIVE SUBGROUP SPECIFIC CELLS OF ORIGIN FOR MEDULLOBLASTOMA (2018) (1)
- Identification of Distinct Prognostic Groups: Implications for Patient Selection to Targeted Therapies Among Anti-Endocrine Therapy-Resistant Early Breast Cancers. (2019) (1)
- Copy-number and targeted sequencing analyses to identify distinct prognostic groups: Implications for patient selection to targeted therapies amongst anti-endocrine therapy resistant early breast cancers. (2017) (1)
- The GA4GH Tool Registry Service (TRS) Dockstore – year one (2019) (1)
- Exome sequencing identifies nonsegregating nonsense ATM and PALB2variants in familial pancreatic cancer (2013) (1)
- X Window System Survival Guide (2007) (1)
- Abstract 3005: International Cancer Genome Consortium (2018) (1)
- CORRIGENDUM: InterMOD: integrated data and tools for the unification of model organism research (2013) (1)
- Abstract 5221: Linking the molecular profile of colorectal tumors to germline genetic and environmental risk factors (2016) (1)
- 1 DISTINCT MUTATIONAL SIGNATURES ARE ASSOCIATED WITH CORRELATES OF 1 INCREASED IMMUNE ACTIVITY IN PANCREATIC DUCTAL ADENOCARCINOMA 2 3 (2016) (1)
- Accurate Discrimination of 23 Major Cancer Types via Whole Genome Somatic Mutation Patterns (2017) (1)
- Combined EsophaCap Cytology with MUC2 Immunohistochemistry for Screening Barrett’s Esophagus and Diagnosing Esophageal Dysplasia and Carcinoma (2016) (1)
- Identification of Transcription Factor GEI-1::GFP Binding Regions in L4 (2011) (1)
- Unix Survival Guide (2002) (1)
- Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process (2013) (1)
- Caenorhabditis elegans genome of Conservation and functional significance of gene topology in the Material Supplemental (2006) (1)
- Real-time clinical application of next-generation sequencing (NGS): Results from a multicenter program. (2013) (1)
- JBrowse Connect: A server API to connect JBrowse instances and users (2019) (1)
- Author Correction: Integrative pathway enrichment analysis of multivariate omics data (2020) (1)
- PDTM-21. MATCHING OF SINGLE CELL TRANSCRIPTOMICS FROM CEREBELLAR DEVELOPMENT IDENTIFIES PUTATIVE SUBGROUP SPECIFIC CELLS OF ORIGIN FOR MEDULLOBLASTOMA (2018) (1)
- LabBase: Data and Workflow Management for Large Scale Biological Research (2002) (1)
- Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower (2020) (1)
- Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower (2020) (1)
- Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig (2020) (1)
- Author Correction: A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns (2020) (1)
- Author Correction: A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns (2020) (1)
- Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes (2020) (1)
- Pathprinting: An integrative approach to understand the functional basis of disease (2013) (1)
- Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 (2011) (1)
- Corrigendum: Insights into cancer severity from biomolecular interaction mechanisms (2017) (1)
- Dockstore 2.0: Enhancing a community platform for sharing cloud-agnostic research tools (2019) (1)
- H3K4-specific histone methyltransferase MLL3 regulates EMT in pancreatic cancer cells (2016) (1)
- 104 Tumor Microenvironment and Genetic Association With Colorectal Cancer Risk (2012) (1)
- Web Apollo: a web-based genomic annotation editing platform (2013) (1)
- Identification of Transcription Factor LIN-15B::GFP Binding Regions in L3 (2011) (1)
- Abstract A27: Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma (2016) (1)
- Neuroinformatics for C. elegans: Relating Mind and Body in Wormbase (2003) (1)
- Databases and ontologies Reactome enhanced pathway visualisation (2017) (0)
- The Gene Ontology Annotation database ( GOA ) : A community re source of GO annotations to the UniProt Knowledgebase (2005) (0)
- X Window Survival Guide (2003) (0)
- R interface to the reactome graph database (2021) (0)
- Neutral tumor evolution? (2018) (0)
- The evolutionary history of 2,658 cancers (2020) (0)
- Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE (2013) (0)
- Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer (2019) (0)
- The U1 spliceosomal RNA is recurrently mutated in multiple cancers (2019) (0)
- PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2 (2022) (0)
- Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution (2020) (0)
- The International Cancer Genome Consortium Data Portal (2019) (0)
- Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (2020) (0)
- P-184PERSISTENCE OF GENETIC MUTATIONS IN THE NEOSQUAMOUS EPITHELIUM AFTER ABLATION THERAPY FOR BARRETT’S OESOPHAGUS AND OESOPHAGEAL DYSPLASIA (2017) (0)
- Inferring structural variant cancer cell fraction (2020) (0)
- PP 2 Generation of a panel of “actionable” cancer genes for molecular profiling (MP) in a feasibility study of targeted and genome wide sequencing (TGWS) (2011) (0)
- Designing a web application for personalized medicine trials. (2012) (0)
- Exploring CGI with Perl (1997) (0)
- Of mice and men: navigating public physical mapping databases. (1998) (0)
- Abstract 1224: Deep targeted tumor sequencing of colorectal cancer cases to study associations of molecular subtypes with clinical, genetic, and lifestyle risk factors (2018) (0)
- Abstract P5-08-14: Deregulated histone and cell cycle pathways are associated with anthracycline resistance in breast cancer (2013) (0)
- Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data (2012) (0)
- E-GEOD-25800.processed.1.zip (2011) (0)
- The U1 Spliceosomal RNA: A Novel Non-Coding Hotspot Driver Mutation Independently Associated with Clinical Outcome in Chronic Lymphocytic Leukemia (2019) (0)
- A GWAS platform built on iPlant cyber-infrastructure (2014) (0)
- E-GEOD-25798.additional.1.zip (2011) (0)
- Abstract 2727: The premalignant state captured in the landscape of somatic mutations can reveal the cancer cell-of-origin (2019) (0)
- Organism System Database The Generic Genome Browser: A Building Block for a Model (2006) (0)
- A network module-based method for identifying cancer prognostic signatures (2012) (0)
- Abstract B18: Genomic analysis of pancreatic ductal adenocarcinoma. (2012) (0)
- Abstract P4-10-03: The genomic landscape of male breast cancers using the oncomine comprehensive assay for actionable mutations (2020) (0)
- Reactome: new services and widgets to ease third-party integration (2016) (0)
- Whole genome sequencing reveals mechanisms of carcinogenesis in pancreatic ductal adenocarcinoma (2016) (0)
- WormBase website: supporting the biocuration process (2014) (0)
- - Mieg Sequence and Other ACEDB Databases Genome Caenorhabditis elegans (1998) (0)
- Targeted sequencing in a phase III trial of luminal breast cancer: Identification of novel targets. (2017) (0)
- MANAGING LABORATORY WORKFLOW WITH LABBASE (2006) (0)
- Author Correction: Inferring structural variant cancer cell fraction (2022) (0)
- Pathway Analysis Tool Suite (2014) (0)
- Author Correction: Inferring structural variant cancer cell fraction (2022) (0)
- Abstract LB-230: A prospective clinical trial to evaluate DNA sequencing as a diagnostic tool to guide cancer therapy: results from the initial 50 patients (2012) (0)
- ISOWN: accurate somatic mutation identification in the absence of normal tissue controls (2017) (0)
- Wang , the Human Genome Genotyping of Single-Nucleotide Polymorphisms in Large-Scale Identification , Mapping (2007) (0)
- TBIO-27. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER ADVANCING GENETIC RESEARCH IN CHILDHOOD CANCER AND STRUCTURAL BIRTH DEFECTS THROUGH LARGE SCALE INTEGRATED DATA-DRIVEN DISCOVERY AND CLOUD-BASED PLATFORMS FOR COLLABORATIVE ANALYSIS (2018) (0)
- Autophagy Targeted Curation (2019) (0)
- Abstract 5046: DeepTumour: Identify tumor origin from whole genome sequences (2022) (0)
- F-044DETECTION OF TUMOUR-SPECIFIC MUTATIONS IN PLASMA DEOXYRIBONUCLEIC ACID: A POTENTIAL OESOPHAGEAL ADENOCARCINOMA BIOMARKER (2017) (0)
- Tello-RuizGramene2016Comparative.pdf (2017) (0)
- Inferring clonal evolution of tumors from single nucleotide somatic mutations (2014) (0)
- Innate Immune Signaling Pathways in Reactome (2010) (0)
- 1 – Introduction to Human Genome Computing Via the World Wide Web (1998) (0)
- Combined Esophacap Cytology with MUC2 Immunohistochemistry for Screening Barrett's Esophagus, Dysplasia and Carcinoma (2017) (0)
- Abstract A1-17: Genomic analysis of metachronous pancreatic ductal adenocarcinoma (2015) (0)
- Abstract 3184: Whole genome sequencing of low-input fresh frozen prostate cancer biopsies (2012) (0)
- Identification of Transcription Factor MEP-1::GFP Binding Regions in Embryos (2011) (0)
- WormBase private instances via Amazon's Cloud infrastructure (2011) (0)
- Abstract 1286: Targeted deep sequencing of colorectal tumor tissues to study associations of tumor subtypes with germline genetic, lifestyle, and environmental risk factors (2017) (0)
- Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic variant detection (2015) (0)
- Familial and Somatic Mutations of Histone-Modifying Enzymes in Cancer (2014) (0)
- Abstract PO-002: Revealing tumour spatial heterogeneity in breast cancer and the impact on clinical management (2020) (0)
- Recurrent noncoding regulatory mutations in pancreatic ductal 1 adenocarcinoma 2 3 4 5 6 7 (2017) (0)
- Illuminating Dark Proteins using Reactome Pathways (2022) (0)
- Network‐Module‐Based Approaches in Cancer Data Analysis (2013) (0)
- Abstract 3825: Prognosis of esophageal adenocarcinoma is dependent on early G1 cyclin-dependent kinase activity (2011) (0)
- Innate Immune Signaling Pathways in Reactome (94.13) (2010) (0)
- Cost-Effectiveness of Sponge-Based Surveillance with Genetic Testing For Early Diagnosis of Esophageal Adenocarcinoma (2015) (0)
- Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer (2016) (0)
- Expansion of reactome functional interaction network to allow exposure of knowledge space of understudied proteins in the context of biological pathways (2020) (0)
- Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution (2020) (0)
- Reactome pathway analysis: a high-performance in-memory approach (2017) (0)
- JBrowse: a dynamic web platform for genome visualization and analysis (2016) (0)
- A cancer cell-line titration series for evaluating somatic classification (2015) (0)
- Abstract B13: Whole-genome mutation landscape in pancreatic ductal adenocarcinoma. (2012) (0)
- Abstract 3124: Prognostic biomarkers for pancreatic cancer (2016) (0)
- Scant Collinearity in Gene Order Shows Arabidopsis Comparative Genomics Between Rice and Material Supplemental (2001) (0)
- Abstract PD4-11: Copy-number and targeted sequencing analyses to identify distinct prognostic groups: Implications for patient selection to targeted therapies amongst anti-endocrine therapy resistant early breast cancers (2018) (0)
- E-GEOD-25798.processed.2.zip (2011) (0)
- Abstract 2746: Detection of tumor-specific mutations in plasma DNA: A potential esophageal adenocarcinoma biomarker (2017) (0)
- Abstract 3605: ICGC in the cloud (2016) (0)
- Abstract 3571: Precise somatic mutation prediction in the absence of matching normal DNA (2017) (0)
- Abstract B31: Establishment and molecular characterization of patient-derived tumor xenografts from resected tumors or ascites fluids of patients with pancreatic/ampullary/bile duct carcinomas (2016) (0)
- Abstract 3131: Tumour spatial heterogeneity in breast cancer and the impact on clinical management (2021) (0)
- Abstract IA-17: Plumbing the depths of the non-coding cancer genome (2021) (0)
- MEDU-39. HIGHLY RECURRENT U1 SMALL NUCLEAR RNA HOTSPOT MUTATIONS DRIVE ALTERNATIVE SPLICING IN SONIC HEDGEHOG MEDULLOBLASTOMA (2019) (0)
- Reactome: A curated knowledgebase of biomolecular pathways (2016) (0)
- The Human Blood Hierarchy Is Shaped By Distinct Progenitor Lineages Across Development (2015) (0)
- Abstract 2003: A molecular portrait of potentially curable prostate cancer. (2013) (0)
- GENE-21. A COMMON FETAL DEVELOPMENTAL ORIGIN FOR PFA EPENDYMOMA, PFB EPENDYMOMA, AND CEREBELLAR PILOCYTIC ASTROCYTOMAS? (2018) (0)
- Abstract P2-10-04: Targeted sequencing in early breast cancer: Identification of novel candidate mutations predictive of anthracycline benefit (2018) (0)
- Abstract P3-08-22: The mutational landscape of cancer driver genes in matched primary ductal carcinomain situand recurrent ductal carcinomain situor recurrent invasive cancers (2020) (0)
- Abstract 5185: Redefining the somatic landscape of pancreatic adenocarcinoma (2014) (0)
- Abstract A9: The pancreatic ductal adenocarcinoma project at the Ontario Institute for Cancer Research. (2012) (0)
- TDP-1 , the C . elegans ortholog of TDP-43 , limits the accumulation of double stranded RNA (2014) (0)
- Sequence and Other ACEDB Databases Genome Caenorhabditis elegans Scriptable Access to the (2014) (0)
- Lawrence Berkeley National Laboratory Recent Work Title JBrowse : A dynamic web platform for genome visualization and analysis (2016) (0)
- EPEN-12. A COMMON FETAL DEVELOPMENTAL ORIGIN FOR PFA EPENDYMOMA, PFB EPENDYMOMA, AND CEREBELLAR PILOCYTIC ASTROCYTOMAS (2019) (0)
- Author Correction: scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy (2022) (0)
- Abstract 3814: In CLL the U1 snRNA driver mutation alters splicing in multiple genes and pathways (2023) (0)
- Abstract 6400: JBrowse 2: An extensible open-source platform for modern genome analysis (2022) (0)
- Author Correction: Failure of human rhombic lip differentiation underlies medulloblastoma formation (2022) (0)
- Author Correction: The NCI Genomic Data Commons (2021) (0)
- Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase (2022) (0)
- Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (2020) (0)
- Author Correction: Patterns of somatic structural variation in human cancer genomes (2020) (0)
- Abstract LB503: Using JBrowse 2 plugins to visualize cancer genomic data (2022) (0)
- Author Correction: The evolutionary history of 2,658 cancers (2023) (0)
- Author Correction: The evolutionary history of 2,658 cancers (2023) (0)
- The Reactome reloaded (2010) (0)
- Using the Reactome Database (2023) (0)
- Previously titled: ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis (2014) (0)
- Abstract 4468: Tumor-derived extracellular vesicles transmit retroelement and pericentromeric RNAs to drive proinflammatory and DNA damage responses in stromal fibroblasts and immune cells (2023) (0)
- Identification of Transcription Factor CEH-30::GFP Binding Regions in Late Embyros (2011) (0)
- Evaluating the Predictive Accuracy of Reactome's Curated Biological Pathways (2022) (0)
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