Mark B. Gerstein

Q: What Schools Are Affiliated With Mark B. Gerstein

Mark B. Gerstein is affiliated with the following schools: Boston University, Yale University, University of British Columbia, National University of Singapore, University of Trento, Stanford University, Baylor College of Medicine, University of Toronto, University of Cambridge, Harvard University

Mark B. Gerstein's AcademicInfluence.com Rankings

Mark B. Gerstein

Physics

#1666

World Rank

#2540

Historical Rank

#689

USA Rank

Biophysics

#31

World Rank

#33

Historical Rank

#12

USA Rank

physics Degrees

Mark B. Gerstein

Biology

#1786

World Rank

#2902

Historical Rank

#854

USA Rank

Bioinformatics

#14

World Rank

#14

Historical Rank

USA Rank

biology Degrees

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Why Is Mark B. Gerstein Influential?

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According to Wikipedia, Mark Bender Gerstein is an American scientist working in bioinformatics and Data Science. , he is co-director of the Yale Computational Biology and Bioinformatics program. Mark Gerstein is Albert L. Williams Professor of Biomedical Informatics, Professor of Molecular Biophysics & Biochemistry , Professor of Statistics & Data Science, and Professor of Computer Science at Yale University. In 2018, Gerstein was named co-director of the Yale Center for Biomedical Data Science.

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Mark B. Gerstein'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

RNA-Seq: a revolutionary tool for transcriptomics (2009) (11298)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007) (5196)
Landscape of transcription in human cells (2012) (4392)
Functional profiling of the Saccharomyces cerevisiae genome (2002) (4225)
GENCODE: The reference human genome annotation for The ENCODE Project (2012) (4009)
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae (2006) (2968)
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing (2008) (2513)
The ENCODE (ENCyclopedia Of DNA Elements) Project (2004) (2194)
The Molecular Taxonomy of Primary Prostate Cancer (2015) (2116)
An integrated encyclopedia of DNA elements in the human genome (2012) (2080)
GENCODE reference annotation for the human and mouse genomes (2018) (1848)
An integrated map of structural variation in 2,504 human genomes (2015) (1800)
A Map of the Interactome Network of the Metazoan C. elegans (2004) (1767)
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia (2012) (1701)
Comparing protein abundance and mRNA expression levels on a genomic scale (2003) (1643)
A User's Guide to the Encyclopedia of DNA Elements (ENCODE) (2011) (1467)
Architecture of the human regulatory network derived from ENCODE data (2012) (1393)
A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data (2003) (1355)
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. (2011) (1294)
Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome (2007) (1204)
The genomic complexity of primary human prostate cancer (2010) (1195)
Global Analysis of Protein Activities Using Proteome Chips (2001) (1185)
Guidelines for investigating causality of sequence variants in human disease (2014) (1160)
Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation (2012) (1142)
Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes (2012) (1128)
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes (2012) (1127)
Global Identification of Human Transcribed Sequences with Genome Tiling Arrays (2004) (1102)
Transcriptional Landscape of the Prenatal Human Brain (2014) (1059)
Mapping copy number variation by population scale genome sequencing (2010) (1057)
Global analysis of protein phosphorylation in yeast (2005) (1006)
Genomic analysis of regulatory network dynamics reveals large topological changes (2004) (1005)
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project (2010) (931)
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. (2016) (931)
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics (2007) (925)
Unlocking the secrets of the genome (2009) (832)
FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders (2015) (825)
Structure and evolution of transcriptional regulatory networks. (2004) (811)
Analysis of yeast protein kinases using protein chips (2000) (777)
Expanded encyclopaedias of DNA elements in the human and mouse genomes (2020) (765)
Subcellular localization of the yeast proteome. (2002) (740)
Spectral biclustering of microarray data: coclustering genes and conditions. (2003) (723)
Structural mechanisms for domain movements in proteins. (1994) (712)
Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. (2011) (706)
What is a gene, post-ENCODE? History and updated definition. (2007) (699)
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis (2019) (698)
Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) (687)
Relating whole-genome expression data with protein-protein interactions. (2002) (681)
KBase: The United States Department of Energy Systems Biology Knowledgebase (2018) (659)
Defining functional DNA elements in the human genome (2014) (647)
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls (2009) (611)
Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. (2000) (597)
Variation in Transcription Factor Binding Among Humans (2010) (595)
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. (2004) (575)
Comprehensive functional genomic resource and integrative model for the human brain (2018) (575)
Getting connected: analysis and principles of biological networks. (2007) (560)
Multi-platform discovery of haplotype-resolved structural variation in human genomes (2017) (550)
A standard reference frame for the description of nucleic acid base-pair geometry. (2001) (549)
Large-scale analysis of the yeast genome by transposon tagging and gene disruption (1999) (548)
A cis-regulatory map of the Drosophila genome (2011) (514)
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. (2005) (491)
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. (2007) (484)
Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights (2006) (480)
Volume changes on protein folding. (1994) (475)
The packing density in proteins: standard radii and volumes. (1999) (474)
Integrative functional genomic analysis of human brain development and neuropsychiatric risks (2018) (464)
Diverse Cellular Functions of the Hsp90 Molecular Chaperone Uncovered Using Systems Approaches (2007) (462)
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. (2009) (461)
What is Bioinformatics? A Proposed Definition and Overview of the Field (2001) (452)
The Reality of Pervasive Transcription (2011) (418)
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. (2003) (417)
Annotating non-coding regions of the genome (2010) (416)
3V: cavity, channel and cleft volume calculator and extractor (2010) (407)
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. (2000) (406)
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. (1999) (395)
Divergence of Transcription Factor Binding Sites Across Related Yeast Species (2007) (382)
Role of non-coding sequence variants in cancer (2016) (380)
The real cost of sequencing: higher than you think! (2011) (378)
Patterns of somatic structural variation in human cancer genomes (2020) (377)
Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs (2010) (368)
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics (2013) (366)
Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays (2007) (358)
The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies (2009) (355)
A database of macromolecular motions. (1998) (354)
Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cells (2012) (354)
Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly-made proteins with complex topologies (2008) (347)
Genomic analysis of essentiality within protein networks. (2004) (335)
A unified statistical framework for sequence comparison and structure comparison. (1998) (330)
A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. (2009) (326)
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing (2006) (324)
Genomic analysis of the hierarchical structure of regulatory networks (2006) (321)
AlleleSeq: analysis of allele-specific expression and binding in a network framework (2011) (311)
Performance comparison of whole-genome sequencing platforms (2011) (310)
The transcriptional activity of human Chromosome 22. (2003) (309)
The GENCODE pseudogene resource (2012) (309)
Distribution of NF-κB-binding sites across human chromosome 22 (2003) (307)
The geometry of the ribosomal polypeptide exit tunnel. (2006) (306)
Identification of a Disease-Defining Gene Fusion in Epithelioid Hemangioendothelioma (2011) (305)
The PsychENCODE project (2015) (303)
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. (2002) (295)
Structural proteomics of an archaeon (2000) (295)
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer (2014) (293)
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data (2009) (286)
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. (2005) (280)
The minimum information required for reporting a molecular interaction experiment (MIMIx) (2007) (279)
Genomic analysis of gene expression relationships in transcriptional regulatory networks. (2003) (272)
Comparative Analysis of the Transcriptome across Distant Species (2014) (268)
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. (2000) (266)
Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. (2001) (265)
Conformational changes associated with protein-protein interactions. (2004) (263)
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic (2002) (260)
Organizational Architecture: Designs for Changing Organizations (1992) (256)
A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation (2019) (255)
The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. (1995) (254)
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. (2003) (251)
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors (2012) (249)
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins (1998) (248)
Modeling gene expression using chromatin features in various cellular contexts (2012) (248)
GENCODE 2021 (2020) (240)
Bridging structural biology and genomics: assessing protein interaction data with known complexes. (2002) (240)
Haplotype-resolved diverse human genomes and integrated analysis of structural variation (2021) (239)
Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. (2014) (239)
The real cost of sequencing: scaling computation to keep pace with data generation (2016) (237)
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. (2011) (236)
Regulation of Gene Expression by a Metabolic Enzyme (2004) (236)
Assessing the limits of genomic data integration for predicting protein networks. (2005) (231)
Molecular sampling of prostate cancer: a dilemma for predicting disease progression (2010) (227)
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. (2007) (225)
Computational analysis of membrane proteins: the largest class of drug targets. (2009) (224)
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (2020) (220)
Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. (2011) (218)
The role of disorder in interaction networks: a structural analysis (2008) (217)
Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches (2011) (217)
Packing at the protein-water interface. (1996) (216)
A question of size: the eukaryotic proteome and the problems in defining it. (2002) (215)
Comparative analysis of processed pseudogenes in the mouse and human genomes. (2004) (214)
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. (2001) (212)
Mapping accessible chromatin regions using Sono-Seq (2009) (211)
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. (2002) (211)
MolMovDB: analysis and visualization of conformational change and structural flexibility (2003) (209)
TOS9 Regulates White-Opaque Switching in Candidaalbicans (2006) (208)
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. (2007) (204)
Predicting interactions in protein networks by completing defective cliques (2006) (202)
The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes (2013) (201)
Structured RNAs in the ENCODE selected regions of the human genome. (2007) (201)
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. (2002) (200)
Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins (2009) (199)
Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses (2010) (199)
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability (2005) (198)
Comprehensive molecular characterization of mitochondrial genomes in human cancers (2017) (197)
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing (2010) (196)
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. (2001) (194)
Transcriptome and epigenome landscape of human cortical development modeled in organoids (2018) (192)
Quantifying environmental adaptation of metabolic pathways in metagenomics (2009) (191)
Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts (2002) (191)
Close association of RNA polymerase II and many transcription factors with Pol III genes (2010) (191)
Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. (2002) (190)
Volume changes in protein evolution. (1994) (188)
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. (2005) (185)
Information assessment on predicting protein-protein interactions (2004) (185)
Protein folding: the endgame. (1997) (183)
CREB Binds to Multiple Loci on Human Chromosome 22 (2004) (181)
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (2020) (180)
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. (2004) (179)
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation (2006) (178)
Target hub proteins serve as master regulators of development in yeast. (2006) (177)
Comparative analysis of regulatory information and circuits across distant species (2014) (177)
exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids (2019) (177)
PseudoPipe: an automated pseudogene identification pipeline (2006) (176)
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library (2010) (176)
Distribution of NF-kappaB-binding sites across human chromosome 22. (2003) (176)
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis (2017) (175)
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. (2000) (171)
Diverse human extracellular RNAs are widely detected in human plasma (2016) (170)
Understanding transcriptional regulation by integrative analysis of transcription factor binding data (2012) (170)
A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. (2000) (169)
GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis (2002) (169)
Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response (2010) (168)
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing (2009) (167)
A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. (1997) (163)
Large-scale analysis of pseudogenes in the human genome. (2004) (163)
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. (2009) (163)
Molecular and cellular reorganization of neural circuits in the human lineage (2017) (162)
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes (2004) (162)
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data (2010) (161)
Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis (2010) (159)
Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures (1996) (158)
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates (2010) (158)
Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. (2013) (157)
Analyzing cellular biochemistry in terms of molecular networks. (2003) (157)
Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. (2015) (156)
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. (2003) (156)
Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines (2017) (156)
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. (2006) (155)
What is bioinformatics? An introduction and overview (2001) (153)
Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. (2004) (152)
Interpretation of Genomic Variants Using a Unified Biological Network Approach (2013) (150)
Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. (2008) (150)
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data (2003) (147)
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. (2008) (147)
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. (2004) (145)
Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. (2018) (145)
Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool (2005) (144)
Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context (2007) (140)
The Database of Macromolecular Motions: new features added at the decade mark (2005) (139)
Use of Thioredoxin as a Reporter To Identify a Subset of Escherichia coli Signal Sequences That Promote Signal Recognition Particle-Dependent Translocation (2005) (138)
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. (2004) (138)
The stability of thermophilic proteins: a study based on comprehensive genome comparison (2000) (138)
Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase. (1991) (136)
Personal genome sequencing: current approaches and challenges. (2010) (136)
Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. (2002) (135)
Insights into genetics, human biology and disease gleaned from family based genomic studies (2019) (135)
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. (2005) (133)
RNA expression patterns change dramatically in human neutrophils exposed to bacteria. (2001) (133)
Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces. (1993) (132)
Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. (2001) (132)
Advances in structural genomics. (1999) (132)
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets (2011) (131)
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb (2012) (130)
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) (128)
Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly. (2005) (128)
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics (2001) (128)
How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. (1998) (127)
YeastHub: a semantic web use case for integrating data in the life sciences domain (2005) (127)
Defining Genes in the Genomics Era (2003) (125)
Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. (2000) (125)
N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. (2009) (124)
Strategic selection: matching executives to business conditions. (1983) (123)
A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes (2003) (122)
Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci (2018) (122)
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties (2002) (122)
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays (2010) (121)
The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors (2017) (121)
The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research (2019) (120)
The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research (2019) (120)
Detecting and annotating genetic variations using the HugeSeq pipeline (2012) (120)
Patterns of protein‐fold usage in eight microbial genomes: A comprehensive structural census (1998) (120)
Predicting essential genes in fungal genomes. (2006) (119)
Global changes in STAT target selection and transcription regulation upon interferon treatments. (2005) (118)
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing (2015) (117)
Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. (1993) (117)
Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data (2010) (117)
Genomic analysis of membrane protein families: abundance and conserved motifs (2002) (116)
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. (2002) (116)
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. (2005) (115)
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells (2011) (115)
The current excitement about copy-number variation: how it relates to gene duplications and protein families. (2008) (115)
A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. (2002) (113)
An integrated approach for finding overlooked genes in yeast (2002) (113)
Genomic and proteomic analysis of the myeloid differentiation program. (2001) (112)
A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites (1992) (112)
The Centers for Mendelian Genomics: A new large‐scale initiative to identify the genes underlying rare Mendelian conditions (2012) (110)
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements (2003) (109)
The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? (2007) (108)
Average core structures and variability measures for protein families: application to the immunoglobulins. (1995) (107)
Getting Started in Gene Orthology and Functional Analysis (2010) (107)
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries (2010) (107)
Dynamic and complex transcription factor binding during an inducible response in yeast. (2009) (106)
High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution (2008) (106)
Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair. (2020) (105)
Measuring the Evolutionary Rewiring of Biological Networks (2011) (105)
Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. (2001) (105)
Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation (2016) (104)
mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer (2009) (103)
Identification of pseudogenes in the Drosophila melanogaster genome. (2003) (103)
A structural census of the current population of protein sequences. (1997) (103)
Genomics: Protein fossils live on as RNA (2008) (103)
Integration of genomic datasets to predict protein complexes in yeast (2004) (102)
Seeking a New Biology through Text Mining (2008) (101)
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes (2009) (98)
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome (2007) (98)
A Multiregional Proteomic Survey of the Postnatal Human Brain (2017) (97)
Understanding Modularity in Molecular Networks Requires Dynamics (2009) (97)
Measuring the reproducibility and quality of Hi-C data (2017) (96)
Tcf7 Is an Important Regulator of the Switch of Self-Renewal and Differentiation in a Multipotential Hematopoietic Cell Line (2012) (96)
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. (2004) (96)
Integrative pathway enrichment analysis of multivariate omics data (2018) (96)
DNA recognition code of transcription factors. (1995) (95)
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data (2011) (95)
EBNA1 regulates cellular gene expression by binding cellular promoters (2009) (94)
Distinct genomic aberrations associated with ERG rearranged prostate cancer (2009) (93)
Comparing genomes in terms of protein structure: surveys of a finite parts list. (1998) (92)
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision (2011) (92)
The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function? (2000) (92)
Data mining crystallization databases: Knowledge‐based approaches to optimize protein crystal screens (2003) (91)
Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line. (2002) (91)
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification (2007) (90)
An integrated system for studying residue coevolution in proteins (2008) (90)
Modeling ChIP Sequencing In Silico with Applications (2008) (89)
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks (2010) (88)
Machine learning and genome annotation: a match meant to be? (2013) (87)
Integrated pseudogene annotation for human chromosome 22: evidence for transcription. (2005) (86)
exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling. (2019) (86)
Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity (2014) (85)
Structural proteomics: prospects for high throughput sample preparation. (2000) (84)
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project (2011) (84)
Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides (2012) (83)
Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer. (2007) (82)
Publishing perishing? Towards tomorrow's information architecture (2007) (82)
An ensemble approach to accurately detect somatic mutations using SomaticSeq (2015) (81)
A comprehensive nuclear receptor network for breast cancer cells. (2013) (81)
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis (2020) (80)
The relationship between the evolution of microRNA targets and the length of their UTRs (2009) (80)
Genomics and Privacy: Implications of the New Reality of Closed Data for the Field (2011) (79)
Perspectives on ENCODE (2020) (79)
Keeping the shape but changing the charges: A simulation study of urea and its iso-steric analogs (1996) (78)
Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome (2007) (78)
Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X‐ray crystallography approaches (2003) (78)
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals (2016) (78)
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks (2006) (78)
Identification of genomic indels and structural variations using split reads (2011) (77)
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels (2010) (76)
Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression (2014) (76)
Targeting the Human Cancer Pathway Protein Interaction Network by Structural Genomics* (2008) (76)
Pangolin genomes and the evolution of mammalian scales and immunity (2016) (75)
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. (2011) (74)
A Genome-Wide Analysis of Blue-Light Regulation of Arabidopsis Transcription Factor Gene Expression during Seedling Development (2003) (73)
Small RNAs Originated from Pseudogenes: cis- or trans-Acting? (2009) (73)
Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity (2018) (72)
Genome-wide analysis relating expression level with protein subcellular localization. (2000) (72)
An integrative ENCODE resource for cancer genomics (2019) (72)
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. (2007) (71)
Stereochemical basis of DNA recognition by Zn fingers. (1994) (71)
Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery (2005) (71)
Robust-linear-model normalization to reduce technical variability in functional protein microarrays. (2009) (71)
Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators (2010) (71)
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment (2012) (70)
Exploring the range of protein flexibility, from a structural proteomics perspective. (2004) (69)
Quantification of private information leakage from phenotype-genotype data: linking attacks (2016) (69)
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes (2017) (69)
Integrating Interactomes (2002) (68)
Structured digital abstract makes text mining easy (2007) (68)
Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms (2011) (67)
Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma (2016) (67)
Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. (2011) (67)
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations (2015) (66)
Integrative database analysis in structural genomics (2000) (65)
Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci (2018) (64)
The DOE Systems Biology Knowledgebase (KBase) (2016) (63)
Comparative analysis of pseudogenes across three phyla (2014) (63)
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences (2020) (63)
Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. (2004) (62)
Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing (2013) (62)
SPINE 2: a system for collaborative structural proteomics within a federated database framework. (2003) (62)
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome (2008) (61)
Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate (2009) (61)
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps (2016) (61)
Design optimization methods for genomic DNA tiling arrays. (2005) (61)
PubNet: a flexible system for visualizing literature derived networks (2005) (60)
Comparing classical pathways and modern networks: towards the development of an edge ontology. (2007) (60)
Data Mining on the Web (2006) (60)
Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum: amino acid sequence and structural interpretation. (1992) (59)
How far can sequences diverge? (1997) (59)
A comprehensive catalog of predicted functional upstream open reading frames in humans (2018) (59)
Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions (2004) (59)
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles (2011) (59)
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications (2014) (59)
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics (2007) (58)
Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins (2001) (58)
Simulating water and the molecules of life. (1998) (58)
Creating competitive advantage with computer technology. (1982) (57)
Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level. (2003) (57)
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework (2014) (57)
modENCODE Project Genome by the Caenorhabditis elegans Integrative Analysis of the (2011) (57)
A Genome-Wide Analysis of Blue-Light Regulation of Arabidopsis Transcription Factor Gene Expression during Seedling Development1[w] (2003) (56)
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications (2007) (56)
Integrative data mining: the new direction in bioinformatics (2001) (56)
Design and Implementation of the International Genetics and Translational Research in Transplantation Network (2015) (56)
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence (1998) (55)
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. (2001) (55)
The Spread of Scientific Information: Insights from the Web Usage Statistics in PLoS Article-Level Metrics (2011) (55)
MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos. (2017) (54)
Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel (2005) (54)
One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin. (2017) (54)
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms (2015) (54)
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. (2008) (54)
Tilescope: online analysis pipeline for high-density tiling microarray data (2007) (53)
Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) (53)
ProCAT: a data analysis approach for protein microarrays (2006) (52)
Personal phenotypes to go with personal genomes (2009) (52)
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity (2009) (51)
Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism. (2004) (51)
StoneHinge: Hinge prediction by network analysis of individual protein structures (2009) (51)
Calculations of protein volumes: sensitivity analysis and parameter database (2002) (51)
Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs (2013) (50)
Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition (2017) (50)
Bridging structural biology and genomics: assessing protein interaction data with known complexes. (2002) (50)
Assessing the need for sequence-based normalization in tiling microarray experiments (2007) (50)
Integration of curated databases to identify genotype-phenotype associations (2006) (50)
A computational approach for identifying pseudogenes in the ENCODE regions (2006) (49)
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution (2013) (49)
Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation. (2016) (49)
Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division (2013) (49)
The real life of pseudogenes. (2006) (48)
The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse. (2003) (48)
Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor β receptor (2004) (48)
Developing a similarity measure in biological function space (2007) (47)
Genomics: ENCODE leads the way on big data (2012) (47)
Quantum computing at the frontiers of biological sciences (2019) (47)
Hinge Atlas: relating protein sequence to sites of structural flexibility (2007) (47)
Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes (2017) (46)
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies (2015) (45)
Spectral biclustering of microarray cancer data : co-clustering genes and conditions (2003) (45)
The human proteome – a scientific opportunity for transforming diagnostics, therapeutics, and healthcare (2012) (45)
Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer (2008) (45)
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation (2018) (44)
Getting Started in Text Mining: Part Two (2009) (44)
Genomics. Defining genes in the genomics era. (2003) (44)
ExpressYourself: a modular platform for processing and visualizing microarray data (2003) (44)
Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. (2010) (44)
Structural Genomics: Current Progress (2003) (44)
OrthoClust: an orthology-based network framework for clustering data across multiple species (2014) (44)
Relationship between gene co-expression and probe localization on microarray slides (2003) (44)
Simulating the minimum core for hydrophobic collapse in globular proteins (1997) (44)
Pseudofam: the pseudogene families database (2008) (43)
MSB: a mean-shift-based approach for the analysis of structural variation in the genome. (2008) (43)
HingeMaster: Normal mode hinge prediction approach and integration of complementary predictors (2008) (42)
FlexOracle: predicting flexible hinges by identification of stable domains (2007) (41)
MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions (2016) (41)
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge (2006) (41)
Annual Research Review: The promise of stem cell research for neuropsychiatric disorders. (2011) (41)
Structural genomics analysis: Characteristics of atypical, common, and horizontally transferred folds (2002) (41)
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. (2007) (41)
DNA recognition and superstructure formation by helix-turn-helix proteins. (1995) (41)
Measuring Shifts in Function and Evolutionary Opportunity Using Variability Profiles: A Case Study of the Globins (2000) (40)
Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets (2010) (40)
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms (2005) (40)
Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden (2020) (39)
LPFC: An internet library of protein family core structures (1997) (39)
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures (2004) (39)
FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods (2018) (37)
Revealing the brain's molecular architecture. (2018) (37)
Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. (2021) (37)
ACT: aggregation and correlation toolbox for analyses of genome tracks (2011) (37)
Genomics and data science: an application within an umbrella (2019) (37)
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks (2020) (37)
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes (2017) (36)
An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits (2006) (36)
Global Survey of Human T Leukemic Cells by Integrating Proteomics and Transcriptomics Profiling*S (2007) (35)
Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations (2017) (35)
Regulatory element copy number differences shape primate expression profiles (2012) (35)
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. (2007) (35)
High-order neural networks and kernel methods for peptide-MHC binding prediction (2015) (34)
Protein evolution. How far can sequences diverge? (1997) (34)
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations (2020) (34)
microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis (2018) (34)
Sequencing The Transcriptional Landscape of the Yeast Genome Defined by RNA (2013) (34)
Gene inactivation and its implications for annotation in the era of personal genomics. (2011) (34)
Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome. (2003) (34)
Integrated prediction of the helical membrane protein interactome in yeast. (2006) (33)
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains (2010) (33)
Germline determinants of the somatic mutation landscape in 2,642 cancer genomes (2017) (33)
RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes (2010) (33)
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions (2008) (33)
Rapid Evolution by Positive Darwinian Selection in T-Cell Antigen CD4 in Primates (2008) (32)
Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources (2016) (32)
Studying Macromolecular Motions in a Database Framework: From Structure to Sequence (2002) (32)
The protein target list of the Northeast Structural Genomics Consortium (2004) (32)
Closure of the NCBI SRA and implications for the long-term future of genomics data storage (2011) (31)
Combined burden and functional impact tests for cancer driver discovery using DriverPower (2020) (31)
Identification and correction of spurious spatial correlations in microarray data. (2003) (31)
Network Analysis as a Grand Unifier in Biomedical Data Science (2018) (31)
Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories. (2007) (31)
What is the natural boundary of a protein in solution? (1993) (31)
Predicting the frequencies of drug side effects (2020) (31)
Standardized annotation of translated open reading frames (2022) (31)
Segmental duplications in the human genome reveal details of pseudogene formation (2010) (30)
On sports and genes. (2012) (30)
Semantic Web Approach to Database Integration in the Life Sciences (2007) (30)
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms (2007) (30)
Genomic Anonymity: Have We Already Lost It? (2008) (29)
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. (2002) (29)
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human (2007) (29)
Manually structured digital abstracts: A scaffold for automatic text mining (2008) (29)
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. (2007) (29)
Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders (2021) (28)
Stroke and Circulating Extracellular RNAs (2017) (28)
Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts (2019) (28)
An NMR study on the DNA-binding SPKK motif and a model for its interaction with DNA. (1993) (28)
Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. (2016) (27)
Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome. (2000) (27)
Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions (2018) (26)
Protein geometry: volumes, areas and distances (2012) (26)
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions (2011) (26)
Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions (2018) (26)
Thermostability of membrane protein helix–helix interaction elucidated by statistical analysis (2002) (26)
Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis (2013) (25)
Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae (2006) (25)
Artificial Transmembrane Oncoproteins Smaller than the Bovine Papillomavirus E5 Protein Redefine Sequence Requirements for Activation of the Platelet-Derived Growth Factor β Receptor (2009) (25)
Using a measure of structural variation to define a core for the globins (1995) (24)
Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures (2018) (24)
Child development and structural variation in the human genome. (2013) (24)
An efficient pseudomedian filter for tiling microrrays (2007) (24)
Flirting with Disaster: Why Accidents Are Rarely Accidental (2008) (24)
Finding an Average Core Structure: Application to the Globins (1994) (24)
What's next for humanity? (2018) (23)
An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome (2015) (23)
Determining the minimum number of types necessary to represent the sizes of protein atoms (2001) (23)
Landscape and variation of novel retroduplications in 26 human populations (2017) (23)
A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs. (2003) (23)
YMD: a microarray database for large-scale gene expression analysis (2002) (23)
An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective (2007) (22)
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (2020) (22)
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (2020) (22)
Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique (2010) (22)
Protein surfaces and volumes: measurement and use (2006) (22)
Design principles of molecular networks revealed by global comparisons and composite motifs (2006) (22)
Data Sanitization to Reduce Private Information Leakage from Functional Genomics (2020) (22)
STARRPeaker: uniform processing and accurate identification of STARR-seq active regions (2020) (22)
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search (2002) (21)
PARE: A tool for comparing protein abundance and mRNA expression data (2007) (21)
Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body (2014) (21)
Protein folds in the worm genome. (1999) (20)
Using semantic web rules to reason on an ontology of pseudogenes (2010) (20)
Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood (2020) (20)
Multi-platform discovery of haplotype-resolved structural variation in human genomes (2019) (20)
Binding geometry of α‐helices that recognize DNA (1995) (20)
Interpretable Sparse High-Order Boltzmann Machines (2014) (20)
Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq. (2018) (20)
Toward a systematic definition of protein function that scales to the genome level: defining function in terms of interactions (2002) (19)
Protein fold and family occurrence in genomes : power-law behaviour and evolutionary model Running title : Power-law behaviour and evolutionary model (2001) (19)
SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes. (2002) (19)
Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps (2011) (19)
The Development of a Practical Artificial Intelligence Tool for Diagnosing and Evaluating Autism Spectrum Disorder: Multicenter Study (2020) (19)
Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours (2017) (19)
Centers for Mendelian Genomics: A decade of facilitating gene discovery (2021) (18)
A Pilot Study of Transcription Unit Analysis in Rice Using Oligonucleotide Tiling-path Microarray (2005) (18)
Extending gene ontology in the context of extracellular RNA and vesicle communication (2016) (18)
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants (2009) (18)
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development (2018) (18)
SVFX: a machine learning framework to quantify the pathogenicity of structural variants (2019) (17)
Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors (2011) (17)
Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors (2015) (17)
Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes. (2002) (17)
Novel insights through the integration of structural and functional genomics data with protein networks. (2012) (17)
Proteins in Motion (1999) (17)
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements (2019) (17)
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels (2009) (17)
Structuring supplemental materials in support of reproducibility (2017) (16)
Estimating growth patterns and driver effects in tumor evolution from individual samples (2019) (16)
Open Access: Taking Full Advantage of the Content (2008) (16)
Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor. (2004) (16)
An integrated systems approach to structure-function relationships of glycans (2005) (16)
TopicNet: a framework for measuring transcriptional regulatory network change (2019) (16)
The Role of Cloud Computing in Managing the Deluge of Potentially Private Genetic Data (2011) (15)
The Technology Connection: Strategy and Change in the Information Age: Strategy and Change in the In (1987) (15)
Sequences and topology. (2001) (15)
Extending gene ontology in the context of extracellular RNA and vesicle communication (2016) (15)
Nearly all new protein-coding predictions in the CHESS database are not protein-coding (2018) (15)
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease (2014) (15)
Uncovering trends in gene naming (2008) (15)
A new tool for technical standardization of the Ki67 immunohistochemical assay (2021) (14)
Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods (2015) (14)
Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs. (2016) (14)
Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. (2006) (14)
Using blockchain to log genome dataset access: efficient storage and query (2020) (14)
Establishing a Global Standard for Wearable Devices in Sport and Fitness: Perspectives from the New England Chapter of the American College of Sports Medicine Members. (2020) (13)
Simulation of water around a model protein helix. 1. Two-dimensional projections of solvent structure (1993) (13)
Epigenome-based splicing prediction using a recurrent neural network (2020) (13)
Cancer genomics: Less is more in the hunt for driver mutations (2017) (13)
Storing and analyzing a genome on a blockchain (2020) (13)
Transcriptional activity and strain-specific history of mouse pseudogenes (2020) (13)
Methods for displaying macromolecular structural uncertainty: application to the globins. (1995) (13)
Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool (2006) (13)
Reconstructing genetic networks in yeast (2003) (13)
Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010) (13)
Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms (2015) (13)
Estimation of the carrier frequency of fumarate hydratase alterations and implications for kidney cancer risk in hereditary leiomyomatosis and renal cancer (2020) (12)
Localized structural frustration for evaluating the impact of sequence variants (2013) (12)
Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays (2008) (12)
Systematic identification of transcription factors associated with patient survival in cancers (2009) (12)
Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences. (2003) (12)
Editorial overviewSequences and topology (2003) (12)
Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD (2022) (12)
The effects of common structural variants on 3D chromatin structure (2020) (12)
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins (2006) (11)
Assessing the Limits of Genomic Data Integration for Predicting Protein-Protein Interactions (2005) (11)
Assessing the Limits of Genomic Data Integration for Predicting Protein-Protein Interactions (2005) (11)
Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci (2018) (11)
Relating protein conformational changes to packing efficiency and disorder (2009) (11)
An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping (2009) (11)
Structured digital tables on the Semantic Web: toward a structured digital literature (2010) (11)
A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq (2021) (11)
Simulation of water around a model protein helix. II: The relative contributions of packing, hydrophobicity, and hydrogen bonding (1993) (10)
Tiling array data analysis: a multiscale approach using wavelets (2011) (10)
STARRPeaker: Uniform processing and accurate identification of whole human STARR-seq active regions (2019) (10)
Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption (2021) (10)
Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi. (2000) (10)
Novel transcribed regions in the human genome. (2006) (10)
Predicting protein ligand binding motions with the conformation explorer (2011) (10)
Digging for Dead Genes: An Analysis of the Characteristics of the Pseudogene Population in the C. elegans Genome (2000) (9)
Repeated tertiary fold of RNA polymerase II and implications for DNA binding. (1998) (9)
Protein fossils live on as RNA (2008) (9)
Identification of yeast cell cycle regulated genes based on genomic features (2013) (9)
Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation (2016) (9)
Power-law behavior applies to a wide variety of genomic properties (2002) (9)
Functional genomics data: privacy risk assessment and technological mitigation (2021) (9)
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics (2007) (9)
Temporal Dynamics of Collaborative Networks in Large Scientific Consortia. (2016) (9)
Corrigendum: Performance comparison of whole-genome sequencing platforms (2012) (9)
IQSeq: Integrated Isoform Quantification Analysis Based on Next-Generation Sequencing (2012) (9)
Network security and data integrity in academia: an assessment and a proposal for large-scale archiving (2005) (9)
Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences (2018) (8)
Chemistry Nobel Rich in Structure (2007) (8)
Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions (2020) (8)
E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics. (1999) (8)
A universal legal framework as a prerequisite for database interoperability (2003) (8)
Blurring the boundaries between the scientific 'papers' and biological databases (2001) (8)
De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation (2020) (8)
The GENCODE human gene set (2010) (8)
Sixty years of genome biology (2013) (8)
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model (2010) (8)
To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq (2019) (7)
RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins (2018) (7)
A method using active‐site sequence conservation to find functional shifts in protein families: Application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens (2004) (7)
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome (2022) (7)
Origins and characterization of variants shared between databases of somatic and germline human mutations (2020) (7)
Abstract 5359: Regulatory germline variants in 10,389 adult cancers (2018) (7)
Analytical Evolutionary Model for Protein Fold Occurrence in Genomes, Accounting for the Effects of Gene Duplication, Deletion, Acquisition and Selective Pressure (2006) (7)
SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments (2020) (7)
Perspectives: signal transduction. Proteins in motion. (1999) (7)
Grand Challenges for Biological and Environmental Research: A Long-Term Vision (2010) (7)
Broad transcriptomic dysregulation across the cerebral cortex in ASD (2020) (7)
Privacy-preserving genotype imputation with fully homomorphic encryption (2020) (7)
A Review of the Morph Server and the Macromolecular Motions Database: A Standardized System for Analyzing and Visualizing Macromolecular Motions in a Database Framework (2003) (7)
Next-Generation Sequencing to Diagnose Suspected Genetic Disorders. (2019) (7)
Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (2020) (6)
Multi-tissue integrative analysis of personal epigenomes (2021) (6)
RNAi Development (2007) (6)
Inferring protein-protein interactions using interaction network topologies (2005) (6)
Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research (2022) (6)
Privacy-preserving genotype imputation with fully homomorphic encryption. (2021) (6)
Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis (2005) (6)
Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions. (2019) (6)
Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly (2020) (6)
DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations (2022) (6)
Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology (2018) (6)
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool (2017) (6)
Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond (2001) (6)
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (2020) (6)
mRNA expression profiles show differential regulatory effects of microRNAs between ER + and ER-breast cancer (2009) (6)
Proposed social and technological solutions to issues of data privacy in personal genomics (2014) (5)
Forging links in an electronic paper chain (1999) (5)
Social Networking and Personal Genomics: Suggestions for Optimizing the Interaction (2009) (5)
Reads meet rotamers: structural biology in the age of deep sequencing. (2015) (5)
Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors (2021) (5)
An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping (2009) (5)
GENCODE: reference annotation for the human and mouse genomes in 2023 (2022) (5)
Using FunSeq2 for Coding and Non‐Coding Variant Annotation and Prioritization (2017) (5)
Sensitive information leakage from functional genomics data: Theoretical quantifications & practical file formats for privacy preservation (2018) (5)
Recovering genotypes and phenotypes using allele-specific genes (2021) (5)
Dependent Type Networks: A Probabilistic Logic via the Curry-Howard Correspondence in a System of Probabilistic Dependent Types (2018) (5)
DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring (2020) (5)
Solution structure of the DNA binding octapeptide repeat of the K10 gene product. (1994) (5)
DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks (2016) (5)
Annotation transfer for genomics : assessing the transferability of protein-protein and protein-DNA interactions between organisms (2004) (4)
Shaping the nebulous enhancer in the era of high-throughput assays and genome editing (2020) (4)
Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers (2021) (4)
The database of macromolecular motions: a standardized system for analyzing and visualizing macromolecular motions in a database framework (2001) (4)
Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses. (2021) (4)
Annotation of the Human Genome (2000) (4)
Bridging structural biology and genomics : assessing protein – protein interaction datasets (2002) (4)
Cyclic and multilevel causation in evolutionary processes (2019) (4)
Pollen-derived RNAs Are Found in the Human Circulation (2019) (4)
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays (2021) (4)
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Understanding genome structural variations (2015) (4)
FANCY: fast estimation of privacy risk in functional genomics data (2019) (4)
Private information leakage from functional genomics data: Quantification with calibration experiments and reduction via data sanitization protocols (2018) (4)
SigLASSO: a LASSO approach jointly optimizing sampling likelihood and cancer mutation signatures (2018) (4)
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Genomics Confounds Gene Classification (2008) (4)
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Network propagation-based prioritization of long tail genes in 17 cancer types (2021) (4)
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Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses (2020) (3)
Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites (2005) (3)
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Abstract 1279: Passenger mutation landscape in cancer genomes (2018) (2)
Social Considerations in Research: Consider Them but Don't Use Them (2011) (2)
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The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics (2011) (2)
Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations (2021) (2)
Information assessment on predicting protein-protein interactions BMC Bioinformatics 2004 (2004) (2)
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models (2022) (2)
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SVFX: a machine learning framework to quantify the pathogenicity of structural variants (2020) (2)
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework (2014) (2)
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Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes (2022) (2)
Network propagation-based prioritization of long tail genes in 17 cancer types (2021) (2)
Recurrent repeat expansions in human cancer genomes (2022) (2)
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Minor intron splicing efficiency increases with the development of lethal prostate cancer (2021) (2)
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The human proteome – a scientific opportunity for transforming diagnostics, therapeutics, and healthcare (2012) (1)
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Interactions Relating Whole-Genome Expression Data with Protein-Protein (2011) (1)
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Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 (2011) (1)
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The effects of common structural variants on 3D chromatin structure (2020) (1)
Cancer relevance of human genes (2021) (1)
Workshop I – Global Analysis of Protein Activities Using Protein Chips (2003) (1)
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Insights from incorporating quantum computing into drug design workflows (2022) (1)
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Building integrative functional maps of gene regulation. (2022) (1)
Abstract 4854: A computational framework for prioritizing noncoding regulatory variants in cancer (2015) (1)
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Nodal Modulator is required to sustain endoplasmic reticulum morphology (2021) (1)
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OrthoClust: an orthology-based network framework for clustering data across multiple species (2014) (1)
An analysis of the present system of scientific publishing: what's wrong and where to go from here (2003) (1)
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Structural Genomics Analysis : Phylogenetic Patterns of Unique , Shared , and Common Folds in 20 Genomes (2001) (1)
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Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research (2006) (0)
sigLASSO: optimizing cancer mutation signatures jointly with sampling likelihood (2018) (0)
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Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes (2022) (0)
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Hierarchical PAC-Bayes Bounds via Deep Probabilistic Programming (2019) (0)
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GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome (2009) (0)
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analysis of transcription , and evolution Pseudogenes in the ENCODE regions : Consensus annotation , Material Supplemental (2007) (0)
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Interpretable Sparse High-Order Boltzmann Machines ( Supplementary Materials ) (2014) (0)
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An important aspect of structural genomics is connecting coordinate data with whole-genome information related to phylogenetic occurrence, protein function, gene expression, and protein-protein interactions. Integrative database analysis allows one to survey the 'finite parts list' of protein folds (2000) (0)
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Introduction to program subject: Fireproofing (1971) (0)
GATTACA is still pertinent 25 years later (2022) (0)
Binding peptide generation for MHC Class I proteins with deep reinforcement learning (2023) (0)
Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph (2010) (0)
An invitation to NHS Organisations to explore learning about innovation within complex , networked organizations (2009) (0)

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