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List of works by Mark Bender Gerstein

3V: cavity, channel and cleft volume calculator and extractor

scientific article

A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome

scientific article

A Comprehensive Nuclear Receptor Network for Breast Cancer Cells ⬇️

scientific article published on January 31, 2013

A Review of the Morph Server and the Macromolecular Motions Database: A Standardized System for Analyzing and Visualizing Macromolecular Motions in a Database Framework

article

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation

scientific article published on 11 July 2019

A cis-regulatory map of the Drosophila genome.

scientific article

A comprehensive catalog of predicted functional upstream open reading frames in humans.

scientific article published on 19 March 2018

A computational approach for identifying pseudogenes in the ENCODE regions

scientific article (publication date: 2006)

A database of macromolecular motions ⬇️

scientific article published on September 15, 1998

A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development

scientific article published on 6 November 2003

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

scientific article

A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies

scientific article

A map of the interactome network of the metazoan C. elegans

scientific article (publication date: 23 January 2004)

A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes

scientific article

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

scientific article published on May 2004

A multiregional proteomic survey of the postnatal human brain.

scientific article published on 13 November 2017

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

scientific article

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

scientific article published in September 2005

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

scientific article published on March 2002

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

scientific article published in February 2002

A standard reference frame for the description of nucleic acid base-pair geometry.

scientific article

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

scientific article

A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure ⬇️

scientific article published on December 12, 1997

A structural census of the current population of protein sequences ⬇️

scientific article published on October 28, 1997

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

scientific article

A systematic survey of loss-of-function variants in human protein-coding genes

scientific article (publication date: 17 February 2012)

A unified statistical framework for sequence comparison and structure comparison ⬇️

scientific article published on May 26, 1998

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

scientific article published on 18 April 2016

A universal legal framework as a prerequisite for database interoperability

scientific article published in September 2003

A ‘PolyORFomic’ Analysis of Prokaryote Genomes Using Disabled-homology Filtering Reveals Conserved But Undiscovered Short ORFs ⬇️

scientific article published on November 7, 2003

ACT: aggregation and correlation toolbox for analyses of genome tracks.

scientific article

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

scientific article

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

scientific article

Advances in structural genomics

scientific article

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

scientific article published in Science

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

scientific article published on 2 August 2011

An NMR study on the DNA-binding SPKK motif and a model for its interaction with DNA.

scientific article

An analysis of the present system of scientific publishing: what's wrong and where to go from here

An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome

scientific article published on 31 March 2015

An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping

scientific article published on 21 October 2009

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping

scientific article

An efficient pseudomedian filter for tiling microrrays

scientific article

An ensemble approach to accurately detect somatic mutations using SomaticSeq

scientific article

An integrated approach for finding overlooked genes in yeast

scientific article published in January 2002

An integrated map of structural variation in 2,504 human genomes

scientific article

An integrated system for studying residue coevolution in proteins

scientific article

An integrative ENCODE resource for cancer genomics

scientific article published on 29 July 2020

An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits

scholarly article by Yang Liu published in January 2005

An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits

scientific article published on 17 November 2006

An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective

scientific article

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Analysis of Nuclear Receptor Pseudogenes in Vertebrates: How the Silent Tell Their Stories

article

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets

scientific article

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

scientific article published on 08 October 2008

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms ⬇️

scientific article published on June 2015

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels

scientific article

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

scientific article (publication date: September 2011)

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

scientific article

Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families

scientific article

Analysis of protein loop closure

article

Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase

scientific article

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.

scientific article published on 22 June 2018

Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins

scientific article

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

scientific article (publication date: December 2013)

Analysis of yeast protein kinases using protein chips.

scientific article

Analyzing cellular biochemistry in terms of molecular networks

scientific article published on January 2004

Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction

scientific article published in October 2004

Annotating non-coding regions of the genome

scientific article

Annotation of the human genome

scientific article published on 01 June 2000

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs

scientific article

Annotation transfer for genomics: measuring functional divergence in multi-domain proteins

scientific article

Annual Research Review: The promise of stem cell research for neuropsychiatric disorders

scientific article

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

scientific article

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients

scientific article published on 22 June 2020

Architecture of the human regulatory network derived from ENCODE data

scientific article (publication date: 6 September 2012)

Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor

scientific article published on 15 July 2009

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores

scientific article published in March 2000

Assessing the limits of genomic data integration for predicting protein networks

scientific article published in July 2005

Assessing the need for sequence-based normalization in tiling microarray experiments

scientific article published on 25 March 2007

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

scientific article published on 21 November 2006

Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing

scientific article

Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer

article published in 2008

Author Correction: Functional genomics data: privacy risk assessment and technological mitigation

correction of a scholarly article

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

scientific article published on 30 November 2020

Average Core Structures and Variability Measures for Protein Families: Application to the Immunoglobulins ⬇️

scientific article published on August 4, 1995

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

scientific article

Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions

scientific article published on 23 August 2021

Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions ⬇️

scientific article published on December 14, 2001

Binding geometry of alpha-helices that recognize DNA

scientific article published on 01 December 1995

Biochemical and genetic analysis of the yeast proteome with a movable ORF collection

scientific article (publication date: December 2005)

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

scientific article published on January 2006

Bridging structural biology and genomics: assessing protein interaction data with known complexes

scientific article

Bridging structural biology and genomics: assessing protein interaction data with known complexes

scientific article published on 01 October 2002

Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions

scientific article published on 03 July 2019

Building the future of biocomputing

scientific article published in Nature

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

scientific article

CREB binds to multiple loci on human chromosome 22.

scientific article published on May 2004

Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly

scientific article

Calculations of protein volumes: sensitivity analysis and parameter database

scientific article published in July 2002

Cancer genomics: Less is more in the hunt for driver mutations.

scientific article published on 28 June 2017

Cellular superspreaders: an epidemiological perspective on HIV infection inside the body

scientific article (publication date: May 2014)

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

scientific article

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features

scientific article

Chemistry Nobel rich in structure

scientific article published in January 2007

Child development and structural variation in the human genome

scientific article published on 13 January 2013

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

scientific article

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

scientific article

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

scientific article

Closure of the NCBI SRA and implications for the long-term future of genomics data storage

scientific article

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human

scientific article

Comparative analysis of processed pseudogenes in the mouse and human genomes

scientific article published on February 2004

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes

scientific article

Comparative analysis of pseudogenes across three phyla

scientific article

Comparative analysis of regulatory information and circuits across distant species

scientific article

Comparative analysis of the transcriptome across distant species

scientific article

Comparing Technological Development and Biological Evolution from a Network Perspective

scientific article published on 01 March 2020

Comparing classical pathways and modern networks: towards the development of an edge ontology

scientific article published on 20 June 2007

Comparing genomes in terms of protein structure: surveys of a finite parts list.

scientific article

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

scientific article

Comparing protein abundance and mRNA expression levels on a genomic scale

scientific article

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

scientific article

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

scientific article

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

scientific article published on 4 November 2015

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes

scientific article

Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes

scientific article

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

scientific article (publication date: 16 October 2009)

Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins ⬇️

scientific article published on February 1, 1998

Comprehensive functional genomic resource and integrative model for the human brain

scientific article published on 01 December 2018

Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions

scientific article

Computational analysis of membrane proteins: the largest class of drug targets.

scientific article

Computer security in academia-a potential roadblock to distributed annotation of the human genome

scientific article published on 01 June 2004

Conformational changes associated with protein-protein interactions

scientific article published on February 2004

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

scientific article

Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma

scientific article published on 3 June 2016

Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs

scientific article

DNA recognition and superstructure formation by helix-turn-helix proteins

scientific article published on 01 April 1995

DNA recognition code of transcription factors

scientific article

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

scientific article

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks

scientific article

Data Sanitization to Reduce Private Information Leakage from Functional Genomics

scientific article published on 01 November 2020

Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens

scientific article

Data mining on the web

scientific article published on 01 December 2006

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

scientific article

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy

scientific article published on 28 October 2014

Deep Inside Champions, Just Genes?

scientific article published in Science

Defining functional DNA elements in the human genome

scientific article

Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies

scientific article

Defining the human reference protein-coding gene set.

scientific article published on 11 October 2010

Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair

scientific article published on 15 April 2020

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

Design optimization methods for genomic DNA tiling arrays

scientific article

Design principles of molecular networks revealed by global comparisons and composite motifs

scientific article published on January 2006

Detecting and annotating genetic variations using the HugeSeq pipeline

scientific article

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model ⬇️

scientific article published on October 31, 2010

Determining the impact of putative loss-of-function variants in protein-coding genes

article

Determining the minimum number of types necessary to represent the sizes of protein atoms

scientific article

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring

scientific article published on 02 July 2020

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

scholarly article

Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes

scientific article published in November 2002

Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome

scientific article published on February 2001

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources

scientific article

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

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing

scientific article

Distinct genomic aberrations associated with ERG rearranged prostate cancer

scientific article published on April 2009

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

scientific article

Divergence of transcription factor binding sites across related yeast species

scientific article

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches

scientific article

Diverse human extracellular RNAs are widely detected in human plasma.

scientific article published on 26 April 2016

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

scientific article

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

scientific article

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

scientific article

Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers

scientific article published on 01 January 1993

Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces

scientific article published on November 1993

Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition

scientific article published on 5 April 2017

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

scientific article published on June 2009

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

scientific article

E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics

scientific article published on 01 June 1999

EBNA1 regulates cellular gene expression by binding cellular promoters

scientific article

ENCODE leads the way on big data ⬇️

scientific article published on September 13, 2012

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

scientific article

Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.

scientific article published on January 1993

Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions

scientific article published on 11 June 2018

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

scientific article

Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression

scientific article published on 11 December 2012

Epigenome-based splicing prediction using a recurrent neural network

scientific article published on 25 June 2020

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

scientific article published on 28 April 2016

Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

scientific article published in Nature Communications

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

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

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

scientific article published on 01 February 2020

Estimating growth patterns and driver effects in tumor evolution from individual samples

scientific article published on 05 February 2020

Estimation of the carrier frequency of fumarate hydratase alterations and implications for kidney cancer risk in hereditary leiomyomatosis and renal cancer

scientific article published on 15 May 2020

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

scientific article published on 06 November 2019

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Exploring the range of protein flexibility, from a structural proteomics perspective

scientific article

ExpressYourself: A modular platform for processing and visualizing microarray data

scientific article

Extending gene ontology in the context of extracellular RNA and vesicle communication

scientific article published on 12 April 2016

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation ⬇️

scientific article (publication date: 20 January 2012)

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

scientific article

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies

scientific article published on January 2006

FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data

scientific article published on 29 July 2020

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders

scientific article (publication date: 16 July 2015)

Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption

scientific article published on 28 June 2021

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

scientific article published in January 2004

Finding an average core structure: application to the globins

scientific article published on January 1, 1994

FlexOracle: predicting flexible hinges by identification of stable domains

scientific article

Forging links in an electronic paper chain

scientific article published in Nature

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer

scientific article

Functional genomics data: privacy risk assessment and technological mitigation

scientific article published in 2021

Functional profiling of the Saccharomyces cerevisiae genome

scientific article (publication date: 25 July 2002)

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

scientific article (publication date: 2010)

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

scientific article published on 20 March 2018

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

scientific article

GENCODE 2021 ⬇️

scientific article published on 03 December 2020

GENCODE reference annotation for the human and mouse genomes

scientific article published on 01 January 2019

GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome

GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome

GENCODE: the reference human genome annotation for The ENCODE Project

scientific article

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner

scientific article published on 30 August 2019

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

scientific article

Gene Tracer: A smart, interactive, voice-controlled Alexa skill for gene information retrieval and browsing, mutation annotation, and network visualization

scientific article published in 2021

Gene inactivation and its implications for annotation in the era of personal genomics

scientific article (publication date: 2011)

Gene names can confound most-searched listings

scientific article published in January 2018

GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing ⬇️

scientific article published on October 2002

Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi

scientific article published on 01 October 2000

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors ⬇️

scientific article published on November 7, 2011

Genome-wide analysis relating expression level with protein subcellular localization

scientific article published on 01 October 2000

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

scientific article

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

scientific article

Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique

scientific article

Genomic analysis of essentiality within protein networks

scientific article published on June 2004

Genomic analysis of gene expression relationships in transcriptional regulatory networks

scientific article published on August 2003

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

scientific article published on 28 April 2006

Genomic analysis of membrane protein families: abundance and conserved motifs

scientific article

Genomic analysis of regulatory network dynamics reveals large topological changes

scientific article

Genomic analysis of the hierarchical structure of regulatory networks

scholarly article

Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides

scientific article

Genomic and proteomic analysis of the myeloid differentiation program

scientific article

Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line

scientific article published on November 2002

Genomic anonymity: have we already lost it?

article published in 2008

Genomics and data science: an application within an umbrella.

scientific article

Genomics and privacy: implications of the new reality of closed data for the field

scientific article

Genomics. Defining genes in the genomics era.

scientific article published in April 2003

Genomics: protein fossils live on as RNA.

scientific article

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

article

Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden

scientific article published on 15 May 2020

Getting connected: analysis and principles of biological networks

scientific article published on May 2007

Getting started in gene orthology and functional analysis

scientific article published in March 2010

Getting started in text mining: part two.

scientific article

Global Survey of Human T Leukemic Cells by Integrating Proteomics and Transcriptomics Profiling

scientific article published on 21 May 2007

Global analysis of protein activities using proteome chips

scientific article (publication date: 14 September 2001)

Global analysis of protein phosphorylation in yeast

scientific article (publication date: December 2005)

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

scientific article

Global identification and characterization of transcriptionally active regions in the rice genome

scientific article

Global identification of human transcribed sequences with genome tiling arrays

scientific article (publication date: 24 December 2004)

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

scientific article

Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins

scientific article published on 23 October 2006

HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps

scientific article

High-order neural networks and kernel methods for peptide-MHC binding prediction

scientific article published on 23 July 2015

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

scientific article

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

scientific article

Hinge Atlas: relating protein sequence to sites of structural flexibility

scientific article

HingeMaster: normal mode hinge prediction approach and integration of complementary predictors.

scientific article

How far can sequences diverge?

scientific article published in Nature

How representative are the known structures of the proteins in a complete genome? A comprehensive structural census

scientific article

IQSeq: integrated isoform quantification analysis based on next-generation sequencing

scientific article

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

scientific article published in June 2007

Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome

scientific article (publication date: October 2002)

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

scientific article

Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome☆ ⬇️

scientific article (publication date: May 2003)

Identification and correction of spurious spatial correlations in microarray data

scientific article

Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity

scientific article

Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma

scientific article

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

scientific article

Identification of genomic indels and structural variations using split reads

scientific article

Identification of novel functional elements in the human genome

scientific article

Identification of pseudogenes in the Drosophila melanogaster genome

scientific article

Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps

scientific article published on 11 August 2011

Identification of yeast cell cycle regulated genes based on genomic features

scientific article

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation

scientific article

Impediments to database interoperation: legal issues and security concerns

scientific article

Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data

scientific article

Information assessment on predicting protein-protein interactions

scientific article

Insights into genetics, human biology and disease gleaned from family based genomic studies

scientific article published on 18 January 2019

Insights into genetics, human biology and disease gleaned from family based genomic studies

article

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

scientific article

Integrated assessment of genomic correlates of protein evolutionary rate

scientific article

Integrated prediction of the helical membrane protein interactome in yeast

scientific article

Integrated pseudogene annotation for human chromosome 22: evidence for transcription

scientific article

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

scientific article

Integration of curated databases to identify genotype-phenotype associations

scientific article

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

scientific article

Integration of genomic datasets to predict protein complexes in yeast

scientific article published in January 2002

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions

scientific article published on 15 September 2011

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

scientific article published on 16 January 2018

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

Integrative annotation of variants from 1092 humans: application to cancer genomics

scientific article

Integrative data mining: the new direction in bioinformatics.

scientific article

Integrative database analysis in structural genomics

scientific article published on 01 November 2000

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

scientific article published on 01 December 2018

Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer

scientific article published in November 2007

Intensification: A Resource for Amplifying Population-Genetic Signals with Protein Repeats

scientific article

Interpretation of genomic variants using a unified biological network approach

scientific article

Interrelating different types of genomic data, from proteome to secretome: 'oming in on function

scientific article

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq

article

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

scientific article published on August 2005

KBase: The United States Department of Energy Systems Biology Knowledgebase

article

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations

scientific article published on 24 August 2015

LPFC: an Internet library of protein family core structures

scientific article

Landscape and variation of novel retroduplications in 26 human populations.

scientific article

Landscape of transcription in human cells

scientific article (publication date: 6 September 2012)

Large-scale analysis of pseudogenes in the human genome

scientific article

Large-scale analysis of the yeast genome by transposon tagging and gene disruption

scientific article

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

scientific article

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

scientific article

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients

scientific article published on 15 October 2020

Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods

scientific article

Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures

scientific article published on 28 August 2019

Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics

scientific article published on 07 October 2007

Localized structural frustration for evaluating the impact of sequence variants

scientific article published on 18 October 2016

Loregic: a method to characterize the cooperative logic of regulatory factors

scientific article

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays

scientific article published on 18 December 2008

MOAT: Efficient Detection of Highly Mutated Regions with the Mutations Overburdening Annotations Tool

scientific article

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

scientific article

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

scientific article published on 26 November 2008

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.

scientific article

Machine learning and genome annotation: a match meant to be? ⬇️

scientific article published on May 29, 2013

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

scientific article published in June 2004

Manually structured digital abstracts: a scaffold for automatic text mining

scientific article

Mapping accessible chromatin regions using Sono-Seq

scientific article

Mapping copy number variation by population-scale genome sequencing

scientific article

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

scientific article published on 8 April 2022

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

scientific article

Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence ⬇️

scientific article published on January 1, 1998

Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins

scientific article published on 01 September 2000

Measuring the evolutionary rewiring of biological networks

scientific article

Measuring the reproducibility and quality of Hi-C data

article by Galip Gürkan Yardımcı et al published 19 March 2019 in Genome Biology

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

scientific article published on 10 April 2015

MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis

scientific article published on 11 February 2019

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos.

scientific article

Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome

scientific article (publication date: December 2003)

Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis

scientific article published in February 2004

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

scientific article

Modeling ChIP sequencing in silico with applications

scientific article

Modeling gene expression using chromatin features in various cellular contexts

scientific article (publication date: 13 June 2012)

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells ⬇️

scientific article published on September 16, 2011

MolMovDB

describes the motions that occur in proteins and other macromolecules

MolMovDB: analysis and visualization of conformational change and structural flexibility

scientific article

Molecular and cellular reorganization of neural circuits in the human lineage.

scientific article published in November 2017

Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets

scientific article

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22

scientific article

Molecular sampling of prostate cancer: a dilemma for predicting disease progression

scientific article

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

scientific article

Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels

scientific article

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Multi-platform discovery of haplotype-resolved structural variation in human genomes

scientific article published on 16 April 2019

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

scientific article

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology

scientific article published on 5 April 2017

N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer

scientific article

NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis

scientific article published on 22 October 2020

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis

scientific article

Network security and data integrity in academia: an assessment and a proposal for large-scale archiving

scientific article

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

scientific article published on March 2007

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

scientific article (publication date: September 2002)

Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool

scientific article

Novel Transcribed Regions in the Human Genome

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Novel approaches for bioinformatic analysis of salivary RNA Sequencing data in the biomarker development process

scientific article published on 14 August 2017

Novel insights through the integration of structural and functional genomics data with protein networks ⬇️

scientific article published on February 11, 2012

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

scientific article

Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements

scientific article

On sports and genes

scientific article published on December 2012

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.

scientific article

Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level

scientific article

Open access: taking full advantage of the content

scientific article

Origins and characterization of variants shared between databases of somatic and germline human mutations

scientific article published on 04 June 2020

OrthoClust: an orthology-based network framework for clustering data across multiple species

scientific article

PARE: a tool for comparing protein abundance and mRNA expression data

scientific article

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

scientific article (publication date: 23 February 2009)

Packing at the protein-water interface

scientific article published on September 1996

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

scientific article

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

scientific article published on 05 February 2020

Pangolin genomes and the evolution of mammalian scales and immunity

scientific article published on 10 August 2016

PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

scientific article published on April 2001

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences

scientific article published on 20 February 2020

Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences

Patients with urologic cancer and other nonurologic malignancies: analysis of a sample and review of the literature ⬇️

scientific article published on December 1, 2001

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes

scientific article

Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census

scientific article

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

scientific article

Performance comparison of whole-genome sequencing platforms

scientific article

Personal genome sequencing: current approaches and challenges

scientific article

Personal omics profiling reveals dynamic molecular and medical phenotypes

scientific article (publication date: 16 March 2012)

Personal phenotypes to go with personal genomes

scientific article published on 19 May 2009

Perspectives on ENCODE

scientific article published on 29 July 2020

Perspectives: signal transduction. Proteins in motion

scientific article published on 01 September 1999

Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum: amino acid sequence and structural interpretation ⬇️

scientific article published on May 15, 1992

Pollen-derived RNAs Are Found in the Human Circulation

scientific article published on 24 August 2019

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

scientific article published on 7 December 2006

Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context

scientific article (publication date: 12 December 2007)

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

scientific article published on 30 November 2020

Predicting essential genes in fungal genomes

scientific article published on 9 August 2006

Predicting interactions in protein networks by completing defective cliques

scientific article published on 2 February 2006

Predicting protein ligand binding motions with the conformation explorer ⬇️

scientific article published on October 27, 2011

Predicting the frequencies of drug side effects

scientific article published on 11 September 2020

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

scientific article

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data

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ProCAT: a data analysis approach for protein microarrays

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Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model ⬇️

scientific article published on 01 November 2001

Protein folding: the endgame

scientific article

Protein folds in the worm genome

scientific article published on 01 January 2000

Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome

scientific article published on August 2000

Proteomics. Integrating interactomes

scientific article

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

PseudoPipe: an automated pseudogene identification pipeline

scientific article published on 30 March 2006

Pseudofam: the pseudogene families database

scientific article (publication date: 2009)

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation

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

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Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

PubNet: a flexible system for visualizing literature derived networks

scientific article

Publishing perishing? Towards tomorrow's information architecture

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Quantification of private information leakage from phenotype-genotype data: linking attacks

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Quantifying environmental adaptation of metabolic pathways in metagenomics

scientific article

Quantum computing at the frontiers of biological sciences

scientific article published on 4 January 2021

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins

scientific article published on 30 July 2020

RNA expression patterns change dramatically in human neutrophils exposed to bacteria

scientific article published on April 2001

RNA-Seq: a revolutionary tool for transcriptomics

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RNAi development

scientific article published on April 2007

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

scientific article

Rapid Evolution by Positive Darwinian Selection in T-Cell Antigen CD4 in Primates

Reads meet rotamers: structural biology in the age of deep sequencing

scientific article

Reconstructing genetic networks in yeast ⬇️

scientific article published on 01 November 2003

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines

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Regulation of gene expression by a metabolic enzyme

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Regulatory element copy number differences shape primate expression profiles.

scientific article

Relating protein conformational changes to packing efficiency and disorder

scientific article published on June 2009

Relating three-dimensional structures to protein networks provides evolutionary insights

scientific article

Relating whole-genome expression data with protein-protein interactions

scientific article

Relationship between gene co-expression and probe localization on microarray slides

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Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity

scientific article published on 01 November 2018

Remodeling of hippocampal GABAergic system in adult offspring after maternal hypoxia and magnesium sulfate load: immunohistochemical study

scientific article published on 2 August 2005

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

scientific article published on 21 March 2018

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Repeated tertiary fold of RNA polymerase II and implications for DNA binding

scientific article

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

scientific article published on August 2014

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

scientific article published on 21 September 2020

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

scientific article

Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators.

scientific article published on 2 November 2010

RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes

scientific article published in February 2010

Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium

scientific article published in January 2005

Robust-linear-model normalization to reduce technical variability in functional protein microarrays

scientific article published on 01 December 2009

Role of non-coding sequence variants in cancer

scientific article

SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes

scientific article published on 01 May 2002

SPINE 2: a system for collaborative structural proteomics within a federated database framework

scientific article

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics

scientific article

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

scientific article published on 08 December 2020

SVFX: a machine learning framework to quantify the pathogenicity of structural variants

scientific article published on 09 November 2020

Seeking a new biology through text mining

scientific article published on July 2008

Segmental duplications in the human genome reveal details of pseudogene formation

scientific article (publication date: November 2010)

Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor.

scientific article

Sensitive information leakage from functional genomics data: Theoretical quantifications & practical file formats for privacy preservation

article published in 2018

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms

scientific article

Sequences and topology

scientific article

Shaping the nebulous enhancer in the era of high-throughput assays and genome editing

scientific article published on 20 March 2019

SigLASSO: a LASSO approach jointly optimizing sampling likelihood and cancer mutation signatures

scholarly article published 10 July 2018

Simulating the minimum core for hydrophobic collapse in globular proteins ⬇️

scientific article published on December 1, 1997

Simulating water and the molecules of life

scientific article published on 01 November 1998

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

scientific article published on 01 October 2018

Sixty years of genome biology

scientific article published on 25 April 2013

Small RNAs originated from pseudogenes: cis- or trans-acting?

scientific article (publication date: July 2009)

Social considerations in research: consider them but don't use them

scientific article published in May 2011

Social networking and personal genomics: suggestions for optimizing the interaction

scientific article published in January 2009

Solution structure of the DNA binding octapeptide repeat of the K10 gene product

scientific article published in April 1994

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

scientific article

Spectral biclustering of microarray data: coclustering genes and conditions

scientific article

Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.

scientific article published in February 2000

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

scientific article published in June 2007

Stereochemical basis of DNA recognition by Zn fingers

scientific article published on August 1994

StoneHinge: hinge prediction by network analysis of individual protein structures

scientific article published on February 2009

Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches

scientific article published in February 2003

Stroke and Circulating Extracellular RNAs

scientific article published on 13 March 2017

Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds

scientific article published in May 2002

Structural genomics: a new era for pharmaceutical research

scientific article

Structural genomics: current progress

scientific article

Structural mechanisms for domain movements in proteins

scientific article

Structural proteomics of an archaeon

scientific article

Structural proteomics: prospects for high throughput sample preparation

scientific article

Structure and evolution of transcriptional regulatory networks

scientific article

Structured RNAs in the ENCODE selected regions of the human genome

scientific article

Structured digital abstract makes text mining easy

scientific article

Structured digital tables on the Semantic Web: toward a structured digital literature

scientific article (publication date: 24 August 2010)

Structuring supplemental materials in support of reproducibility

scientific article

Studying Macromolecular Motions in a Database Framework: From Structure to Sequence

scholarly article

Studying genomes through the aeons: protein families, pseudogenes and proteome evolution

scientific article

Subcellular localization of the yeast proteome

scientific article (publication date: 15 March 2002)

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

scientific article published on 29 July 2020

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

scientific article published on 3 January 2008

Systematic control of protein interactions for systems biology ⬇️

scientific article published on December 12, 2011

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

scientific article published on 7 February 2008

Systematic identification of transcription factors associated with patient survival in cancers

scientific article

Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons

scientific article

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

scholarly article

TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles

scientific article published on 29 October 2011

TOS9 regulates white-opaque switching in Candida albicans

scientific article published on September 2006

Target hub proteins serve as master regulators of development in yeast

scientific article

Targeting the human cancer pathway protein interaction network by structural genomics

scientific article published on 18 May 2008

Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line

scientific article

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements

scientific article published on 19 August 2019

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

scientific article

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

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The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions.

scientific article published on 24 May 2012

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

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The Database of Macromolecular Motions: new features added at the decade mark

scientific article

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research

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The GENCODE human gene set

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The GENCODE human gene set

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The GENCODE pseudogene resource

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The Geometry of the Ribosomal Polypeptide Exit Tunnel

scientific article published on 30 May 2006

The PsychENCODE project

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The Spread of Scientific Information: Insights from the Web Usage Statistics in PLoS Article-Level Metrics ⬇️

scientific article published on May 16, 2011

The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?

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The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data

scientific article published on 29 May 2020

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

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The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?

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The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties

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

scholarly article

The genomic complexity of primary human prostate cancer

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The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse

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The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare

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The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics

scientific article published on 14 February 2007

The minimum information required for reporting a molecular interaction experiment (MIMIx).

scientific article published on August 2007

The modERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors

scientific article published on 28 December 2017

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework

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The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

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The packing density in proteins: standard radii and volumes.

scientific article published in July 1999

The protein target list of the Northeast Structural Genomics Consortium

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The real cost of sequencing: higher than you think!

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The real cost of sequencing: scaling computation to keep pace with data generation

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The real life of pseudogenes

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The reality of pervasive transcription

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The relationship between protein structure and function: a comprehensive survey with application to the yeast genome

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The relationship between the evolution of microRNA targets and the length of their UTRs

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The role of cloud computing in managing the deluge of potentially private genetic data

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The role of disorder in interaction networks: a structural analysis

scientific article published on 25 March 2008

The stability of thermophilic proteins: a study based on comprehensive genome comparison

scientific article (publication date: May 2000)

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks

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The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans

scientific article (publication date: March 2005)

The transcriptional activity of human Chromosome 22

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The transcriptional landscape of the yeast genome defined by RNA sequencing

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The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra

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Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis

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

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Tiling array data analysis: a multiscale approach using wavelets

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

scientific article published on 23 January 2013

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq

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Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences

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Tools needed to navigate landscape of the genome

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TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics

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TopicNet: a framework for measuring transcriptional regulatory network change

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Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications

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Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification

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Towards developing a practical artificial intelligence tool for diagnosing and evaluating autism spectrum disorder: A study using multicenter ABIDE II datasets

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Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

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Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions

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Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability

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

scientific article published on 19 July 2007

Transcriptional activity and strain-specific history of mouse pseudogenes

scientific article published on 29 July 2020

Transcriptional landscape of the prenatal human brain

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Transcriptome and epigenome landscape of human cortical development modeled in organoids

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Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

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Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

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Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism

scholarly article

Transmembrane protein oxygen content and compartmentalization of cells

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Uncovering trends in gene naming

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Understanding genome structural variations

scientific article published on 7 December 2015

Understanding modularity in molecular networks requires dynamics

scientific article published on 28 July 2009

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

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Unlocking the secrets of the genome

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Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation

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Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures

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Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes

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Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts

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Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization

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Using a measure of structural variation to define a core for the globins

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Using blockchain to log genome dataset access: efficient storage and query

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Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures

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Using semantic web rules to reason on an ontology of pseudogenes

scientific article (publication date: 15 June 2010)

Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood

scientific article published on 17 July 2020

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

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VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

scientific article published on 17 December 2014

Variation in transcription factor binding among humans

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Volume changes in protein evolution

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Volume changes on protein folding

scientific article published in July 1994

What is a gene, post-ENCODE? History and updated definition

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What is bioinformatics? A proposed definition and overview of the field.

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What is bioinformatics? An introduction and overview.

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What is the natural boundary of a protein in solution?

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Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations

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Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers

scientific article published on 26 April 2021

Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels

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

scientific article

YeastHub: a semantic web use case for integrating data in the life sciences domain

scientific article

Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization

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exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

scientific article published on 01 April 2019

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling

scientific article published on 04 April 2019

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data

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mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer

scientific article published on September 2009

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