Gerstein, Mark - Department of Molecular Biophysics and Biochemistry, Yale University

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Gerstein, Mark - Department of Molecular Biophysics and Biochemistry, Yale University

Supplementary online material Jansen et al. A Bayesian networks approach for predicting protein-protein interactions
GeneCensus: Genome Comparisons in terms of Metabolic Pathway Activity and Protein Family Sharing
Positive selection at the protein network periphery: Evaluation in terms of structural constraints and
commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch Genome Biology 2006, 7(Suppl 1):S13
Positional artifacts in microarrays: experimental verification and construction of COP,
Global analysis of protein phosphorylation in yeast Jason Ptacek1
Structural Genomics Analysis: Characteristics of atypical, typical,
/ www.sciencexpress.org / 26 July 2001 / Page 1/ 10.1126/science.1062191 To facilitate studies of the yeast proteome, we have cloned
Identification of pseudogenes in the Drosophila melanogaster genome
U:\GENOME\CONTENT\PRIMARY\Luscombe\Edited\L0302201bp2.doc 13/06/02 Typesetter: there are 'picture' equations as display items in text and in text in Figure 1
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures
nature biotechnology volume 28 number 1 january 2010 47 r e s o u r c e
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms
Conformational changes associated with proteinprotein interactions
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS HingeMaster: Normal mode hinge
Mapping accessible chromatin regions using Sono-Seq
BPC Disk Usage Information Form Manuscript Number: 5343
Protein Engineering vol.7 DO.4 pp.461 -470, 1994 Solution structure of the DNA binding octapeptide repeat of the
The Packing Density in Proteins: Standard Radii and Volumes
Predicting interactions in protein networks by completing defective cliques
Message from ISCB Getting Started in Gene Orthology and Functional
Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome
2 Muramatsu, M. et al. (1999) Specific expression of activation-induced cytidinedeaminase(AID),anovelmemberoftheRNA-editingdeaminase
A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaeal Genomes in Terms
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality
Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function
Gene expression Assessing the need for sequencebased normalization in tiling
Published online 7 August 2007 Nucleic Acids Research, 2007, Vol. 35, No. 15 e99 doi:10.1093/nar/gkm549
Patterns of ProteinFold Usage in Eight Microbial Genomes
Beyond Synexpression Relationships: Local Clustering of Time-shifted and Inverted Gene
Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis
*Corresponding Author: Mark Gerstein--Department of Molecular Biophysics and Biochemis-try, and Department of Computer Science, Yale University, 266 Whitney Avenue, P.O. Box
A small reservoir of disabled ORFs in the Saccharomyces cerevisiae genome and its implications for the dynamics of
*Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA;
Nucleic Acids Research, 1994, Vol. 22, No. 16 3397-3405 Stereochemical basis of DNA recognition by Zn fingers
BioMed Central Page 1 of 5
Our implementation of the SCA method Introduction
Beyond Synexpression Relationships: Local Clustering of Time-shifted and Inverted Gene
Differential binding of calmodulin-related proteins to their targets revealed through high-density
J. Mol. Biol. (1991) 220, 133-149 Analysis of Protein Loop Closure
894 VOLUME 25 NUMBER 8 AUGUST 2007 NATURE BIOTECHNOLOGY The minimum information required for reporting a
GENOME/2006/055863 Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis
Available online at www.sciencedirect.com The current excitement about copy-number variation: how it
The completion and near completion of the sequencing phase of genome projects has ushered in the age of proteomics, the
YMD: A microarray database for large-scale gene expression analysis Kei-Hoi Cheung, PhD1
JOURNAL OF COMPUTATIONAL BIOLOGY Volume 11, Number 4, 2004
BIOINFORMATICS A Supervised Hidden Markov Model Framework for
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Structural Genomics Analysis: Phylogenetic Patterns of Unique, Shared, and Common Folds in 20 Genomes
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS RigidFinder: A fast and sensitive
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction
HANS GRIMMER 271 and the form of 7r given in Table 3 then show that
An analysis of the present system of scientific publishing: what's wrong and
We investigate the relationship between protein subcellular localization and gene expression for a variety of whole-
Artificial transmembrane oncoproteins smaller than the2 bovine papillomavirus E5 protein redefine sequence requirements3
10. Y. Gu et al., Mol. Cell Biol. 22, 7645 (2002). 11. A. J. Ridley, H. F. Paterson, C. L. Johnston, D. Diek-
Protein Geometry: Volumes, Areas, and Distances
10.1101/gad.1740009Access the most recent version at doi: published online December 18, 2008Genes Dev.
RESEARCH Open Access Identification and analysis of unitary
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10.1101/gr.075804.107Access the most recent version at doi: published online May 16, 2008;Genome Res.
Protein Engineering vol.8 no.4 pp.319-328, 1995 DNA recognition code of transcription factors
Rapid Evolution by Positive Darwinian Selection in T-cell Antigen CD4 in Zhengdong D. Zhang 1
Mapping of Transcription Factor Binding Regions in Mammalian Cells by ChIP: Comparison of Array and Sequencing Based Technologies
www.sciencemag.org SCIENCE VOL 315 5 JANUARY 2007 39 Another Nail
Quantifying environmental adaptation of metabolic pathways in metagenomics
3V: cavity, channel and cleft volume calculator and extractor
Digging Deep for Ancient Relics: A Survey of Protein Motifs in the Intergenic Sequences of Four Eukaryotic Genomes
Background: Different Perspectives in Comparing Genomes and Structures While there is a well-established practice of comparing protein structures --often focusing on clustering
Analysis of Membrane Proteins in Metagenomics: Networks of correlated environmental features and protein families
Online ISSN: 1097461X Print ISSN: 00207608 International Journal of Quantum
Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from
Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome
http://genomebiology.com/2002/3/8/research/0040.1 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
10.1101/gad.1371305Access the most recent version at doi: 2005 19: 2953-2968; originally published online Nov 30, 2005;Genes & Dev.
Design principles of molecular networks revealed by global comparisons and composite motifs
lnthel9[7scienufidionnilelfall1eraUilliamfii[sonfflntffiizsdafirtrrreirthflhrted tUFl[hrrrhldEtheirhruinsdirurtlUinhrgiantrnmputernetunrliandplungetheir
The transcriptome is the complete set of transcripts in a cell, and their quantity, for
SEMANTIC WEB APPROACH TO DATABASE INTEGRATION IN THE LIFE SCIENCES
MARK B GERSTEIN || Change Password || View/Change User Information || CiteTrack Personal Alerts || Subscription HELP || SIGNAL TRANSDUCTION
Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation
Digging Deep for Ancient Relics: A Survey of Protein Motifs in the Intergenic Sequences of Four
Beyond Synexpression Relationships: Local Clustering of Time-shifted and Inverted Gene
BioMed Central Open Access
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family
An analysis of the present system of scientific publishing
FULL TEXT (TEXT + FULL FIGURES) Vol. 2, No. 7, 15 July 1994
10.1101/gad.1781909Access the most recent version at doi: 2009 23: 1351-1363Genes Dev.
TopNet: a tool for comparing biological sub-networks, correlating protein properties with
Assessing the Limits of Genomic Data Integration for Predicting Protein-Protein Interactions
Transcription regulation (in YEAST ): a genomic network
DOI: 10.1126/science.1140748 , 815 (2007);317Science
Protein Science (1998), 7: 445-456. Cambridge University Press. Printed in the USA. Copyright 1998 The Protein Society
Analysis of single nucleotide polymorphisms in human chromosomes 21 and 22 Suganthi Balasubramanian, Paul Harrison, Hedi Hegyi, Paul Bertone, Nicholas
BMC Bioinformatics Genome-wide sequence-based prediction of peripheral proteins
Volume Changes in Protein Evolution A method to weight protein sequences
Conformational Changes Associated with Protein-Protein Interactions
Genomic analysis of essentiality within protein networks Haiyuan Yu, Dov Greenbaum, Hao Xin Lu, Xiaowei Zhu and Mark Gerstein
An Interdepartmental Ph.D. Program in Computational Biology and Bioinformatics: The Yale Perspective
Impediments to database interoperation: legal issues and security concerns The significant growth of this annual over the past decade is testament to the importance of databases to scientific research in
10.1101/gad.1760209Access the most recent version at doi: 2009 23: 619-632 originally published online February 24, 2009Genes Dev.
Genome Biology 2008, 9:R3 Open Access2008Wuet al.Volume 9, Issue 1, Article R3Research
Structured RNAs in the ENCODE Selected Regions of the Human Genome
Assessing the Performance of Different High-density Tiling Microarray Strategies for Mapping Transcribed Regions of the Human Genome
Patterns of Protein-Fold Usage in Eight Microbial Genomes: A Comprehensive Structural Census
A reprint from American Scientistthe magazine of Sigma Xi, The Scientific Research Society
The transcriptional activity of human Chromosome 22
Genome-wide analysis of gene expression relationships in transcriptional regulatory networks
THE NEXUS OF STANDARD SETTING ORGANIZATIONS, INTELLECTUAL PROPERTY, ANTITRUST
Automatic Classification of a Database of Macromolecular Motions based on Normal Mode
Genome Analyses of Spirochetes: A Study of the Protein Structures, Functions and Metabolic
The Geometry of the Ribosomal Polypeptide Exit , M. Gerstein1
Genome Biology 2003, 4:117 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
Genomic analysis of essentialityGenomic analysis of essentialityGenomic analysis of essentialityGenomic analysis of essentiality within protein networkswithin protein networkswithin protein networkswithin protein networks
CORRESPONDENCE NATURE|Vol 440|6 April 2006 Avoidinghazardsofbest-
HEMATOPOIESIS Genomic and proteomic analysis of the myeloid differentiation program: global
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 59135920, May 1998
Thermostability of membrane protein helix^helix interaction elucidated by statistical analysis
new technology nature genetics volume 26 november 2000 283
Relating protein conformational changes to packing efficiency and disorder
doi:10.1182/blood-2008-06-162164 Prepublished online Jan 14, 2009;
1999 Macmillan Magazines Ltd 15. Ohta, T. An examination of the generation-time effect on molecular evolution. Proc. Natl. Acad. Sci.
Application Note The tYNA Platform for Comparative Interactomics: A Web Tool for
Proc. Nati. Acad. Sci. USA Vol. 89, pp. 4638-4642, May 1992
Statistical Analysis of the Genomic Distribution and Correlation of Regulatory Elements in the ENCODE Regions
PERSPECTIVE Personal genome sequencing: current
Prediction of Regulatory Networks: Genome-wide identification of transcription factor targets from gene expression data
Zhang et al. Identification and Analysis of Over 2000 Ribosomal Protein
10.1101/gad.1362105Access the most recent version at doi: 2005 19: 2816-2826Genes & Dev.
DOI: 10.1126/science.1196914 , 1775 (2010);330Science
DOI: 10.1126/science.1158441 , 1344 (2008);320Science
N E W S A N D V I E W S NATURE BIOTECHNOLOGY VOLUME 21 NUMBER 11 NOVEMBER 2003 3
Revisiting the CAI from a whole-genome perspective: analyzing the relationship between gene expression and
(81), pe44. [DOI: 10.1126/scisignal.281pe44]2Science Signaling Roger P. Alexander, Philip M. Kim, Thierry Emonet and Mark B. Gerstein (28 July
Studying Protein Flexibility in a Statistical Framework: Tools and Databases for Analyzing Structures and Approaches for Mapping
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short,
The EMBO Journal vol. 12 no. 1 pp. 1 -8, 1993 Electron diffraction analysis of structural changes in the
Transmembrane Protein Oxygen Content and Compartmentalization of Cells
Leading Edge Cell 134, July 11, 2008 2008 Elsevier Inc. 9
Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed
Toward a Systematic Definition of Protein Function That Scales to the Genome Level
Integrated Prediction of the Helical Membrane Protein Interactome in Yeast
Annotation Transfer for Genomics: Measuring Functional Divergence
EUKARYOTIC CELL, Oct. 2006, p. 16741687 Vol. 5, No. 10 1535-9778/06/$08.00 0 doi:10.1128/EC.00252-06
JOURNAL OF BACTERIOLOGY, May 2005, p. 29832991 Vol. 187, No. 9 0021-9193/05/$08.00 0 doi:10.1128/JB.187.9.29832991.2005
New computational techniques have allowed protein folds to be assigned to all or parts of between a quarter (Caenorhabditis
The Relationship Between Protein Structure and Function: A Comprehensive Survey Focusing
The Relationship Between Protein Structure and Function: A Comprehensive Survey with Application
1999 Macmillan Magazines Ltd for the nucleus to be reprogrammed. But
How representative are the known structures of the proteins encoded by [AU:OK?] a complete genome? A comprehensive
How Representative are the Known Structures of the Proteins in a Complete
Patterns of Protein-Fold Usage in Eight Microbial Genomes
COMMUNICATION A `PolyORFomic' Analysis of Prokaryote Genomes
Identication of pseudogenes in the Drosophila melanogaster genome
Studying Genomes Through the Aeons: Protein Families, Pseudogenes and Proteome Evolution
2002 Oxford University Press Nucleic Acids Research, 2002, Vol. 30, No. 5 10831090 SURVEY AND SUMMARYSURVEY AND SUMMARY
COMMUNICATION A Small Reservoir of Disabled ORFs in the Yeast
Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes
Sequences and topology Editorial overview
V I E W P O I N T The ENCODE (ENCyclopedia Of
TopNet: a tool for comparing biological sub-networks, correlating protein properties with
Assessing the Limits of Genomic Data Integration for Predicting Protein Networks
Subcellular localization of the yeast Anuj Kumar,1
10.1101/gr.7080508Access the most recent version at doi: published online Feb 7, 2008;Genome Res.
Vol. 22 no. 12 2006, pages 14371439 doi:10.1093/bioinformatics/btl116BIOINFORMATICS ORIGINAL PAPER
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The Relationship between Protein Structure and Function: a Comprehensive Survey with Application
Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate
The role of disorder in interaction networks: a structural analysis
ANALYZING CELLULAR BIOCHEMISTRY IN TERMS OF MOLECULAR NETWORKS
Annotation Transfer Between Genomes: ProteinProtein Interologs and
10.1101/gr.6339607Access the most recent version at doi: 2007 17: 669-681Genome Res.
Digging for Dead Genes: An Analysis of the Characteristics of the Pseudogene Population in the C. elegans Genome
ProteinfossilsliveonasRNA Rajkumar Sasidharan and Mark Gerstein
GENES, CHROMOSOMES & CANCER 48:366380 (2009) Distinct Genomic Aberrations Associated with ERG
Manuscript prepared for submission to J. Molecular Evolution Title: MEASURING SHIFTS IN FUNCTION AND EVOLUTIONARY OPPORTUNITY
Genomic analysis of regulatory network dynamics reveals large topological changes
Welcome (Institutional Subscriber : Yale University) Please login or August 2006
Protein Engineering vol.6 DO.6 pp.565-574, 1993 An NMR study on the DNA-binding SPKK motif and a model for
Digging for Dead Genes: An Analysis of the Characteristics of the Pseudogene Population in the C. elegans Genome
DNA replication-timing analysis of human chromosome 22 at high resolution and
SPINE: An Integrated Tracking Database and Data Mining Approach for Identifying Feasible Targets in High-throughput Structural Proteomics
GATA-1 binding sites mapped in the -globin locus by using mammalian chIp-chip analysis
Proteins: Structure, Function, and Genetics Article No. 7e0847
Protein Engineering vol.8 no.4 pp.329-338, 1995 DNA recognition and superstructure formation by
Review Paper 83Yearbook of Medical Informatics 2001
Supplementary material Dataset Data set
STUDYING MACROMOLECULAR MOTIONS IN A DATABASE FRAMEWORK: FROM STRUCTURE TO SEQUENCE
Correspondence Dog as an Outgroup to Human
Analysis of the Yeast Transcriptome with Structural and Functional Categories
Ontologies for proteomics --Towards a systematic definition of structure & function that scales to the
Close association of RNA polymerase II and many transcription factors with Pol III genes
Design Optimization Methods for Genomic DNA Tiling Arrays
EDITOR'S CORNER The Protein Target List of the Northeast Structural
48 SCIENTIFIC AMERICAN AUGUST 2006 www.sciam.com SCIENTIFIC AMERICAN 49
RNAexpression patterns change dramatically in human neutrophils exposed to bacteria
When it was realized in the late 1960s1 how much of the
BioMed Central Page 1 of 15
The Database of Macromolecular Motions: new features added at the decade mark
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements
Proteomics Of Mycoplasma Genitalium: Identification And Characterization Of Unannotated And Atypical Proteins In A Small Model Genome
Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures
Genome Analyses of T. pallidum and B. burgdorferi 387 Genome Analyses of Spirochetes: A Study of the
REVISED manuscript (PEW 32/95) for J. Mol. Biol. (sent 25 Apr 1995)
Calculation of Standard Atomic Volumes for RNA Cores and Comparison with Proteins: RNA is packed more
Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray
DNA replication timing analysis of human chromosome 22 at high resolution and different developmental states
Structural Genomics Analysis: Characteristics of Atypical, Typical, and Horizontally Transferred Folds
2001 Schattauer GmbH Method Inform Med 4/2001
BioMed Central Page 1 of 21
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed
genome is defined as the entire col-lection of genes encoded by a partic-
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
Studying Genomes Through the Aeons: Protein Families, Pseudogenes and Proteome Evolution
Tilescope: online analysis pipeline for high-density tiling microarray data Zhengdong D. Zhang1
6 Gerlai, R. (2001) Gene targeting: technical confounds and potential solutions in behavioral brain research. Behav. Brain Res. 125,
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Structural Genomics Analysis: Characteristics of Atypical, Common, and Horizontally Transferred Folds
Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of
The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse
How representative are the known structures of the proteins in a complete genome? A comprehensive structural census
Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with
Protein fold and family occurrence in genomes: power-law behaviour and evolutionary model
DOI: 10.1126/science.1136174 , 1938 (2006);314Science
10.1101/gr.110189.110Access the most recent version at doi: published online December 22, 2010Genome Res.
(146), ra79. [DOI: 10.1126/scisignal.2001014]3Science Signaling Nitin Bhardwaj, Philip M. Kim and Mark B. Gerstein (2 November 2010)
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Comparing genomes to computer operating systems in terms of the topology and evolution of
Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies
/ www.sciencexpress.org / 18 March 2010 / Page 1 / 10.1126/science.1183621 Differences in gene expression may play a major role in
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Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/
(109), ra12. [DOI: 10.1126/scisignal.2000482]3Science Signaling Benjamin E. Turk (16 February 2010)
Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation
9 JANUARY 2009 VOL 323 SCIENCE www.sciencemag.org210 CREDIT:JOESUTLIFF
EBNA1 regulates cellular gene expression by binding cellular promoters
PLEASE SCROLL DOWN FOR ARTICLE This article was downloaded by: [Yale Univ Library]
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Robust-Linear-Model Normalization To Reduce Technical Variability in Functional Protein Microarrays
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UNCORRECTEDPROOF Please cite this article in press as: Arinaminpathy, Y. et al. Computational analysis of membrane proteins: the largest class of drug targets, Drug Discov Today (2009), doi:10.1016/
Message from ISCB Getting Started in Text Mining: Part Two
N-myc Downstream Regulated Gene 1 (NDRG1) Is Fused to
Small RNAs Originated from Pseudogenes: cis-or trans-Xingyi Guo1
The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis
Genome Biology 2009, 10:R23 Open Access2009Korbelet al.Volume 10, Issue 2, Article R23Software
StoneHinge: Hinge prediction by network analysis of individual protein structures
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Genome Biology 2009, 10:R2 Open Access2009Balasubramanianet al.Volume 10, Issue 1, Article R2Research
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
10.1101/gr.080069.108Access the most recent version at doi: published online November 26, 2008Genome Res.
BIOINFORMATICS Vol. 00 no. 00 2008
BioMed Central Page 1 of 14
PLEASE SCROLL DOWN FOR ARTICLE This article was downloaded by: [Yale Univ Library]
High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution
Modeling ChIP Sequencing In Silico with Applications Zhengdong D. Zhang1
MCP Submitted Targeting the Human Cancer Pathway Protein
Open Access: Taking Full Advantage of the Content Philip E. Bourne1
Invited Editorial Manually structured digital abstracts: A scaffold for automatic
Genome BBiioollooggyy 2008, 99
Analysis of nuclear receptor pseudogenes in vertebrates: How the silent tell their stories
Seq/Site 1 2 31 2 3 4 5 ...6 I F W T C-F
Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostate Cancer
Vol. 23 no. 22 2007, pages 30733079 BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm452
Diverse Cellular Functions of the Hsp90 Molecular Chaperone
/ www.sciencexpress.org / 13 September 2007 / Page 1 / 10.1126/science.1149504 Structural variation of the genome involves kilobase-to
ORIGINAL PAPER Transcription factor binding site identification in yeast
Comparing classical pathways and modern networks: towards the
The DART Classification of Unannotated Transcription within the ENCODE Regions: Associating Transcription with Known and Novel
INTEGRATED ANALYSIS OF EXPERIMENTAL DATASETS REVEALS MANY NOVEL PROMOTERS IN 1% OF THE HUMAN GENOME
in the human genome Systematic prediction and validation of breakpoints associated with copy-number variants
Associate Editor: Dr. Alex Bateman Bioinformatics Advance Access published May 31, 2007
Global Survey of Human T Leukemic Cells by Integrating Proteomic and Transcriptomic Profiling
Tilescope: online analysis pipeline for high-density tiling microarray data Zhengdong D. Zhang1
BioMed Central Page 1 of 12
10.1101/gad.1528707Access the most recent version at doi: 2007 21: 1010-1024Genes & Dev.
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The human genome project has revealed the DNA sequence that governs all biological processes in humans
DOI: 10.1126/science.314.5806.1682b , 1682b (2006);314Science
An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits
Oxford University Press 2005 1 Original paper
Genomic analysis of the hierarchical structure of regulatory networks
10.1101/gr.5144106Access the most recent version at doi: published online Aug 9, 2006;Genome Res.
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling
10.1101/gad.1389306Access the most recent version at doi: 2006 20: 435-448; originally published online Jan 31, 2006;Genes & Dev.
Design Optimization Methods for Genomic DNA Tiling Arrays
Inferring Protein-Protein Interactions Using Interaction Network Topologies
Genome Biology 2005, 6:119 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
Genome Biology 2005, 6:R80 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation
Issues in the analysis of oligonucleotide tiling microarrays
Integrated Pseudogene Annotation for Human Chromosome 22: Evidence for Transcription
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed
Normal modes for predicting protein motions: A comprehensive database assessment and
Calculation of Standard Atomic Volumes for RNA and Comparison with Proteins: RNA is Packed More Tightly
/ www.sciencexpress.org / 11 November 2004 / Page 1/ 10.1126/science.1103388 Elucidating the transcribed regions of the genome
BMC Bioinformatics This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted
Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
Genome Biology 2004, 5:R64 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation
Large-scale Analysis of Pseudogenes in the Human Genome ZhaoLei Zhang and Mark Gerstein*
Major Molecular Differences Between Mammalian Sexes are involved in Drug Metabolism and Renal Function
MOLECULAR AND CELLULAR BIOLOGY, May 2004, p. 38043814 Vol. 24, No. 9 0270-7306/04/$08.00 0 DOI: 10.1128/MCB.24.9.38043814.2004
Evolutionary Use of Domain Recombination: A Distinction Between Membrane and Soluble Proteins
Recently, a nearly complete draft of the human genome has been determined, producing an enormous wealth of
BMC Genomics This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted
Distribution of NF-B-binding sites across human chromosome 22
ExpressYourself: a modular platform for processing and visualizing microarray data
Data Mining Crystallization Databases: Knowledge-Based Approaches to Optimize Protein Crystal Screens
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the
MolMovDB: analysis and visualization of conformational change and structural flexibility
11 JANUARY 2002 VOL 295 SCIENCE www.sciencemag.org284 nosity during the same pe-
Toward a Systematic Definition of Protein Function That Scales to the Genome Level
JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS (JSFG) Dear Author(s),
Complex transcriptional circuitry at the G1/S transition in
Normal Mode Analysis of Macromolecular Motions in a Database Framework: Developing Mode Concentration as a
commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch http://genomebiology.com/2002/3/2/reports/4004.1
Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins
Online ISSN: 1097-461X Print ISSN: 0020-7608 International Journal of Quantum
A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry
An XML application for genomic data interoperation Kei-Hoi Cheung1
Progress in Biophysics & Molecular Biology 73 (2000) 339345 Structural proteomics: prospects for high throughput
Whole-genome expression profiles provide a rich new data-trove for bioinformatics. Initial analyses of the profiles have
A Bayesian System Integrating Expression Data with Sequence Patterns for Localizing Proteins
PROTEIN FOLDS IN THE WORM GENOME M. GERSTEIN, J. LIN, H. HEGYI
Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing
Comparing Genomes in terms of Protein Structure
1998 Oxford University Press42804290 Nucleic Acids Research, 1998, Vol. 26, No. 18 A database of macromolecular motions
COMMUNICATION Repeated Tertiary Fold of RNA Polymerase II and
Proc. Natl. Acad. Sci. USA Vol. 94, pp. 1191111916, October 1997
Protein Science (1997), 6: 246-248. Cambridge University Press. Printed in the USA. Copyright 1997 The Protein Society
Keeping the shape but changing the charges: A simulation study of urea and its iso-steric analogs
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 1016710172, September 1996
J. Mol. Biol. (1995) 249, 955966 The Volume of Atoms on the Protein Surface
I~UTTERWORTH E 1 N E M A N N
Finding an average core structure: Application to the globins Russ B. Altman
J. Phys. Chem. 1993,97, 2991-2999 2991 Simulationof Water around a Model Protein Helix. 2. The Relative Contributions of Packing,
Supplementary material Emanuelsson et al. EXPERIMENTAL METHODS
Additional Table 2. Gideon Labs Analyzed and their Descriptions Abbreviations Lab Description Criteria Used to Score Lab as Positive
A Supervised Hidden Markov Model Framework for Efficiently Segmenting Tiling Array Data in
48 SCIENTIFIC AMERICAN AUGUST 2006 COPYRIGHT 2006 SCIENTIFIC AMERICAN, INC.
Assessing Annotation Transfer for Genomics: Quantifying the Relations between Protein Sequence,
Assessing the Performance of Different High-density Tiling Microarray Strategies for Mapping Transcribed Regions of the Human Genome
Integrated Prediction of the Helical Membrane Protein Interactome in Yeast
BMC Bioinformatics This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted
Transcription regulation: a genomic network
Genomic analysis of regulatory network dynamics reveals
ANALYZING CELLULAR BIOCHEMISTRY IN TERMS OF MOLECULAR NETWORKS
Analyzing Cellular Biochemistry in Terms of Molecular Networks , Haiyuan Yu1,5
Annotation transfer for genomics: assessing the transferability of protein-protein and protein-DNA interactions between
|Genome Analysis Comparative analysis of processed pseudogenes in the
Zhang, Carriero and Gerstein Comparative analysis of processed pseudogenes in the mouse and
Running Title: Mining the Structural Genomics Pipeline Mining the Structural Genomics Pipeline
A Bayesian networks approach for predicting protein-protein interactions from genomic data
"bio139" --2003/7/28 --page 1 --#1 BIOINFORMATICS
Distribution of NF-B-binding sites across human chromosome 22
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