| no |
title |
author |
magazine |
year |
volume |
issue |
page(s) |
type |
| 1 |
A computational approach for genome-wide mapping of splicing factor binding sites
|
Akerman, Martin
|
|
2009
|
|
3 |
|
article
|
| 2 |
A DNA microarray survey of gene expression in normal human tissues
|
Shyamsundar, Radha
|
|
2005
|
|
3 |
|
article
|
| 3 |
A genome-wide view of mutation rate co-variation using multivariate analyses
|
Ananda, Guruprasad
|
|
2011
|
|
3 |
|
article
|
| 4 |
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
|
Small, Kerrin S
|
|
2007
|
|
3 |
|
article
|
| 5 |
Alternative ion channel splicing in mesial temporal lobe epilepsy and Alzheimer's disease
|
Heinzen, Erin L
|
|
2007
|
|
3 |
|
article
|
| 6 |
Analysis of 142 genes resolves the rapid diversification of the rice genus
|
Zou, Xin-Hui
|
|
2008
|
|
3 |
|
article
|
| 7 |
Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics
|
Horlock, Claire
|
|
2007
|
|
3 |
|
article
|
| 8 |
Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome
|
Wang, Suzhi
|
|
2008
|
|
3 |
|
article
|
| 9 |
An integrative probabilistic model for identification of structural variation in sequencing data
|
Sindi, Suzanne S
|
|
2012
|
|
3 |
|
article
|
| 10 |
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms
|
Li, Jun
|
|
2006
|
|
3 |
|
article
|
| 11 |
Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox
|
Brochier, Céline
|
|
2004
|
|
3 |
|
article
|
| 12 |
A scaling normalization method for differential expression analysis of RNA-seq data
|
Robinson, Mark D
|
|
2010
|
|
3 |
|
article
|
| 13 |
A sequence-based survey of the complex structural organization of tumor genomes
|
Raphael, Benjamin J
|
|
2008
|
|
3 |
|
article
|
| 14 |
A vertebrate case study of the quality of assemblies derived from next-generation sequences
|
Ye, Liang
|
|
2011
|
|
3 |
|
article
|
| 15 |
Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells
|
Albert, Thomas K
|
|
2010
|
|
3 |
|
article
|
| 16 |
CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts
|
Katayama, Shintaro
|
|
2007
|
|
3 |
|
article
|
| 17 |
Characterizing regulatory path motifs in integrated networks using perturbational data
|
Joshi, Anagha
|
|
2010
|
|
3 |
|
article
|
| 18 |
Characterizing the stress/defense transcriptome of Arabidopsis
|
Mahalingam, Ramamurthy
|
|
2003
|
|
3 |
|
article
|
| 19 |
Closure of the NCBI SRA and implications for the long-term future of genomics data storage
|
,
|
|
2011
|
|
3 |
|
article
|
| 20 |
Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities
|
Stewart, Frank J
|
|
2011
|
|
3 |
|
article
|
| 21 |
Comparative context analysis of codon pairs on an ORFeome scale
|
Moura, Gabriela
|
|
2005
|
|
3 |
|
article
|
| 22 |
Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single cell level
|
Subkhankulova, Tatiana
|
|
2006
|
|
3 |
|
article
|
| 23 |
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
|
Weinberg, Zasha
|
|
2010
|
|
3 |
|
article
|
| 24 |
Comparative profiling of the sense and antisense transcriptome of maize lines
|
Ma, Jiong
|
|
2006
|
|
3 |
|
article
|
| 25 |
Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks
|
Kun, Ádám
|
|
2008
|
|
3 |
|
article
|
| 26 |
Conserved developmental transcriptomes in evolutionarily divergent species
|
Parikh, Anup
|
|
2010
|
|
3 |
|
article
|
| 27 |
CRAC: an integrated approach to the analysis of RNA-seq reads
|
Philippe, Nicolas
|
|
2013
|
|
3 |
|
article
|
| 28 |
Cross-kingdom patterns of alternative splicing and splice recognition
|
McGuire, Abigail M
|
|
2008
|
|
3 |
|
article
|
| 29 |
DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels
|
Zhao, Huiying
|
|
2013
|
|
3 |
|
article
|
| 30 |
Deciphering cellular states of innate tumor drug responses
|
Graudens, Esther
|
|
2006
|
|
3 |
|
article
|
| 31 |
Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach
|
Solana, Jordi
|
|
2012
|
|
3 |
|
article
|
| 32 |
Detection and correction of false segmental duplications caused by genome mis-assembly
|
Kelley, David R
|
|
2010
|
|
3 |
|
article
|
| 33 |
Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation
|
Ren, Lichen
|
|
2007
|
|
3 |
|
article
|
| 34 |
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
|
Lemmens, Karen
|
|
2009
|
|
3 |
|
article
|
| 35 |
DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes
|
Aran, Dvir
|
|
2013
|
|
3 |
|
article
|
| 36 |
DNA signatures for detecting genetic engineering in bacteria
|
Allen, Jonathan E
|
|
2008
|
|
3 |
|
article
|
| 37 |
Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest
|
Keeling, Christopher I
|
|
2013
|
|
3 |
|
article
|
| 38 |
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
|
Giannoukos, Georgia
|
|
2012
|
|
3 |
|
article
|
| 39 |
Evaluation of next generation sequencing platforms for population targeted sequencing studies
|
Harismendy, Olivier
|
|
2009
|
|
3 |
|
article
|
| 40 |
Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA
|
Benítez-Bellón, Esperanza
|
|
2002
|
|
3 |
p. research0013.1-research0013.16
|
article
|
| 41 |
Exploratory differential gene expression analysis in microarray experiments with no or limited replication
|
Loguinov, Alexander V
|
|
2004
|
|
3 |
|
article
|
| 42 |
Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation
|
Sempere, Lorenzo F
|
|
2004
|
|
3 |
|
article
|
| 43 |
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors
|
Iyer, Lakshminarayan M
|
|
2002
|
|
3 |
p. research0012.1-research0012.11
|
article
|
| 44 |
Feminizing chicks: a model for avian sex determination based on titration of Hint enzyme activity and the predicted structure of an Asw-Hint heterodimer
|
Pace, Helen C
|
|
2003
|
|
3 |
|
article
|
| 45 |
FlyGEM, a full transcriptome array platform for the Drosophila community
|
Johnston, Rick
|
|
2004
|
|
3 |
|
article
|
| 46 |
Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis
|
Ashelford, Kevin
|
|
2011
|
|
3 |
|
article
|
| 47 |
Functional diversification of duplicate genes through subcellular adaptation of encoded proteins
|
Marques, Ana C
|
|
2008
|
|
3 |
|
article
|
| 48 |
Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments
|
Manikandan, Karuppasamy
|
|
2008
|
|
3 |
|
article
|
| 49 |
Functions, structure, and read-through alternative splicing of feline APOBEC3 genes
|
Münk, Carsten
|
|
2008
|
|
3 |
|
article
|
| 50 |
Gene expression-based screening for inhibitors of PDGFR signaling
|
Antipova, Alena A
|
|
2008
|
|
3 |
|
article
|
| 51 |
Gene expression changes during murine postnatal brain development
|
Clinton, M
|
|
2000
|
|
3 |
p. research0005.1-research0005.11
|
article
|
| 52 |
Genome assembly forensics: finding the elusive mis-assembly
|
Phillippy, Adam M
|
|
2008
|
|
3 |
|
article
|
| 53 |
Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription
|
Nakaya, Helder I
|
|
2007
|
|
3 |
|
article
|
| 54 |
Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude
|
Cai, Qingle
|
|
2013
|
|
3 |
|
article
|
| 55 |
Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite
|
Denoeud, France
|
|
2011
|
|
3 |
|
article
|
| 56 |
Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function
|
Zhang, Xiaoming
|
|
2012
|
|
3 |
|
article
|
| 57 |
Genome-wide assessment of imprinted expression in human cells
|
Morcos, Lisanne
|
|
2011
|
|
3 |
|
article
|
| 58 |
Genome-wide functional analysis of human 5' untranslated region introns
|
Cenik, Can
|
|
2010
|
|
3 |
|
article
|
| 59 |
Genomic structure of the gene for mouse germ cell nuclear factor (GCNF)
|
Süsens, Ute
|
|
2000
|
|
3 |
p. research0006.1-research0006.3
|
article
|
| 60 |
Global and unbiased detection of splice junctions from RNA-seq data
|
Ameur, Adam
|
|
2010
|
|
3 |
|
article
|
| 61 |
GOTax: investigating biological processes and biochemical activities along the taxonomic tree
|
Schlicker, Andreas
|
|
2007
|
|
3 |
|
article
|
| 62 |
Hawkeye: an interactive visual analytics tool for genome assemblies
|
Schatz, Michael C
|
|
2007
|
|
3 |
|
article
|
| 63 |
High-resolution transcription atlas of the mitotic cell cycle in budding yeast
|
Granovskaia, Marina V
|
|
2010
|
|
3 |
|
article
|
| 64 |
hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets
|
Johnson, Todd A
|
|
2011
|
|
3 |
|
article
|
| 65 |
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates
|
Zhang, Zhengdong D
|
|
2010
|
|
3 |
|
article
|
| 66 |
Identification of expressed genes linked to malignancy of human colorectal carcinoma by parametric clustering of quantitative expression data
|
Muro, Shizuko
|
|
2003
|
|
3 |
|
article
|
| 67 |
Improving RNA-Seq expression estimates by correcting for fragment bias
|
Roberts, Adam
|
|
2011
|
|
3 |
|
article
|
| 68 |
Indirect genomic effects on survival from gene expression data
|
Ferkingstad, Egil
|
|
2008
|
|
3 |
|
article
|
| 69 |
Integrated analysis of breast cancer cell lines reveals unique signaling pathways
|
Heiser, Laura M
|
|
2009
|
|
3 |
|
article
|
| 70 |
ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes
|
Varani, Alessandro M
|
|
2011
|
|
3 |
|
article
|
| 71 |
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
|
Tung, Chi-Hua
|
|
2007
|
|
3 |
|
article
|
| 72 |
Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)
|
Sabater-Muñoz, Beatriz
|
|
2006
|
|
3 |
|
article
|
| 73 |
Long terminal repeat retrotransposons of Mus musculus
|
McCarthy, Eugene M
|
|
2004
|
|
3 |
|
article
|
| 74 |
MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
|
Shao, Zhen
|
|
2012
|
|
3 |
|
article
|
| 75 |
MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues
|
Blackshaw, Seth
|
|
2003
|
|
3 |
|
article
|
| 76 |
Mobilization of pro-inflammatory lipids in obese Plscr3-deficient mice
|
Mutch, David M
|
|
2007
|
|
3 |
|
article
|
| 77 |
Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells
|
Cecil, Alexander
|
|
2011
|
|
3 |
|
article
|
| 78 |
Modulation of the transcription regulatory program in yeast cells committed to sporulation
|
Friedlander, Gilgi
|
|
2006
|
|
3 |
|
article
|
| 79 |
Molecular genetics and structural genomics of the human protein kinase C gene module
|
Kofler, Kurt
|
|
2002
|
|
3 |
p. research0014.1-research0014.10
|
article
|
| 80 |
MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins
|
Maurer-Stroh, Sebastian
|
|
2004
|
|
3 |
|
article
|
| 81 |
New genes in the evolution of the neural crest differentiation program
|
Martinez-Morales, Juan-Ramon
|
|
2007
|
|
3 |
|
article
|
| 82 |
'Next-generation' sequencing becomes 'now-generation'
|
Neafsey, Daniel E
|
|
2011
|
|
3 |
|
article
|
| 83 |
Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships
|
Dabney, Alan R
|
|
2007
|
|
3 |
|
article
|
| 84 |
Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea
|
Kulkarni, Resham D
|
|
2005
|
|
3 |
|
article
|
| 85 |
Osprey: a network visualization system
|
Breitkreutz, Bobby-Joe
|
|
2003
|
|
3 |
|
article
|
| 86 |
Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology
|
Liu, Tao
|
|
2009
|
|
3 |
|
article
|
| 87 |
Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue
|
Mayrhofer, Markus
|
|
2013
|
|
3 |
|
article
|
| 88 |
Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins
|
Meraldi, Patrick
|
|
2006
|
|
3 |
|
article
|
| 89 |
Ranked prediction of p53 targets using hidden variable dynamic modeling
|
Barenco, Martino
|
|
2006
|
|
3 |
|
article
|
| 90 |
Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues
|
Casati, Paula
|
|
2004
|
|
3 |
|
article
|
| 91 |
Reactome: a knowledge base of biologic pathways and processes
|
Vastrik, Imre
|
|
2007
|
|
3 |
|
article
|
| 92 |
Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions
|
Venancio, Thiago M
|
|
2009
|
|
3 |
|
article
|
| 93 |
Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes
|
Reddington, James P
|
|
2013
|
|
3 |
|
article
|
| 94 |
Reduced reliance on the trace element selenium during evolution of mammals
|
Lobanov, Alexey V
|
|
2008
|
|
3 |
|
article
|
| 95 |
Repetitive DNA is associated with centromeric domains in Trypanosoma brucei but not Trypanosoma cruzi
|
Obado, Samson O
|
|
2007
|
|
3 |
|
article
|
| 96 |
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
|
Ewing, Adam D
|
|
2013
|
|
3 |
|
article
|
| 97 |
RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome
|
Ayers, Katie L
|
|
2013
|
|
3 |
|
article
|
| 98 |
Sense-antisense pairs in mammals: functional and evolutionary considerations
|
Galante, Pedro AF
|
|
2007
|
|
3 |
|
article
|
| 99 |
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
|
Salzberg, Steven L
|
|
2005
|
|
3 |
|
article
|
| 100 |
Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation
|
Weber, Claudia C
|
|
2011
|
|
3 |
|
article
|
| 101 |
Survey of transcripts in the adult Drosophila brain
|
Posey, Karen L
|
|
2001
|
|
3 |
p. research0008.1-research0008.16
|
article
|
| 102 |
Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action
|
Hillenmeyer, Maureen E
|
|
2010
|
|
3 |
|
article
|
| 103 |
Systems biology-defined NF-κB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status
|
Yan, Bin
|
|
2008
|
|
3 |
|
article
|
| 104 |
TFCat: the curated catalog of mouse and human transcription factors
|
Fulton, Debra L
|
|
2009
|
|
3 |
|
article
|
| 105 |
The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes
|
Sheps, Jonathan A
|
|
2004
|
|
3 |
|
article
|
| 106 |
The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data
|
Hayamizu, Terry F
|
|
2005
|
|
3 |
|
article
|
| 107 |
The cohesin complex: sequence homologies, interaction networks and shared motifs
|
Jones, Susan
|
|
2001
|
|
3 |
p. research0009.1-research0009.12
|
article
|
| 108 |
The contributions of normal variation and genetic background to mammalian gene expression
|
Pritchard, Colin
|
|
2006
|
|
3 |
|
article
|
| 109 |
The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics
|
Gianoulis, Tara A
|
|
2011
|
|
3 |
|
article
|
| 110 |
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases
|
Aravind, L
|
|
2001
|
|
3 |
p. research0007.1-research0007.8
|
article
|
| 111 |
The fine-scale architecture of structural variants in 17 mouse genomes
|
Yalcin, Binnaz
|
|
2012
|
|
3 |
|
article
|
| 112 |
The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome
|
Cook, R Kimberley
|
|
2012
|
|
3 |
|
article
|
| 113 |
The GRID: The General Repository for Interaction Datasets
|
Breitkreutz, Bobby-Joe
|
|
2003
|
|
3 |
|
article
|
| 114 |
The impact of the neisserial DNA uptake sequences on genome evolution and stability
|
Treangen, Todd J
|
|
2008
|
|
3 |
|
article
|
| 115 |
The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum
|
Martin, Rowena E
|
|
2005
|
|
3 |
|
article
|
| 116 |
The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers
|
Koonin, Eugene V
|
|
2003
|
|
3 |
|
article
|
| 117 |
The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes
|
Änkö, Minna-Liisa
|
|
2012
|
|
3 |
|
article
|
| 118 |
The role of imprinted genes in humans
|
Moore, Gudrun
|
|
2011
|
|
3 |
|
article
|
| 119 |
The Transcription Factor Encyclopedia
|
Yusuf, Dimas
|
|
2012
|
|
3 |
|
article
|
| 120 |
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
|
Bradley Shaffer, H
|
|
2013
|
|
3 |
|
article
|
| 121 |
Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays
|
Li, Lei
|
|
2008
|
|
3 |
|
article
|
| 122 |
Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression
|
Baranov, Pavel V
|
|
2005
|
|
3 |
|
article
|
| 123 |
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
|
Langmead, Ben
|
|
2009
|
|
3 |
|
article
|
| 124 |
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes
|
Kastenmüller, Gabi
|
|
2009
|
|
3 |
|
article
|
| 125 |
Vector algebra in the analysis of genome-wide expression data
|
Kuruvilla, Finny G
|
|
2002
|
|
3 |
p. research0011.1-research0011.11
|
article
|
| 126 |
Visualization of the phylogenetic content of five genomes using dekapentagonal maps
|
Zhaxybayeva, Olga
|
|
2004
|
|
3 |
|
article
|
| 127 |
Weighting by heritability for detection of quantitative trait loci with microarray estimates of gene expression
|
Manly, Kenneth F
|
|
2005
|
|
3 |
|
article
|
| 128 |
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
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Swertz, Morris A
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2010
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3 |
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article
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Journal description