From single cells to whole organisms

Silke Sperling

Correction: Multiclass classification of microarray data with repeated measurements: application to cancer

Ka Yeung, Roger E Bumgarner

The genome of Rhizobium leguminosarum has recognizable core and accessory components

J Peter W Young, Lisa C Crossman, Andrew WB Johnston, Nicholas R Thomson, Zara F Ghazoui, Katherine H Hull, Margaret Wexler, Andrew RJ Curson, Jonathan D Todd, Philip S Poole, Tim H Mauchline, Alison K East, Michael A Quail, Carol Churcher, Claire Arrowsmith, Inna Cherevach, Tracey Chillingworth, Kay Clarke, Ann Cronin, Paul Davis, Audrey Fraser, Zahra Hance, Heidi Hauser, Kay Jagels, Sharon Moule, Karen Mungall, Halina Norbertczak, Ester Rabbinowitsch, Mandy Sanders, Mark Simmonds, Sally Whitehead, Julian Parkhill

EGASP: the human ENCODE Genome Annotation Assessment Project

Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E Lewis, Martin G Reese

GENCODE: producing a reference annotation for ENCODE

Jennifer Harrow, France Denoeud, Adam Frankish, Alexandre Reymond, Chao-Kung Chen, Jacqueline Chrast, Julien Lagarde, James GR Gilbert, Roy Storey, David Swarbreck, Colette Rossier, Catherine Ucla, Tim Hubbard, Stylianos E Antonarakis, Roderic Guigo

Functional genomics of early cortex patterning

David Chambers, Gord Fishell

Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart

Rong Mao, Xiaowen Wang, Edward L Spitznagel, Laurence P Frelin, Jason C Ting, Huashi Ding, Jung-whan Kim, Ingo Ruczinski, Thomas J Downey, Jonathan Pevsner

Where is the difference between the genomes of humans and annelids?

Alexei Fedorov, Larisa Fedorova

Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference

Ben Lehner, Andrea Calixto, Catriona Crombie, Julia Tischler, Angelo Fortunato, Martin Chalfie, Andrew G Fraser

Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains

Elizabeth E Slawson, Christopher D Shaffer, Colin D Malone, Wilson Leung, Elmer Kellmann, Rachel B Shevchek, Carolyn A Craig, Seth M Bloom, James Bogenpohl, James Dee, Emiko TA Morimoto, Jenny Myoung, Andrew S Nett, Fatih Ozsolak, Mindy E Tittiger, Andrea Zeug, Mary-Lou Pardue, Jeremy Buhler, Elaine R Mardis, Sarah CR Elgin

A computational approach for identifying pseudogenes in the ENCODE regions

Deyou Zheng, Mark B Gerstein

Editorial

The expression signature of in vitro senescence resembles mouse but not human aging

Kristian Wennmalm, Claes Wahlestedt, Ola Larsson

iVici: Interrelational Visualization and Correlation Interface

Kirill Tarassov, Stephen W Michnick

The regulation of endocytosis by kinases: cell biology meets genomics

Zita Balklava, Barth D Grant

A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

John S Reece-Hoyes, Bart Deplancke, Jane Shingles, Christian A Grove, Ian A Hope, Albertha JM Walhout

The aquaporins

Elisabeth Kruse, Norbert Uehlein, Ralf Kaldenhoff

Predicting genes for orphan metabolic activities using phylogenetic profiles

Lifeng Chen, Dennis Vitkup

Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress

Anthony D Aragon, Gabriel A Qui？ones, Edward V Thomas, Sushmita Roy, Margaret Werner-Washburne

A novel approach to identifying regulatory motifs in distantly related genomes

Ruth Van Hellemont, Pieter Monsieurs, Gert Thijs, Bart De Moor, Yves Van de Peer, Kathleen Marchal

On the evolution of the standard amino-acid alphabet

Yi Lu, Stephen Freeland

A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones

Clare Gooding, Francis Clark, Matthew C Wollerton, Sushma-Nagaraja Grellscheid, Harriet Groom, Christopher WJ Smith

Polarized monocyte response to cytokine stimulation

Dirk Nagorsen, Sara Deola, Kina Smith, Ena Wang, Vladia Monsurro, Paola Zanovello, Francesco M Marincola, Monica C Panelli

The rarity of gene shuffling in conserved genes

Gavin C Conant, Andreas Wagner

Genomic analysis of early murine mammary gland development using novel probe-level algorithms

Stephen R Master, Alexander J Stoddard, L Charles Bailey, Tien-Chi Pan, Katherine D Dugan, Lewis A Chodosh

The cryptochromes

Chentao Lin, Takeshi Todo

Searching for differentially expressed gene combinations

Marcel Dettling, Edward Gabrielson, Giovanni Parmigiani

A weed for all reasons

Vivian F Irish, Christopher D Day

Articles selected by Faculty of 1000: muscle differentiation regulatory network; the rules of transcriptional regulation; rapid exprimental determination of DNA-binding protein motifs; polymerase poised and ready to go; bacterial tree accounting for lateral transfer

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

Mark G Carter, Alexei A Sharov, Vincent VanBuren, Dawood B Dudekula, Condie E Carmack, Charlie Nelson, Minoru SH Ko

Articles selected by Faculty of 1000: meiosis evolution; picoeukaryote cell-cycle genes; identifying targets of small molecules; rice genome evolution; circadian gene expression cyanobacteria

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization

Francis D Gibbons, Markus Proft, Kevin Struhl, Frederick P Roth

A non-parametric approach for identifying differentially expressed genes in factorial microarray experiments

Qihua Tan, Jesper Dahlgaard, Werner Vach, Basem M Abdallah, Moustapha Kassem, Torben A Kruse

Sequence complementarity of U2 snRNA and U2A' intron predicts intron function

Maria Lundin

Relations in biomedical ontologies

Barry Smith, Werner Ceusters, Bert Klagges, Jacob K？hler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector, Cornelius Rosse

Ulysses - an application for the projection of molecular interactions across species

Danielle Kemmer, Yong Huang, Sohrab P Shah, Jonathan Lim, Jochen Brumm, Macaire MS Yuen, John Ling, Tao Xu, Wyeth W Wasserman, BF Francis Ouellette

PubNet: a flexible system for visualizing literature derived networks

Shawn M Douglas, Gaetano T Montelione, Mark Gerstein

Conservation versus variation of dinucleotide frequencies across genomes: Evolutionary implications

Shang-Hong Zhang, Jian-Hua Yang

All motifs are NOT created equal: structural properties of transcription factor-DNA interactions and the inference of sequence specificity

Michael B Eisen

Evidence of functional selection pressure for alternative splicingevents that accelerate evolution of protein subsequences

Yi Xing, Christopher Lee

Transcriptional networking

Sarah A Teichmann, Erich Bornberg-Bauer, Nicholas M Luscombe

Quality control in the nucleus

Graciela Flores

Migration events play significant role in genetic differentiation: A microsatellite-based study on Sikkim settlers

Saurav Guha, R Trivedi, V K Kashyap

The cyclophilins

Ping Wang, Joseph Heitman

Articles selected by Faculty of 1000: microRNA-target interactions; hominid gene control regions; pre-mRNA splicing; gene silencing during pathogenesis; multiple use of microarrays

The microbial selenoproteome of the Sargasso Sea

Yan Zhang, Dmitri E Fomenko, Vadim N Gladyshev

Correction: Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture

Lei Li, Xiangfeng Wang, Mian Xia, Viktor Stolc, Ning Su, Zhiyu Peng, Waraporn Tongprasit, Songgang Li, Jun Wang, Xiping Wang, Xing Deng

Human genome research enters a new phase

Harukazu Suzuki, Yoshihide Hayashizaki

The genomic response to 20-hydroxyecdysone at the onset of Drosophila metamorphosis

Robert B Beckstead, Geanette Lam, Carl S Thummel

Tandem repeat copy-number variation in protein-coding regions of human genes

Colm T O'Dushlaine, Richard J Edwards, Stephen D Park, Denis C Shields