Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

Arun K Ramani, Razvan C Bunescu, Raymond J Mooney, Edward M Marcotte

Articles selected by Faculty of 1000: enhancer evolution in flies; modeling nuclear import; cell-cycle kinase substrates; transgenic plants change little; early embryo epigenetics

Articles selected by Faculty of 1000: similar embryos from divergent genomes; gene expression variation in twins; the E. coli stress response network; adaptive immune system evolution; alloployploid tobacco evolution

The diversity of bacterial pathogenicity mechanisms

Eugene Rosenberg

Males can grow egg cells, too

Laura M Hrastar

Large-scale discovery and validation of functional elements in the human genome

Bradley E Bernstein, Manolis Kellis

A full menu for stem-cell research

Francesca M Spagnoli, Ali H Brivanlou

A novel scheme to assess factors involved in the reproducibility of DNA-microarray data

Sacha van Hijum, Anne de Jong, Richard Baerends, Harma A Karsens, Naomi E Kramer, Rasmus Larsen, Chris D den Hengst, Casper J Albers, Jan Kok, Oscar P Kuipers

Making systems biology work in the 21st century

Athel Cornish-Bowden

Genomic studies of mood disorders - the brain as a muscle?

Alexander B Niculescu

SINEs point to abundant editing in the human genome

Joshua DeCerbo, Gordon G Carmichael

The Sequence Ontology: a tool for the unification of genome annotations

Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin, Michael Ashburner

Variation in tissue-specific gene expression among natural populations

Andrew Whitehead, Douglas L Crawford

Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?

Celine Brochier, Simonetta Gribaldo, Yvan Zivanovic, Fabrice Confalonieri, Patrick Forterre

An evolutionary and functional assessment of regulatory network motifs

Aurélien Mazurie, Samuel Bottani, Massimo Vergassola

Quantitative genomics of starvation stress resistance in Drosophila

Susan T Harbison, Sherman Chang, Kim P Kamdar, Trudy FC Mackay

Ways to get from plant genomes to phenomes: via yeast

Pablo D Rabinowicz, Willem Rensink

Marsupials and monotremes sort genome treasures from junk

Matthew J Wakefield, Jennifer AM Graves

Contribution of transcriptional regulation to natural variations in Arabidopsis

Wenqiong J Chen, Sherman H Chang, Matthew E Hudson, Wai-King Kwan, Jingqiu Li, Bram Estes, Daniel Knoll, Liang Shi, Tong Zhu

Articles selected by Faculty of 1000: nuclear microRNA processing; transposon mutagenesis in Helicobacter; Saccharomyces gene expression regulation; molecular convergent evolution; linkage disequilibrium in dogs

A genomic view of methane oxidation by aerobic bacteria and anaerobic archaea

Ludmila Chistoserdova, Julia A Vorholt, Mary E Lidstrom

E. coli ages

Graciela Flores

Phylogeny of the M superhaplogroup inferred from complete mitochondrial genome sequence of Indian specific lineages

Revathi Rajkumar, Jheelam Banerjee, Hima Gunturi, R Trivedi, VK Kashyap

Histones: should I stay or should I go?

Bing Li, Chun Ruan, Jerry L Workman

The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum

Rowena E Martin, Roselani I Henry, Janice L Abbey, John D Clements, Kiaran Kirk

HIF-1α hinders mismatch repair

Clementine Wallace

Mammals feed off yeast pathway

Melissa Phillips

Epithelial pathway revealed

Charles Q Choi

Articles selected by Faculty of 1000: plant comparative mitochondrial genomics; open source proteomics database; identifying disease-associated enzymes; predicting microRNA targets; genome annotation using polymorphisms

Circadian clocks are seeing the systems biology light

Kevin R Hayes, Julie E Baggs, John B Hogenesch

Why genes persist in organelle genomes

Daniel O Daley, James Whelan

Single-feature polymorphism discovery in the barley transcriptome

Nils Rostoks, Justin O Borevitz, Peter E Hedley, Joanne Russell, Sharon Mudie, Jenny Morris, Linda Cardle, David F Marshall, Robbie Waugh

Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis

Ran Elkon, Sharon Rashi-Elkeles, Yaniv Lerenthal, Chaim Linhart, Tamar Tenne, Ninette Amariglio, Gideon Rechavi, Ron Shamir, Yosef Shiloh

Feet in mouth disease

Gregory A Petsko

The opsins

Akihisa Terakita

Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions

L Ryan Baugh, Joanne C Wen, Andrew A Hill, Donna K Slonim, Eugene L Brown, Craig P Hunter

Protein degradation, signaling, microRNAs and cancer

Peter Gallant

Human RNA silences viral DNA

Charles Q Choi

A non-random walk through the genome

Brian Oliver, Tom Misteli

Same-sex fungi can mate

Charles Q Choi

A primitive energy pathway in fungus

Charles Q Choi

New evolutionary frontiers from unusual virus genomes

Christopher Desjardins, Jonathan A Eisen, Vishvanath Nene

Flexible peptides and cytoplasmic gels

Dennis Bray

A DNA microarray survey of gene expression in normal human tissues

Radha Shyamsundar, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, Jonathan R Pollack

Genome-wide analysis of the context-dependence of regulatory networks

Balázs Papp, Stephen Oliver

A genomic approach to investigate developmental cell death in woody tissues of Populus trees

Charleen Moreau, Nikolay Aksenov, Maribel Lorenzo, Bo Segerman, Christiane Funk, Peter Nilsson, Stefan Jansson, Hannele Tuominen

X sequence published

Stephen Pincock

Sperm fusion protein identified

Graciela Flores

Tsunami

Gregory A Petsko

The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

Terry F Hayamizu, Mary Mangan, John P Corradi, James A Kadin, Martin Ringwald