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Comments When bigger is better Gregory A Petsko PMCID: PMC2864101 When failure should be the option Gregory A Petsko PMCID: PMC2874522 Commentaries Taming of the shrewd: novel eukaryotic genes from RNA viruses Eugene V Koonin PMCID: PMC2823675 Giant lobelias exemplify convergent evolution Thomas J Givnish PMCID: PMC2826311 Unraveling the mysteries of dog evolution Rodney L Honeycutt PMCID: PMC2841097 Anaerobic Metazoans: No longer an oxymoron Lisa A Levin PMCID: PMC2867776 Anaerobic animals from an ancient, anoxic ecological niche Marek Mentel and William Martin PMCID: PMC2859860 Adherens junctions remain dynamic Matthias M Falk PMCID: PMC2867777 Hybridization and speciation in angiosperms: a role for pollinator shifts? Mark W Chase, Ovidiu Paun, and Michael F Fay PMCID: PMC2858105 Diversity lost: are all Holarctic large mammal species just relict populations? Michael Hofreiter and Ian Barnes PMCID: PMC2858106 A central role for p38 MAPK in the early transcriptional response to stress Alan J Whitmarsh PMCID: PMC2860348 Network integration meets network dynamics Teresa M Przytycka and Yoo-Ah Kim PMCID: PMC2861031 Unraveling bovin phylogeny: accomplishments and challenges Faysal Bibi and Elisabeth S Vrba PMCID: PMC2861646 Ecological genomics: steps towards unraveling the genetic basis of inducible defenses in Daphnia Ralph Tollrian and Florian Leese PMCID: PMC2867779 Transcriptomics and disease vector control John Vontas, Hilary Ranson, and Luke Alphey PMCID: PMC2867780 Hidden reach of the micromanagers Peter S Linsley and Aimee L Jackson PMCID: PMC2867781 A modern circadian clock in the common angiosperm ancestor of monocots and eudicots C Robertson McClung PMCID: PMC2867782 Smart biomaterials - regulating cell behavior through signaling molecules Aneta J Mieszawska and David L Kaplan PMCID: PMC2873335 Systems-biology dissection of eukaryotic cell growth Teresa M Przytycka and Justen Andrews PMCID: PMC2875221 Altered cell cycle regulation helps stem-like carcinoma cells resist apoptosis James Chappell and Stephen Dalton PMCID: PMC2876098 Repetitive elements in parasitic protozoa Christine Clayton PMCID: PMC2875222 On the scent of sexual attraction Peter A Brennan PMCID: PMC2880966 Plastid evolution: gene transfer and the maintenance of 'stolen' organelles Eunsoo Kim and John M Archibald PMCID: PMC2883544 The (r)evolution of cancer genetics Francesca D Ciccarelli PMCID: PMC2883958 A little bit is better than nothing: the incomplete parthenogenesis of salamanders, frogs and fish Kathrin P Lampert and Manfred Schartl PMCID: PMC2914643 Iron testes: sperm mitochondria as a context for dissecting iron metabolism Karen G Hales PMCID: PMC2890511 As you weed, so shall you reap: on the origin of algaculture in damselfish Duur K Aanen PMCID: PMC2887784 The hidden diversity of ribosomal peptide natural products Eric W Schmidt PMCID: PMC2890512 S28 peptidases: lessons from a seemingly 'dysfunctional' family of two John W Kozarich PMCID: PMC2893137 Altered metabolism in cancer Jason W Locasale and Lewis C Cantley PMCID: PMC2892450 Genome-wide association studies in Plasmodium species Bridget Penman, Caroline Buckee, Sunetra Gupta, and Sean Nee PMCID: PMC2903549 Regulation of lipid droplet turnover by ubiquitin ligases Philipp Alberts and Daniela Rotin PMCID: PMC2906420 The global dynamics of RNA stability orchestrates responses to cellular activation Jack D Keene PMCID: PMC2900241 A question of scale: Human migrations writ large and small Murray P Cox and Michael F Hammer PMCID: PMC2908064 Mitochondrial dynamics: quantifying mitochondrial fusion in vitro Alexis Jourdain and Jean-Claude Martinou PMCID: PMC2909948 Losing the desire: selection can promote obligate asexuality Kayla C King and Gregory DD Hurst PMCID: PMC2911426 Vertebrate Hedgehog signaling: cilia rule Christopher W Wilson and Didier YR Stainier PMCID: PMC2912248 Insulators and imprinting from flies to mammals Chunhui Hou and Victor G Corces PMCID: PMC2912829 Kinesin-14: the roots of reversal Robert A Cross PMCID: PMC2922096 Paleoclimate and bubonic plague: a forewarning of future risk? Anthony J McMichael PMCID: PMC2929224 Oestrogen shuts the door on SOX9 Lindsey Mork and Blanche Capel PMCID: PMC2930626 Correspondence Rapid progress on the vertebrate tree of life Robert C Thomson and H Bradley Shaffer PMCID: PMC2842240 A New Replicator: A theoretical framework for analysing replication István Zachar and Eörs Szathmáry PMCID: PMC2850328 Editorials The hope of progress Miranda Robertson PMCID: PMC2864097 Plus ça change Miranda Robertson PMCID: PMC2864102 The evolution of gene regulation, the RNA universe, and the vexed questions of artefact and noise Miranda Robertson PMCID: PMC2905359 Focus The architecture of RNA polymerase fidelity Craig D Kaplan PMCID: PMC2889878 Methodology Articles Monitoring the regulation of gene expression in a growing organ using a fluid mechanics formalism Rémy Merret, Bruno Moulia, Irène Hummel, David Cohen, Erwin Dreyer, and Marie-Béatrice Bogeat-Triboulot PMCID: PMC2845557 Controlled spatial and conformational display of immobilised bone morphogenetic protein-2 and osteopontin signalling motifs regulates osteoblast adhesion and differentiation in vitro Elizabeth A Mitchell, Benjamin T Chaffey, Andrew W McCaskie, Jeremy H Lakey, and Mark A Birch PMCID: PMC2880964 A rapid and scalable method for selecting recombinant mouse monoclonal antibodies Cécile Crosnier, Nicole Staudt, and Gavin J Wright PMCID: PMC2898661 Characterization of a heat resistant ß-glucosidase as a new reporter in cells and mice Susan C McCutcheon, Ken Jones, Sarah A Cumming, Richard Kemp, Heather Ireland-Zecchini, John C Saunders, Carol A Houghton, Louise A Howard, and Douglas J Winton PMCID: PMC2909947 A novel cell-free mitochondrial fusion assay amenable for high-throughput screenings of fusion modulators Astrid C Schauss, Huiyan Huang, Seok-Yong Choi, Liqun Xu, Sébastien Soubeyrand, Patricia Bilodeau, Rodolfo Zunino, Peter Rippstein, Michael A Frohman, and Heidi M McBride PMCID: PMC2919466 Opinion The edges of understanding Arthur D Lander PMCID: PMC2864098 Caenorhabditis elegans behavioral genetics: where are the knobs? Leon Avery PMCID: PMC2882361 Question & Answer Q&A: Promise and pitfalls of genome-wide association studies John FY Brookfield PMCID: PMC2864099 Video Q&A: What is autism? - A personal view Martin Raff PMCID: PMC2864100 Q&A: ChIP-seq technologies and the study of gene regulation Edison T Liu, Sebastian Pott, and Mikael Huss PMCID: PMC2871264 Video Q&A: Non-coding RNAs and eukaryotic evolution - a personal view John Mattick PMCID: PMC2905358 Q&A: Life, synthetic biology and risk Steven A Benner PMCID: PMC2885331 Q&A: Robotics as a tool to understand the brain Daniel M Wolpert and J Randall Flanagan PMCID: PMC2909176 Q&A: Single-molecule localization microscopy for biological imaging Ann L McEvoy, Derek Greenfield, Mark Bates, and Jan Liphardt PMCID: PMC2920249 Research Articles Disruption of insulin signalling preserves bioenergetic competence of mitochondria in ageing Caenorhabditis elegans Kristel Brys, Natascha Castelein, Filip Matthijssens, Jacques R Vanfleteren, and Bart P Braeckman PMCID: PMC2914644 Bumblebee foraging rhythms under the midnight sun measured with radiofrequency identification Ralph J Stelzer and Lars Chittka PMCID: PMC2907328 Serious limitations of the QTL/Microarray approach for QTL gene discovery Ricardo A Verdugo, Charles R Farber, Craig H Warden, and Juan F Medrano PMCID: PMC2919467 How 5000 independent rowers coordinate their strokes in order to row into the sunlight: Phototaxis in the multicellular green alga Volvox Noriko Ueki, Shigeru Matsunaga, Isao Inouye, and Armin Hallmann PMCID: PMC2920248 The Drosophila homolog of the mammalian imprint regulator, CTCF, maintains the maternal genomic imprint in Drosophila melanogaster William A MacDonald, Debashish Menon, Nicholas J Bartlett, G Elizabeth Sperry, Vanya Rasheva, Victoria Meller, and Vett K Lloyd PMCID: PMC2922095 Research articles THOC5/FMIP, an mRNA export TREX complex protein, is essential for hematopoietic primitive cell survival in vivo Annalisa Mancini, Susanne C Niemann-Seyde, Rüdiger Pankow, Omar El Bounkari, Sabine Klebba-Färber, Alexandra Koch, Ewa Jaworska, Elaine Spooncer, Achim D Gruber, Anthony D Whetton, and Teruko Tamura PMCID: PMC2806247 Early evolution of the LIM homeobox gene family Mansi Srivastava, Claire Larroux, Daniel R Lu, Kareshma Mohanty, Jarrod Chapman, Bernard M Degnan, and Daniel S Rokhsar PMCID: PMC2828406 Regeneration and reprogramming compared Bea Christen, Vanesa Robles, Marina Raya, Ida Paramonov, and Juan Carlos Izpisúa Belmonte PMCID: PMC2826312 Mild folate deficiency induces genetic and epigenetic instability and phenotype changes in prostate cancer cells Gaia Bistulfi, Erika VanDette, Sei-Ichi Matsui, and Dominic J Smiraglia PMCID: PMC2845099 A role for NRAGE in NF-κB activation through the non-canonical BMP pathway Nicholas Matluk, Jennifer A Rochira, Aldona Karaczyn, Tamara Adams, and Joseph M Verdi PMCID: PMC2829509 Evolution of a unique predatory feeding apparatus: functional anatomy, development and a genetic locus for jaw laterality in Lake Tanganyika scale-eating cichlids Thomas A Stewart and R Craig Albertson PMCID: PMC2828976 Reconstructing the ups and downs of primate brain evolution: implications for adaptive hypotheses and Homo floresiensis Stephen H Montgomery, Isabella Capellini, Robert A Barton, and Nicholas I Mundy PMCID: PMC2825212 Ontogenetic development of auditory sensitivity and sound production in the squeaker catfish Synodontis schoutedeni Walter Lechner, Lidia Eva Wysocki, and Friedrich Ladich PMCID: PMC2824629 Adherens junctions connect stress fibres between adjacent endothelial cells Jaime Millán, Robert J Cain, Natalia Reglero-Real, Carolina Bigarella, Beatriz Marcos-Ramiro, Laura Fernández-Martín, Isabel Correas, and Anne J Ridley PMCID: PMC2845098 Coevolution of activating and inhibitory receptors within mammalian carcinoembryonic antigen families Robert Kammerer and Wolfgang Zimmermann PMCID: PMC2832619 Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence Christopher D Dardick, Ann M Callahan, Remo Chiozzotto, Robert J Schaffer, M Claudia Piagnani, and Ralph Scorza PMCID: PMC2830173 A metabolic signature of long life in Caenorhabditis elegans Silke Fuchs, Jacob G Bundy, Sarah K Davies, Jonathan M Viney, Jonathan S Swire, and Armand M Leroi PMCID: PMC2829508 Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age Chunxiang Li, Hongjie Li, Yinqiu Cui, Chengzhi Xie, Dawei Cai, Wenying Li, Victor H Mair, Zhi Xu, Quanchao Zhang, Idelisi Abuduresule, Li Jin, Hong Zhu, and Hui Zhou PMCID: PMC2838831 The IGF1 small dog haplotype is derived from Middle Eastern grey wolves Melissa M Gray, Nathan B Sutter, Elaine A Ostrander, and Robert K Wayne PMCID: PMC2837629 Identification and characterization of Dlc1 isoforms in the mouse and study of the biological function of a single gene trapped isoform Mohammad G Sabbir, Nichola Wigle, Shauna Loewen, Yuan Gu, Cordula Buse, Geoffrey G Hicks, and Michael RA Mowat PMCID: PMC2839985 Geographic and ecologic heterogeneity in elimination thresholds for the major vector-borne helminthic disease, lymphatic filariasis Manoj Gambhir, Moses Bockarie, Daniel Tisch, James Kazura, Justin Remais, Robert Spear, and Edwin Michael PMCID: PMC2848205 ASB9 interacts with ubiquitous mitochondrial creatine kinase and inhibits mitochondrial function Sanghoon Kwon, Dongbum Kim, Jae Won Rhee, Jeong-A Park, Dae-Won Kim, Doo-Sik Kim, Younghee Lee, and Hyung-Joo Kwon PMCID: PMC2852384 Denitrification in human dental plaque Frank Schreiber, Peter Stief, Armin Gieseke, Ines M Heisterkamp, Willy Verstraete, Dirk de Beer, and Paul Stoodley PMCID: PMC2859859 To signal or not to signal? Chemical communication by urine-borne signals mirrors sexual conflict in crayfish Fiona C Berry and Thomas Breithaupt PMCID: PMC2867775 Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila Carlo G Artieri and Rama S Singh PMCID: PMC2907589 In vivo trans-specific gene silencing in fungal cells by in planta expression of a double-stranded RNA Maria Laine P Tinoco, Bárbara BA Dias, Rebeca C Dall'Astta, João A Pamphile, and Francisco JL Aragão PMCID: PMC2907587 The zebra finch neuropeptidome: prediction, detection and expression Fang Xie, Sarah E London, Bruce R Southey, Suresh P Annangudi, Andinet Amare, Sandra L Rodriguez-Zas, David F Clayton, and Jonathan V Sweedler PMCID: PMC2873334 Gene duplication and fragmentation in the zebra finch major histocompatibility complex Christopher N Balakrishnan, Robert Ekblom, Martin Völker, Helena Westerdahl, Ricardo Godinez, Holly Kotkiewicz, David W Burt, Tina Graves, Darren K Griffin, Wesley C Warren, and Scott V Edwards PMCID: PMC2907588 The first metazoa living in permanently anoxic conditions Roberto Danovaro, Antonio Dell'Anno, Antonio Pusceddu, Cristina Gambi, Iben Heiner, and Reinhardt Møbjerg Kristensen PMCID: PMC2907586 The lethal giant larvae tumour suppressor mutation requires dMyc oncoprotein to promote clonal malignancy Francesca Froldi, Marcello Ziosi, Flavio Garoia, Andrea Pession, Nicola A Grzeschik, Paola Bellosta, Dennis Strand, Helena E Richardson, Annalisa Pession, and Daniela Grifoni PMCID: PMC2877678 Quality prevails over identity in the sexually selected vocalisations of an ageing mammal Elodie Briefer, Elisabetta Vannoni, and Alan G McElligott PMCID: PMC2858104 Localized direction selective responses in the dendrites of visual interneurons of the fly Christian Spalthoff, Martin Egelhaaf, Philip Tinnefeld, and Rafael Kurtz PMCID: PMC2876097 Stepwise mechanism for transcription fidelity Yulia Yuzenkova, Aleksandra Bochkareva, Vasisht R Tadigotla, Mohammad Roghanian, Savva Zorov, Konstantin Severinov, and Nikolay Zenkin PMCID: PMC2874521 Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls Daniela Witten, Robert Tibshirani, Sam Guoping Gu, Andrew Fire, and Weng-Onn Lui PMCID: PMC2880020 Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times Kathryn R Elmer, Topi K Lehtonen, Andreas F Kautt, Chris Harrod, and Axel Meyer PMCID: PMC2880021 Gli2a protein localization reveals a role for Iguana/DZIP1 in primary ciliogenesis and a dependence of Hedgehog signal transduction on primary cilia in the zebrafish Hyejeong Rosemary Kim, Joanna Richardson, Freek van Eeden, and Philip W Ingham PMCID: PMC2890509 Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa Tomislav Domazet-Lošo and Diethard Tautz PMCID: PMC2880965 Nutrient control of eukaryote cell growth: a systems biology study in yeast Alex Gutteridge, Pınar Pir, Juan I Castrillo, Philip D Charles, Kathryn S Lilley, and Stephen G Oliver PMCID: PMC2895586 Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family Daniel H Haft, Malay Kumar Basu, and Douglas A Mitchell PMCID: PMC2887384 Spartin activates atrophin-1-interacting protein 4 (AIP4) E3 ubiquitin ligase and promotes ubiquitination of adipophilin on lipid droplets Christopher Hooper, Swamy S Puttamadappa, Zak Loring, Alexander Shekhtman, and Joanna C Bakowska PMCID: PMC2887783 Darcin: a male pheromone that stimulates female memory and sexual attraction to an individual male's odour Sarah A Roberts, Deborah M Simpson, Stuart D Armstrong, Amanda J Davidson, Duncan H Robertson, Lynn McLean, Robert J Beynon, and Jane L Hurst PMCID: PMC2890510 A new strategy for isolating genes controlling dosage compensation in Drosophila using a simple epigenetic mosaic eye phenotype Mahalakshmi Prabhakaran and Richard L Kelley PMCID: PMC2893135 Downstream of tyrosine kinase/docking protein 6, as a novel substrate of tropomyosin-related kinase C receptor, is involved in neurotrophin 3-mediated neurite outgrowth in mouse cortex neurons Wei qi Li, Lei Shi, Yuan gang You, Yan hua Gong, Bin Yin, Jian gang Yuan, and Xiao zhong Peng PMCID: PMC2901200 Reviews Immune mechanisms of protection: can adjuvants rise to the challenge? Amy S McKee, Megan KL MacLeod, John W Kappler, and Philippa Marrack PMCID: PMC2864095 Biology-driven cancer drug development: back to the future Christopher J Lord and Alan Ashworth PMCID: PMC2864096 Assessing the human immune system through blood transcriptomics Damien Chaussabel, Virginia Pascual, and Jacques Banchereau PMCID: PMC2895587 Software MochiView: versatile software for genome browsing and DNA motif analysis Oliver R Homann and Alexander D Johnson PMCID: PMC2867778 Correction Correction: Exploiting the promiscuity of imatinib Shun J Lee and Jean YJ Wang PMCID: PMC2893136 Corrects: Shun J Lee, et al. Exploiting the promiscuity of imatinib. J Biol. 2009; 8(3): 30. Other Issues: Journal List
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