Creating a critical mass and promoting the diversity of computational biology researchers.

Publications

Most Cited

Ido Amit, Manuel Garber*, Nicolas Chevrier*, Ana Paula Leite*, Yoni Donner*, Thomas Eisenhaure, Mitchell Guttman, Jennifer K. Grenier, Weibo Li, Or Zuk, Lisa A. Schubert, Brian Birditt, Tal Shay, Alon Goren, Xiaolan Zhang, Zachary Smith, Raquel Deering, Rebecca C. McDonald, Moran Cabili, Bradley E. Bernstein, John L. Rinn, Alex Meissner, David E. Root, Nir Hacohen, Aviv Regev. Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses. Science (2009) 326, 257 - 263. [cited 110 times].

Nuno D. Mendes, Ana T. Freitas, Marie-France Sagot. Current tools for the identification of miRNA genes and their targets. Nucleic Acids Research (2009) 37 (8), 2419-2433. [cited 51 times].

Cruz JA & E Westhof. The dynamic landscapes of RNA architecture. Cell (2009) 136, 604-609. [cited 50 times].

Thomas M. Keane, Leo Goodstadt, Petr Danecek, Michael A. White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avigail Agam, Guy Slater, Martin Goodson, Nicholas A. Furlotte, Eleazar Eskin, Christoffer Nellåker, Helen Whitley, James Cleak, Deborah Janowitz, Polinka Hernandez-Pliego, Andrew Edwards, T. Grant Belgard, Peter L. Oliver, Rebecca E. McIntyre, Amarjit Bhomra, Jérôme Nicod, Xiangchao Gan, Wei Yuan, Louise van der Weyden, Charles A. Steward, Sendu Bala, Jim Stalker, Richard Mott, Richard Durbin, Ian J. Jackson, Anne Czechanski, José Afonso Guerra-Assunção, Leah Rae Donahue, Laura G. Reinholdt, Bret A. Payseur, Chris P. Ponting, Ewan Birney, Jonathan Flint & David J. Adams. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 477, 289–294. [cited 48 times].

Nicolas FE, Pais H, Schwach F, Lindow M, Kauppinen S, Moulton V, Dalmay T. Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140. RNA (2008) 14, 2513-2520. [cited 31 times].

All

Fernandes HL, Stevenson IH, Phillips AN, Segraves MA, Kording KP. Saliency and Saccade Encoding in the Frontal Eye Field During Natural Scene Search. Cerebral Cortex (2014) , doi:10.1093/cercor/bht179.

Prôa, M., O'Higgins, P. & Monteiro, L.R. Type I error rates for testing genetic drift with phenotypic covariance matrices: A simulation study. Evolution (2013) 67(1), 185-195.

Yoan Diekmann and José B. Pereira-Leal. Evolution of intracellular Compartmentalization. Biochemical Journal (2013) 449, 319-331.

Kerstin Howe, Matthew D. Clark, Carlos F. Torroja, James Torrance, Camille Berthelot, Matthieu Muffato, John E. Collins, Sean Humphray, Karen McLaren, Lucy Matthews, Stuart McLaren, Ian Sealy, Mario Caccamo, Carol Churcher, Carol Scott, Jeffrey C. Barrett, Romke Koch, Gerd-Jörg Rauch, Simon White, William Chow, Britt Kilian, Leonor T. Quintais, José A. Guerra-Assunção, Yi Zhou, Yong Gu, Jennifer Yen, Jan-Hinnerk Vogel, Tina Eyre, Seth Redmond, Ruby Banerjee, Jianxiang Chi, Beiyuan Fu, Elizabeth Langley, Sean F. Maguire, Gavin K. Laird, David Lloyd, Emma Kenyon, Sarah Donaldson, Harminder Sehra, Jeff Almeida-King, Jane Loveland, Stephen Trevanion, Matt Jones, Mike Quail, Dave Willey, Adrienne Hunt, John Burton, Sarah Sims, Kirsten McLay, Bob Plumb, Joy Davis, Chris Clee, Karen Oliver, Richard Clark, Clare Riddle, David Eliott, Glen Threadgold, Glenn Harden, Darren Ware, Beverly Mortimer, Giselle Kerry, Paul Heath, Benjamin Phillimore, Alan Tracey, Nicole Corby, Matthew Dunn, Christopher Johnson, Jonathan Wood, Susan Clark, Sarah Pelan, Guy Griffiths, Michelle Smith, Rebecca Glithero, Philip Howden, Nicholas Barker, Christopher Stevens, Joanna Harley, Karen Holt, Georgios Panagiotidis, Jamieson Lovell, Helen Beasley, Carl Henderson, Daria Gordon, Katherine Auger, Deborah Wright, Joanna Collins, Claire Raisen, Lauren Dyer, Kenric Leung, Lauren Robertson, Kirsty Ambridge, Daniel Leongamornlert, Sarah McGuire, Ruth Gilderthorp, Coline Griffiths, Deepa Manthravadi, Sarah Nichol, Gary Barker, Siobhan Whitehead, Michael Kay, Jacqueline Brown, Clare Murnane, Emma Gray, Matthew Humphries, Neil Sycamore, Darren Barker, David Saunders, Justene Wallis, Anne Babbage, Sian Hammond, Maryam Mashreghi-Mohammadi, Lucy Barr, Sancha Martin, Paul Wray, Andrew Ellington, Nicholas Matthews, Matthew Ellwood, Rebecca Woodmansey, Graham Clark, James Cooper, Anthony Tromans, Darren Grafham, Carl Skuce, Richard Pandian, Robert Andrews, Elliot Harrison, Andrew Kimberley, Jane Garnett, Nigel Fosker, Rebekah Hall, Patrick Garner, Daniel Kelly, Christine Bird, Sophie Palmer, Ines Gehring, Andrea Berger, Christopher M. Dooley, Zübeyde Ersan-Ürün, Cigdem Eser, Horst Geiger, Maria Geisler, Lena Karotki, Anette Kirn, Judith Konantz, Martina Konantz, Martina Oberländer, Silke Rudolph-Geiger, Mathias Teucke, Kazutoyo Osoegawa, Baoli Zhu, Amanda Rapp, Sara Widaa, Cordelia Langford, Fengtang Yang, Nigel P. Carter, Jennifer Harrow, Zemin Ning, Javier Herrero, Steve M. J. Searle, Anton Enright, Robert Geisler, Ronald H. A. Plasterk, Charles Lee, Monte Westerfield, Pieter J. de Jong, Leonard I. Zon, John H. Postlethwait, Christiane Nüsslein-Volhard, Tim J. P. Hubbard, Hugues Roest Crollius, Jane Rogers & Derek L. Stemple. The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) , http://dx.doi.org/10.1038/nature12111.

Cherian A, Fernandes HL, Miller LE. Primary motor cortical discharge during force field adaptation reflects muscle-like dynamics. Journal of Neurophysiology (2013) 110, 768 –783.

Bruno M.C. Martins, Peter S. Swain. Ultrasensitivity in Phosphorylation-Dephosphorylation Cycles with Little Substrate. PLoS Comput Biol (2013) 9(8) , e1003175.

Rodrigues AMM, Gardner A. Evolution of helping and harming in viscous populations when group size varies. The American Naturalist (2013) 181, 609-622.

Rodrigues AMM, Gardner A. Evolution of helping and harming in heterogeneous groups. Evolution (2013) 67, 2284-2298.

Estrela S, Brown SP . Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities. PLOS Computational Biology (2013) 9, e1003036.

Liberal R, Pinney JW. Simple topological properties predict functional misannotations in a metabolic network.. Bioinformatics (2013) 29, i154-61.

Pinho R, Borenstein E, Feldman MW. Most networks in Wagner's model are cycling. PLoS One (2012) 7, e34285.

Ines de Santiago, Emily Brookes, Daniel Hebenstreit, Kelly J. Morris, Tom Carroll, Sheila Q. Xie, Julie K. Stock, Martin Heidemann, Dirk Eick, Naohito Nozaki, Hiroshi Kimura, Jiannis Ragoussis, Sarah A. Teichmann and Ana Pombo. . Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs. Cell Stem Cell (2012) 10 (2), 157-170.

Avraham G, Nisky I, Fernandes HL, Acuna DE, Kording KP, Loeb GE, and Karniel A. Towards perceiving robots as humans – three handshake models face the Turing-like handshake test. IEEE Transactions on Haptics (2012) , .

Freire P, Vinod PK, Novak B. Interplay of transcriptional and proteolytic regulation in driving robust cell cycle progression. Mol Biosyst. (2012) 8, 863-870.

Rodrigues AMM, Gardner A. Evolution of helping and harming in heterogeneous populations. Evolution (2012) 66, 2065-79.

Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E.. RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 18, 610-625.

Huynen MA, Duarte Isabel, Chrzanowska-Lightowlers ZM, Nabuurs SB. Structure based hypothesis of a mitochondrial ribosome rescue mechanism. Biology Direct (2012) 7, 14.

Duarte Isabel, Nabuurs SB, Magno Ramiro, Huynen MA. Evolution and Diversification of the Organellar Release Factor Family. Molecular Biology and Evolution (2012) in press, .

José Afonso Guerra-Assunção and Anton J Enright. Large-scale analysis of microRNA evolution. BMC Genomics (2012) 13, 218.

Leopold Parts, Åsa K Hedman, Sarah Keildson, Andrew J Knights, Cei Abreu-Goodger, Martijn van de Bunt, José Afonso Guerra-Assunção, Nenad Bartonicek, Stijn van Dongen, Reedik Mägi, James Nisbet, Amy Barrett, Mattias Rantalainen, Alexandra C Nica, Michael A Quail, Kerrin S Small, Daniel Glass, Anton J Enright, John Winn, Panos Deloukas, Emmanouil T Dermitzakis, Mark I McCarthy, Timothy D Spector, Richard Durbin, Cecilia M Lindgren. Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue. PLoS Genetics (2012) 8, e1002704.

Eswarappa SM, Estrela S, Brown SP. Within-host dynamics of multi-species infections: facilitation, competition and virulence. Plos One (2012) 7, e38730.

Gardner A, Alpedrinha J, West SA. Haplodiploidy and the evolution of eusociality: split sex ratios.. Am Nat. (2012) 179, 240-56.

Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.. Nucleic Acids Res. (2012) 40, D91-7.

Pina C, Fugazza C, Tipping AJ, Brown J, Soneji S, Teles J, Peterson C, Enver T. Inferring rules of lineage commitment in haematopoiesis. Nat Cell Biol (2012) 14, 287-94.

Dmochowski JP, Sajda P, Dias J, Parra LC. Correlated components of ongoing EEG point to emotionally laden attention - a possible marker of engagement?. Front Hum Neurosci (2012) 6, 112.

Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, Baulcombe DC. A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell (2012) 24, 859-74.

Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EP. Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens. PLoS Pathogen (2012) 8, e1002503.

Vilares I, Howard JD, Fernandes HL, Gottfried JA, and Kording KP. Differential Representations of Prior and Likelihood Uncertainty in the Human Brain. Current Biology (2012) 22, 1.

Fernandes HL, Stevenson IH, and Kording KP. Generalization of stochastic visuomotor rotations. PLoS ONE (2012) 7, e43016.

Estrela S, Trisos C, Brown SP. From metabolism to ecology: cross-feeding interactions shape the balance between polymicrobial conflict and mutualism. American Naturalist (2012) 180, 566-576.

Rob M. de Graaf, Guenola Ricard, Theo A. van Alen, Isabel Duarte, Bas E. Dutilh, Carola Burgtorf, Jan W.P. Kuiper, Georg W.M. van der Staay, Aloysius G.M. Tielens, Martijn A. Huynen and Johannes H.P. Hackstein. The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis. Molecular Biology and Evolution (2011) 28, 2379-91.

Shivaprasad PV, Dunn RM, Santos BA, Bassett A, Baulcombe DC. Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. EMBO J. (2011) 31, 257-66.

Correia BE, Ban YEA, Friend DJ, Ellingson K, Xu HY, Boni E, Bradley-Hewitt T, Bruhn-Johannsen JF, Stamatatos L, Strong RK, and Schief WR . Computational Protein Design Using Flexible Backbone Remodeling and Resurfacing: Case Studies in Structure-Based Antigen Design. J Mol Biol (2011) 405, 284-297.

S. Schuster, L.F. de Figueiredo, A. Schroeter, C. Kaleta. Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach. Biosystems (2011) 105, 147-153.

C. Kaleta, L.F. de Figueiredo, I. Heiland, S. Klamt and S. Schuster. Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis. Biosystems (2011) 105, 107-108.

R. Mateescu, P.T. Monteiro, E. Dumas and H. de Jong. CTRL: Extension of CTL with Regular Expressions and Fairness Operators to Verify Genetic Regulatory Networks. Theoretical Computer Science (2011) 412, 2854-2883.

C. Kaleta, L.F. de Figueiredo, S. Werner, R. Guthke, M. Ristow, S. Schuster. In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans. PLoS Computational Biology (2011) 7, e1002116.

L.F. de Figueiredo, T.I. Gossmann, M. Ziegler and S. Schuster. Pathway Analysis of NAD+ metabolism. Biochemical Journal (2011) , in press.

McLellan JS, Correia BE, Chen M, Yang Y, Graham BS, Schief WR, Kwong PD. Design and characterization of epitope-scaffold immunogens that present the motavizumab epitope from respiratory syncytial virus. J Mol Biol (2011) 409, 853-66.

Cruz JA & Westhof E. Identification and annotation of noncoding RNAs in Saccharomycotina. Comptes Rendus Biologies (2011) 334, 671-678.

Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang PS, McLellan JS, Kwong PD, Baker D, Strong RK, Schief WR. Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science (2011) 334, 373-376.

Cruz JA & Westhof E. Sequence-based identification of 3D structural modules in RNA with RMDetect. Nature Methods (2011) 8, 513-519.

Martins, Hugo; Villesen, Palle. Improved integration time estimation of endogenous retroviruses with phylogenetic data. PLOS One (2011) 6, 3.

Thomas M. Keane, Leo Goodstadt, Petr Danecek, Michael A. White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avigail Agam, Guy Slater, Martin Goodson, Nicholas A. Furlotte, Eleazar Eskin, Christoffer Nellåker, Helen Whitley, James Cleak, Deborah Janowitz, Polinka Hernandez-Pliego, Andrew Edwards, T. Grant Belgard, Peter L. Oliver, Rebecca E. McIntyre, Amarjit Bhomra, Jérôme Nicod, Xiangchao Gan, Wei Yuan, Louise van der Weyden, Charles A. Steward, Sendu Bala, Jim Stalker, Richard Mott, Richard Durbin, Ian J. Jackson, Anne Czechanski, José Afonso Guerra-Assunção, Leah Rae Donahue, Laura G. Reinholdt, Bret A. Payseur, Chris P. Ponting, Ewan Birney, Jonathan Flint & David J. Adams. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 477, 289–294.

Cruz AV, Mallet N, Magill PJ, Brown P, Averbeck BB. Effects of dopamine depletion on information flow between the subthalamic nucleus and external globus pallidus. Journal of Neurophysiology (2011) in press, .

Lardon LA, Merkey BV, Martins S, Dötsch A, Picioreanu C, Kreft JU & Smets BF. iDynoMiCS: next-generation individual-based modelling of biofilms. Environmental Microbiology (2011) 13, 2416-2434.

Yoan Diekmann, Elsa Seixas, Marc Gouw, Filipe Tavares-Cadete, Miguel C. Seabra and José B. Pereira-Leal. Thousands of Rab GTPases for the Cell Biologist. PLoS Computational Biology (2011) 7(10), e1002217.

Goulao LF, Vieira-Silva S, Jackson PA. Association of hemicellulose- and pectin-modifying gene expression with Eucalyptus globulus secondary growth. Plant Physiol. Biochem. (2011) 49(8), 873-81.

Barbosa S, Black CA, and Hastings A. Challenges in Estimating Insecticide Selection Pressures from Mosquito Field Data. PLoS Neglected Tropical Diseases (2011) 5, e1387.

Bouvignies G, Vallurupalli P, Hansen DF, Correia BE, Lange O, Bah A, Vernon RM, Dahlquist FW, Baker D, Kay LE. Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature (2011) 477, 111-114.

Correia BE, Holmes MA, Huang PS, Strong RK, Schief WR. High-resolution structure prediction of a circular permutation loop. Protein Sci (2011) 20, 1929-1934.

Ramiro RS, Alpedrinha J, Carter L, Gardner A, Reece SE. Sex and death: the effects of innate immune factors on the sexual reproduction of malaria parasites. PLoS Pathog (2011) 7, e1001309.

Abbot P, Abe J, Alcock J, Alizon S, Alpedrinha JA, Andersson M, Andre JB, van Baalen M, Balloux F, Balshine S, Barton N, Beukeboom LW, Biernaskie JM, Bilde T, Borgia G, Breed M, Brown S, Bshary R, Buckling A, Burley NT, Burton-Chellew MN, Cant MA, Chapuisat M, Charnov EL, Clutton-Brock T, Cockburn A, Cole BJ, Colegrave N, Cosmides L, Couzin ID, Coyne JA, Creel S, Crespi B, Curry RL, Dall SR, Day T, Dickinson JL, Dugatkin LA, El Mouden C, Emlen ST, Evans J, Ferriere R, Field J, Foitzik S, Foster K, Foster WA, Fox CW, Gadau J, Gandon S, Gardner A, Gardner MG, Getty T, Goodisman MA, Grafen A, Grosberg R, Grozinger CM, Gouyon PH, Gwynne D, Harvey PH, Hatchwell BJ, Heinze J, Helantera H, Helms KR, Hill K, Jiricny N, Johnstone RA, Kacelnik A, Kiers ET, Kokko H, Komdeur J, Korb J, Kronauer D, Kümmerli R, Lehmann L, Linksvayer TA, Lion S, Lyon B, Marshall JA, McElreath R, Michalakis Y, Michod RE, Mock D, Monnin T, Montgomerie R, Moore AJ, Mueller UG, Noë R, Okasha S, Pamilo P, Parker GA, Pedersen JS, Pen I, Pfennig D, Queller DC, Rankin DJ, Reece SE, Reeve HK, Reuter M, Roberts G, Robson SK, Roze D, Rousset F, Rueppell O, Sachs JL, Santorelli L, Schmid-Hempel P, Schwarz MP, Scott-Phillips T, Shellmann-Sherman J, Sherman PW, Shuker DM, Smith J, Spagna JC, Strassmann B, Suarez AV, Sundström L, Taborsky M, Taylor P, Thompson G, Tooby J, Tsutsui ND, Tsuji K, Turillazzi S, Ubeda F, Vargo EL, Voelkl B, Wenseleers T, West SA, West-Eberhard MJ, Westneat DF, Wiernasz DC, Wild G, Wrangham R, Young AJ, Zeh DW, Zeh JA, Zink A. Inclusive fitness theory and eusociality. Nature (2011) 471, E1-4.

Mourao M, Schnell S, Shaw SL. Macroscopic simulations of microtubule dynamics predict two steady-state processes governing array morphology. Computational biology and chemistry (2011) 35, 269-281.

Min Hu, Qasim Ayub, José Afonso Guerra-Assunção, Quan Long, Zemin Ning, Ni Huang, Irene Gallego Romero, Lira Mamanova, Pelin Akan, Xin Liu, Alison J. Coffey, Daniel J. Turner, Harold Swerdlow, John Burton, Michael A. Quail, Donald F. Conrad, Anton J. Enright, Chris Tyler-Smith and Yali Xue. Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data. Human Genetics (2011) , 10.1007/s00439-011-1111-9.

Bruno M.C Martins, Peter S Swain. Trade-Offs and Constraints in Allosteric Sensing. PLoS Comput Biol (2011) 7 (11), e1002261.

Mourao MA, Srividhya J, McSharry PE, Crampin EJ, Schnell S. A graphical user interface for a method to infer kinetics and network architecture (MIKANA). PLoS One (2011) 6, e27534.

Tenazinha N, Vinga S. A survey on methods for modeling and analyzing integrated biological networks . IEEE/ACM Trans Comput Biol Bioinform (2011 ) 8, 943-58.

Fernandes HL, Albert MV, and Kording KP. Measuring generalization of visuomotor perturbations in wrist movements using mobile phones. PLoS One (2011) 6, e20290.

Vieira-Silva S, Touchon M, Abby SS, Rocha EP. Investment in rapid growth shapes the evolutionary rates of essential proteins. Proc Natl Acad Sci USA (2011) 108, 20030-5.

Freire P, Zhang T. Two legs are better than one. Cell Cycle (2011) 10(8), 1189-90.

Vinod PK*, Freire P*, Rattani A, Ciliberto A, Uhlmann F and Novak B. Computational modelling of mitotic exit in budding yeast – the role of separase and Cdc14 endocycles. J. R. Soc. Interface (2011) 8(61), 1128-41.

G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro and H. de Jong. Efficient parameter search for qualitative models of regulatory networks using symbolic model checking. Bioinformatics (2010) 26(18), i603-i610.

Joao Pessoa, Zsuzsa Sarkany, Frederico Ferreira-da-Silva, Sonia Martins, Maria R Almeida, Jianming Li and Ana M Damas. Functional characterization of Arabidopsis thaliana transthyretin-like protein. BMC Plant Biology (2010) 10, 30.

M.C. Teixeira, P.J. Dias, P.T. Monteiro, A. Sala, A.L. Oliveira, A.T. Freitas and I. Sá-Correia. Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches. Molecular BioSystems (2010) 6(12), 2471-2481.

José Lourenço, Mario Recker. Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes. PLoS Neglected Tropical Diseases (2010) 4(11), e894.

Fernandes HL, and Körding KP. In praise of “false” models and rich data. Journal of Motor Behavior (2010) 42, 343-349.

José Afonso Guerra-Assunção and Anton J. Enright. MapMi: automated mapping of microRNA loci. BMC Bioinformatics (2010) 11, 7.

Like Fokkens, Sandra MC Botelho, Jos Boekhorst, Berend Snel. Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. BMC Bioinformatics (2010) 11, 86.

Amy Lynd,David Weetman,Susana Barbosa,Alexander Egyir Yawson,Sara Mitchell,Joao Pinto,Ian Hastings, and Martin J. Donnelly. Field, Genetic, and Modeling Approaches Show Strong Positive Selection Acting upon an Insecticide Resistance Mutation in Anopheles gambiae s.s.. Molecular Biology and Evolution (2010) 27(5), 1117-1125.

E. Ruppin, J.A. Papin, L.F. de Figueiredo and S. Schuster. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Current Opinion in Biotechnology (2010) 21, 502-510.

K. Bohl, L. F. de Figueiredo, O. Hädicke, S. Klamt, C. Kost, S. Schuster and C. Kaleta. CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks.. Lecture Notes in Informatics - Proceedings (2010) 173, 71-80.

S. Schuster, L. F. de Figueiredo and Christoph Kaleta. Predicting novel pathways in genome-scale metabolic networks.. Biochem Soc Trans (2010) 38, 1202-1205.

Vieira-Silva S, Rocha EP. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet. (2010) 6, e1000808.

Correia BE, Ban YE, Holmes MA, Xu H, Ellingson K, Kraft Z, Carrico C, Boni E, Sather DN, Zenobia C, Burke KY, Bradley-Hewitt T, Bruhn-Johannsen JF, Kalyuzhniy O, Baker D, Strong RK, Stamatatos L, Schief WR. Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure (2010) 8, 1116-1126.

Pais H, Nicolas FE, Soond SM, Swingler TE, Clark IM, Chantry A, Moulton V, Dalmay T. Analyzing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level. RNA (2010) 16, 489-494.

Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark TA, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray JW.. Exon-level microarray analyses identify alternative splicing programs in breast cancer.. Mol Cancer Res. (2010) 8, 961.

Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, Moffatt MF, Cookson WO.. Disordered microbial communities in asthmatic airways.. PLoS ONE (2010) 5;5(1), e8578.

Stephanie M. Willerth, Helder A. M. Pedro, Lior Pachter, Laurent M. Humeau, Adam P. Arkin, David V. Schaffer. Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology. PLoS ONE (2010) 5 issue 10, e13564.

Sylvie Estrela & Ivana Gudelj. Evolution of cooperative cross-feeding could be less challenging than originally thought. Plos One (2010) 5, e14121.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr‐Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.,. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 330(6012), 1787‐97.

Vieira-Silva S, Touchon M, Rocha EP. No evidence for elemental-based streamlining of prokaryotic genomes. Trends Ecol. Evol. (2010) 25(6), 319-20.

Nuno D. Mendes, Ana T. Freitas, Ana T. Vasconcelos, Marie-France Sagot. Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi. BMC Genomics (2010) 11, .

Novak B, Vinod PK, Freire P, Kapuy O.. Systems-level feedback in cell-cycle control. Biochem Soc Trans. (2010) 38(5), 1242-6.

Cruz JA & E Westhof. The dynamic landscapes of RNA architecture. Cell (2009) 136, 604-609.

England P, Wehenkel A, Martins S, Hoos S, André-Leroux G, Villarino A, Alzari PM.. The FHA-containing protein GarA acts as a phosphorylation-dependent molecular switch in mycobacterial signaling.. FEBS letters (2009) 583, 301-7.

L.F. de Figueiredo, S. Schuster, C. Kaleta and D.A. Fell. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics (2009) 25, 152-158.

Rodrigues A, Koeppl H. Ohtsuki H, Satake A. A game theoretical model of deforestation in human–environment relationships. Journal of Theoretical Biology (2009) 258, 127-134.

Gardner A, Arce A & Alpedrinha J . Budding dispersal and the sex ratio. Journal of Evolutionary Biology (2009) 22, 1036.

G. Batt, B. Besson, H. de Jong, E. Dumas, J. Geiselmann, P.T. Monteiro, M. Page and D. Ropers. Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks. Bacterial molecular networks (2009) , .

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Ricardo Águas, José Lourenço, M. Gabriela M. Gomes, Lisa J. White. The Impact of IPTi and IPTc Interventions on Malaria Clinical Burden - In Silico Perspectives. PLoS ONE (2009) 4(8), e6627.

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