Skip Navigation

2011 Feature Articles

SYNTHETIC BIOLOGY AND CHEMISTRY

An exogenous chloroplast genome for complex sequence manipulation in algae
O'Neill BM, Mikkelson KL, Gutierrez NM, Cunningham JL, Wolff KL, Szyjka SJ, Yohn CB, Redding KE, Mendez MJ.
Full Text

Enhancing the cellular uptake of Py-Im polyamides through next-generation aryl turns
Meier JL, Montgomery DC, Dervan PB.
Full Text

Evolutionary genome engineering using a restriction-modification system
Asakura Y, Kojima H, Kobayashi I.
Full Text

Novel post-synthetic generation, isomeric resolution, and characterization of Fapy-dG within oligodeoxynucleotides: differential anomeric impacts on DNA duplex properties
Lukin M, Minetti CA, Remeta DP, Attaluri S, Johnson F, Breslauer KJ, de Los Santos C.
Full Text

COMPUTATIONAL BIOLOGY

pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5′/3′ arm variation including concomitant cleavage and polyuridylation patterns
Burroughs AM, Kawano M, Ando Y, Daub CO, Hayashizaki Y.
Full Text

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems
Iyer LM, Zhang D, Rogozin IB, Aravind L.
Full Text

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N.
Full Text

Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast
Joshi A, Van de Peer Y, Michoel T.
Full Text

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function
Belcastro V, Siciliano V, Gregoretti F, Mithbaokar P, Dharmalingam G, Berlingieri S, Iorio F, Oliva G, Polishchuck R, Brunetti-Pierri N, di Bernardo D.
Full Text

Control of gene expression by modulated self-assembly
Vilar JM, Saiz L.
Full Text

A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems
Zhang D, Iyer LM, Aravind L.
Full Text

RNIE: genome-wide prediction of bacterial intrinsic terminators
Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z.
Full Text

GENE REGULATION, CHROMATIN AND EPIGENETICS

Alternative Splicing and Nonsense-Mediated Decay Modulate Expression of Important Regulatory Genes in Arabidopsis
Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J et al.
Full Text

A preinitiation complex at the 3’ end of genes drives antisense transcription independent of divergent sense transcription
Murray SC, Serra Barros A, Brown DA, Dudek P, Ayling J, Mellor J.
Full Text

The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes
Müller GA, Quaas M, Schümann M, Krause E, Padi M, Fischer M, Litovchick L, Decaprio JA, Engeland K.
Full Text

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset
Feller C, Prestel M, Hartmann H, Straub T, Söding J, Becker PB.
Full Text

RDR6-mediated synthesis of complementary RNA is terminated by miRNA stably bound to template RNA
Rajeswaran R, Pooggin MM.
Full Text

Nuclear hormone 1{alpha},25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy
Heikkinen S, Väisänen S, Pehkonen P, Seuter S, Benes V, Carlberg C.
Full Text

Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms
Chatterjee N, Sinha D, Lemma-Dechassa M, Tan S, Shogren-Knaak MA, Bartholomew B.
Full Text

Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling
Hayashi-Takanaka Y, Yamagata K, Wakayama T, Stasevich TJ, Kainuma T, Tsurimoto T, Tachibana M, Shinkai Y, Kurumizaka H, Nozaki N, Kimura H.
Full Text

Reciprocal roles of DBC1 and SIRT1 in regulating estrogen receptor {alpha} activity and co-activator synerg
Ji Yu E, Kim SH, Heo K, Ou CY, Stallcup MR, Kim JH.
Full Text

Requirement of TFIIH kinase subunit Mat1 for RNA Pol II C-terminal domain Ser5 phosphorylation, transcription and mRNA turnover.
Helenius K, Yang Y, Tselykh TV, Pessa HK, Frilander MJ, Mäkelä TP.
Full Text

The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3'-UTR
Gong F, Sun L, Wang Z, Shi J, Li W, Wang S, Han X, Sun Y.
Full Text

Distant positioning of proteasomal proteolysis relative to actively transcribed genes
Scharf A, Grozdanov PN, Veith R, Kubitscheck U, Meier UT, von Mikecz A.
Full Text

Nucleosome accessibility governed by the dimer/tetramer interface
Böhm, V., Hieb, A.R., Andrews, A.J., Gansen, A., Rocker, A., Tóth, K., Luger, K. and Langowski, J.
Full Text

Differential RNA-binding activity of the hnRNP G protein correlated with the sex genotype in the amphibian oocyte
Kanhoush R, Praseuth D, Perrin C, Chardard D, Vinh J, Penrad-Mobayed M.
Full Text

GENOME INTEGRITY, REPAIR AND REPLICATION

Human telomerase acts as a hTR-independent reverse transcriptase in mitochondria
Sharma NK, Reyes A, Green P, Caron MJ, Bonini MG, Gordon DM, Holt IJ, Santos JH.
Full Text

Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions
Reeves DA, Mu H, Kropachev K, Cai Y, Ding S, Kolbanovskiy A, Kolbanovskiy M, Chen Y, Krzeminski J, Amin S, Patel DJ, Broyde S, Geacintov NE.
Full Text

PARG is recruited to DNA damage sites through poly(ADP-ribose)- and PCNA-dependent mechanisms
Mortusewicz O, Fouquerel E, Amé JC, Leonhardt H, Schreiber V.
Full Text

The FANC pathway is activated by adenovirus infection and promotes viral replication-dependent recombination
Cherubini G, Naim V, Caruso P, Burla R, Bogliolo M, Cundari E, Benihoud K, Saggio I, Rosselli F.
Full Text

A role for the arginine methylation of Rad9 in checkpoint control and cellular sensitivity to DNA damage
He W, Ma X, Yang X, Zhao Y, Qiu J, Hang H.
Full Text

GENOMICS

Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies
Tripp HJ, Hewson I, Boyarsky S, Stuart JM, Zehr JP.
Full Text

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB.
Full Text

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA
Bundschuh R, Altmüller J, Becker C, Nürnberg P, Gott JM.
Full Text

Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes
Reineke AR, Bornberg-Bauer E, Gu J
Full Text

Widespread occurrence of non-canonical transcription termination by human RNA polymerase III
Orioli A, Pascali C, Quartararo J, Diebel KW, Praz V, Romascano D, Percudani R, van Dyk LF, Hernandez N, Teichmann M, Dieci G.
Full Text

Association between translation efficiency and horizontal gene transfer within microbial communities
Tuller T, Girshovich Y, Sella Y, Kreimer A, Freilich S, Kupiec M, Gophna U, Ruppin E
Full Text

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
Nunoura, T., Takaki, Y., Kakuta, J., Nishi, S., Sugahara, J., Kazama, H., Chee, G.-J., Hattori, M., Kanai, A., Atomi, H. et al.
Full Text

MOLECULAR BIOLOGY

RNA-binding protein HuR autoregulates its expression by promoting alternative polyadenylation site usage
Dai W, Zhang G, Makeyev EV.
Full Text

Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation
Vassilenko KS, Alekhina OM, Dmitriev SE, Shatsky IN, Spirin AS.
Full Text

Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation
Xiao B, Zhang H, Johnson RC, Marko JF.
Full Text

c-MYC coordinately regulates ribosomal gene chromatin remodeling and Pol I availability during granulocyte differentiation
Poortinga, G., Wall, M., Sanij, E., Siwicki, K., Ellul, J., Brown, D., Holloway, T.P., Hannan, R.D. and McArthur, G.A.
Full Text

NUCLEIC ACID ENZYMES

Yeast mitochondrial RNase P, RNase Z and the RNA degradosome are part of a stable supercomplex
Daoud R, Forget L, Lang BF.
Full Text

Opening-closing dynamics of the mitochondrial transcription pre-initiation complex
Kim H, Tang GQ, Patel SS, Ha T.
Full Text

The conformation of microRNA seed regions in native microRNPs is prearranged for presentation to mRNA targets
Lambert NJ, Gu SG, Zahler AM.
Full Text

Identification and characterization of the mitochondrial RNA polymerase and transcription factor in the fission yeast Schizosaccharomyces pombe
Jiang H, Sun W, Wang Z, Zhang J, Chen D, Murchie AIH.
Full Text

Human 2'-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover
Poulsen JB, Andersen KR, Kjær KH, Durand F, Faou P, Vestergaard AL, Talbo GH, Hoogenraad N, Brodersen DE, Justesen J, Martensen PM.
Full Text

Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase
Gerasimaite R, Merkiene E, Klimasauskas S.
Full Text

Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering
Ulge UY, Baker DA, Monnat, RJ.
Full Text

RNA

Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis
Cavanagh AT, Sperger JM, Wassarman KM.
Full Text

West Nile virus encodes a microRNA-like small RNA in the 3’ untranslated region which upregulates GATA4 mRNA and facilitates virus replication in mosquito cells
Hussain M, Torres S, Schnettler E, Funk A, Grundhoff A, Pijlman GP, Khromykh AA, Asgari S.
Full Text

A Supramolecular Assembly Formed by Influenza A Virus Genomic RNA Segments
Fournier E, Moules V, Essere B, Paillart JC, Sirbat JD, Isel C, Cavalier A, Rolland JP, Thomas D, Lina B, Marquet R.
Full Text

The Human Translation Initiation Multi-Factor Complex Promotes Methionyl-tRNAi Binding to the 40S Ribosomal Subunit
Sokabe M, Fraser CS, Hershey JW.
Full Text

Unraveling the Structural Complexity in a Single Stranded RNA Tail: Implications for Efficient Ligand Binding in the Prequeuosine Riboswitch
Eichhorn CD, Feng J, Suddala KC, Walter NG, Brooks CL 3rd, Al-Hashimi HM.
Full Text

Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry
Vander Meulen KA, Butcher SE.
Full Text

Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria?
Schrader JM, Uhlenbeck OC.
Full Text

Activation and repression functions of an SR splicing regulator depend on exonic versus intronic-binding position
Shen M, Mattox W.
Full Text

N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD
Okada-Katsuhata Y, Yamashita A, Kutsuzawa K, Izumi N, Hirahara F, Ohno S.
Full Text

The miRNA pathway limits AGO1 availability during siRNA-mediated PTGS defense against exogenous RNA
Martínez de Alba AE, Jauvion V, Mallory AC, Bouteiller N, Vaucheret H.
Full Text

The SRSF1 linker induces semi-conservative ESE binding by cooperating with the RRMs
Cho S, Hoang A, Chakrabarti S, Huynh N, Huang DB, Ghosh G.
Full Text

Correction of the consequences of mitochondrial 3243A>G mutation in the MT-TL1 gene causing the MELAS syndrome by tRNA import into mitochondria
Karicheva OZ, Kolesnikova OA, Schirtz T, Vysokikh MY, Mager-Heckel AM, Lombès A, Boucheham A, Krasheninnikov IA, Martin RP, Entelis N, Tarassov I.
Full Text

Characterization of extracellular circulating microRNA
Turchinovich A, Weiz L, Langheinz A, Burwinkel B.
Full Text

Messenger RNA degradation is initiated at the 5' end and follows sequence- and condition-dependent modes in chloroplasts
Salvador ML, Suay L, Klein U.
Full Text

Reconstitution and characterization of the unconventional splicing of XBP1u mRNA in vitro
Shinya S, Kadokura H, Imagawa Y, Inoue M, Yanagitani K, Kohno K.
Full Text

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage
Bracken CP, Szubert JM, Mercer TR, Dinger ME, Thomson DW, Mattick JS, Michael MZ, Goodall GJ.
Full Text

Activation of a microRNA response in trans reveals a new role for poly(A) in translational repression.
Ricci EP, Limousin T, Soto-Rifo R, Allison R, Pöyry T, Decimo D, Jackson RJ, Ohlmann T.
Full Text

An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine
Su D, Lieberman A, Lang BF, Simonovic M, Söll D, Ling J.
Full Text

Prevention of cross-talk in conserved regulatory systems: identification of specificity determinants in RNA-binding anti-termination proteins of the BglG family
Hübner S, Declerck N, Diethmaier C, Le Coq D, Aymerich S, Stülke J.
Full Text

Depletion of key protein components of the RISC pathway impairs pre-ribosomal RNA processing
Liang XH, Crooke ST.
Full Text

Rescue of non-sense mutated p53 tumor suppressor gene by aminoglycosides
Floquet, C.l., Deforges, J., Rousset, J.-P. and Bidou, L.
Full Text

Elucidation of the assembly events required for the recruitment of Utp20, Imp4 and Bms1 onto nascent pre-ribosomes
J. Pérez-Fernández, P. Martín-Marcos, M. Dosil
Full Text

Translation-competent 48S complex formation on HCV IRES requires the RNA-binding protein NSAP1
Park SM, Paek KY, Hong KY, Jang CJ, Cho S, Park JH, Kim JH, Jan E, Jang SK.
Full Text

STRUCTURAL BIOLOGY

ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex
Möckel C, Lammens K, Schele A, Hopfner KP.
Full Text

Quaternary structure of the specific p53-DNA complex reveals the mechanism of p53 mutant dominance
Aramayo R, Sherman MB, Brownless K, Lurz R, Okorokov AL, Orlova EV.
Full Text

Rescue of non-sense mutated p53 tumor suppressor gene by aminoglycosides
Floquet, C.l., Deforges, J., Rousset, J.-P. and Bidou, L.
Full Text

Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis
Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M
Full Text

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
P. Lutsik, L. Feuerbach, J. Arand, T. Lengauer, J. Walter, C. Bock
Full Text

SURVEY AND SUMMARY

Validation of kinetics similarity in qPCR
Bar T, Kubista M, Tichopad A.
Full Text

Local sensing of global DNA topology: from crossover geometry to type II topoisomerase processivity
Timsit Y.
Full Text

DATABASE SPECIAL ISSUE

DAnCER: Disease-Annotated Chromatin Epigenetics Resource
Turinsky, A.L., Turner, B., Borja, R.C., Gleeson, J.A., Heath, M., Pu, S., Switzer, T., Dong, D., Gong, Y., On, T. et al.
Full Text

genenames.org: the HGNC resources in 2011
Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA.
Full Text

ViralZone: a knowledge resource to understand virus diversity
Hulo C, de Catro E, Masson P, Bouguerelet L, Bairoch A, Xenarios I, Le Mercier P.
Full Text

SuperSweet – a resource on natural and artificial sweetening agents
Ahmed J, Preissner S, Dunkel M, Worth CL, Eckert A, Preissner R.
Full Text

The UCSC Genome Browser database: update 2011
Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A. et al.
Full Text

The Pancreatic Expression database: 2011 update
RJ Cutts, E Gadaleta, SA Han, T Crnogorac-Jurcevic, NR Lemoine, C Chelala
Full Text

TOPSAN: a dynamic web database for structural genomics
Ellrott K, Zmasek CM, Weekes D, Krishna SS, Bakolitsa C, Godzik A, Wolley J.
Full Text

The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research
Homma, K., Suzuki, K. and Sugawara, H.
Full Text

BriX: a database of protein building blocks for structural analysis, modeling and design
Vanhee, P., Verschueren, E., Baeten, L., Stricher, F., Serrano, L., Rousseau, F. and Schymkowitz, J.
Full Text

The RCSB Protein Data Bank: redesigned web site and web services
Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlić, A., Quesada, M., Quinn, G.B., Westbrook, J.D. et al.
Full Text

Indian genetic disease database
Pradhan, S., Sengupta, M., Dutta, A., Bhattacharyya, K., Bag, S.K., Dutta, C. and Ray, K.
Full Text

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
Robasky, K. and Bulyk, M.L.
Full Text

ENCODE whole-genome data in the UCSC genome browser (2011 update)
Raney, B.J., Cline, M.S., Rosenbloom, K.R., Dreszer, T.R., Learned, K., Barber, G.P., Meyer, L.R., Sloan, C.A., Malladi, V.S., Roskin, K.M. et al.
Full Text

YPA: an integrated repository of promoter features in Saccharomyces cerevisiae
Chang, D.T.-H., Huang, C.-Y., Wu, C.-Y. and Wu, W.-S.
Full Text

PDBe: Protein Data Bank in Europe
Velankar, S., Alhroub, Y., Alili, A.l., Best, C., Boutselakis, H.C., Caboche, S., Conroy, M.J., Dana, J.M., van Ginkel, G., Golovin, A. et al.
Full Text

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P. et al.
Full Text

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P. et al.
Full Text

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
Sun, S., Chen, J., Li, W., Altintas, I., Lin, A., Peltier, S., Stocks, K., Allen, E.E., Ellisman, M., Grethe, J. et al.
Full Text

Ensembl 2011
Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al.
Full Text

REPAIRtoire – a database of DNA repair pathways
Milanowska, K., Krwawicz, J., Papaj, G., Kosiński, J., Poleszak, K., Lesiak, J., Osińska, E., Rother, K. and Bujnicki, J.M.
Full Text

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
Gama-Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muñiz-Rascado, L., Solano-Lira, H., Jimenez-Jacinto, V.n., Weiss, V., García-Sotelo, J.S., López-Fuentes, A. et al.
Full Text

Ongoing and future developments at the Universal Protein Resource
The UniProt Consortium
Full Text

Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations
Gonzalez-Galarza, F.F., Christmas, S., Middleton, D. and Jones, A.R.
Full Text

Reactome: a database of reactions, pathways and biological processes
Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B. et al.
Full Text

Rfam: Wikipedia, clans and the "decimal" release
Gardner, P.P., Daub, J., Tate, J., Moore, B.L., Osuch, I.H., Griffiths-Jones, S., Finn, R.D., Nawrocki, E.P., Kolbe, D.L., Eddy, S.R. et al.
Full Text

SUPERFAMILY 1.75 including a domain-centric gene ontology method
de Lima Morais, D.A., Fang, H., Rackham, O.J.L., Wilson, D., Pethica, R., Chothia, C. and Gough, J.
Full Text

ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments
Parkinson, H., Sarkans, U., Kolesnikov, N., Abeygunawardena, N., Burdett, T., Dylag, M., Emam, I., Farne, A., Hastings, E., Holloway, E. et al.
Full Text

A series of PDB related databases for everyday needs
Joosten, R.P., te Beek, T.A.H., Krieger, E., Hekkelman, M.L., Hooft, R.W.W., Schneider, R., Sander, C. and Vriend, G.
Full Text

PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata
Whitmore, L., Woollett, B., Miles, A.J., Klose, D.P., Janes, R.W. and Wallace, B.A.
Full Text

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
Huerta-Cepas, J., Capella-Gutierrez, S., Pryszcz, L.P., Denisov, I., Kormes, D., Marcet-Houben, M. and Gabaldón, T.
Full Text

PHOSIDA 2011: the posttranslational modification database
Gnad, F., Gunawardena, J. and Mann, M.
Full Text

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.
Khorshid, M., Rodak, C. and Zavolan, M.
Full Text

ModBase, a database of annotated comparative protein structure models, and associated resources
Pieper, U., Webb, B.M., Barkan, D.T., Schneidman-Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E.C., Pettersen, E.F., Huang, C.C. et al.
Full Text

EcoCyc: a comprehensive database of Escherichia coli biology
Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muñiz-Rascado, L., Bonavides-Martinez, C.s., Paley, S., Krummenacker, M., Altman, T. et al.
Full Text

WEB SERVER SPECIAL ISSUE

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
P. Di Tommaso, S. Moretti, I. Xenarios, M. Orobitg, A. Montanyola, J.M. Chang, J.F. Taly, C. Notredame
Full Text

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures
C. Blanchet, M. Pasi, K. Zakrzewska, R. Lavery
Full Text

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data
A. Lan, I.Y. Smoly, G. Rapaport, S. Lindquist, E. Fraenkel, E. Yeger-Lotem
Full Text

AnnotQTL: a new tool to gather functional and comparative information on a genomic region
F. Lecerf, A. Bretaudeau, O. Sallou, C. Desert, Y. Blum, S. Lagarrigue, O. Demeure
Full Text

ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry
M. Askenazi, M. Linial
Full Text

R3D-BLAST: a search tool for similar RNA 3D substructures
Y.C. Liu, C.H. Yang, K.T. Chen, J.R. Wang, M.L. Cheng, J.C. Chung, H.T. Chiu, C.L. Lu
Full Text

Back to the top