Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases
Daboussi F, Zaslavskiy M, Poirot L, Loperfido M, Gouble A, Guyot V, Leduc S, Galetto R, Grizot S, Oficjalska D, Perez C, Delacôte F, Dupuy A, Chion-Sotinel I, Le Clerre D, Lebuhotel C, Danos O, Lemaire F, Oussedik K, Cédrone F, Epinat JC, Smith J, Dickson
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Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences
Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA.
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Transgene regulation in plants by alternative splicing of a suicide exon
Hickey SF, Sridhar M, Westermann AJ, Qin Q, Vijayendra P, Liou G, Hammond MC.
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Configuring robust DNA strand displacement reactions for in situ molecular analyses
Dzifa Y. Duose, Ryan M. Schweller, Jan Zimak, Arthur R. Rogers, Walter N. Hittelman, and Michael R. Diehl
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Unrecognized sequence homologies may confound genome-wide association studies
Galichon P, Mesnard L, Hertig A, Stengel B, Rondeau E.
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Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures
Do-Nyun Kim, Fabian Kilchherr, Hendrik Dietz, and Mark Bathe
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Drosophila melanogaster linker histone dH1 is required for transposon silencing and to preserve genome integrity
Vujatovic O, Zaragoza K, Vaquero A, Reina O, Bernués J, Azorín F.
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The HTLV-1-encoded protein HBZ directly inhibits the acetyl transferase activity of p300/CBP
Wurm T, Wright DG, Polakowski N, Mesnard JM, Lemasson I.
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Transcriptional provirus silencing as a crosstalk of de novo DNA methylation and epigenomic features at the integration site
Senigl F, Auxt M, Hejnar J.
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Zinc induced Dnmt1 expression involves antagonism between MTF-1 and nuclear receptor SHP
Zhang Y, Andrews GK, Wang L.
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Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5
Gary Loughran, Matthew S. Sachs, John F. Atkins, and Ivaylo P. Ivanov
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Gli2 and MEF2C activate each other’s expression and function synergistically during cardiomyogenesis in vitro
Anastassia Voronova, Ashraf Al Madhoun, Anna Fischer, Michael Shelton, Christina Karamboulas, and Ilona Sylvia Skerjanc
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Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
Johannes M. Freudenberg, Swati Ghosh, Brad L. Lackford, Sailu Yellaboina, Xiaofeng Zheng, Ruifang Li, Suresh Cuddapah, Paul A. Wade, Guang Hu, and Raja Jothi
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Yin Yang 1 extends the Myc-related Transcription Factors Network in Embryonic Stem Cells
Pietro Vella, Iros Barozzi, Alessandro Cuomo, Tiziana Bonaldi, and Diego Pasini
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Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain
Jinping Liu, Shukun Luo, Hongchang Zhao, Ji Liao, Jing Li, Chunying Yang, Bo Xu, David F. Stern, Xingzhi Xu, and Keqiong Ye
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The molecular basis of ATM-dependent dimerization of the Mdc1 DNA-damage checkpoint mediator
Stephanie Jungmichel, Julie A. Clapperton, Janette Lloyd, Flurina J. Hari, Christoph Spycher, Lucijana Pavic, Jiejin Li, Lesley F. Haire, Mario Bonalli, Dorthe H. Larsen, Claudia Lukas, Jiri Lukas, Derek MacMillan, Michael L. Nielsen, Manuel Stucki, and Stephen J. Smerdon
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Genome-wide occupancy links Hoxa2 to Wnt-beta-catenin signaling in mouse embryonic development
Ian J. Donaldson, Shilu Amin, James J. Hensman, Eva Kutejova, Magnus Rattray, Neil Lawrence, Andrew Hayes, Christopher M. Ward, and Nicoletta Bobola
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A novel phage-encoded transcription antiterminator acts by suppressing pausing by bacterial RNA polymerase
Zhanna Berdygulova, Daria Esyunina, Nataliya Miropolskaya, Damir Mukhamedyarov, Konstantin Kuznedelov, Bryce E. Nickels, Konstantin Severinov, Andrey Kulbachinskiy, and Leonid Minakhin
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P1 AND P2 PROTEIN HETERODIMER BINDING TO THE P0 PROTEIN OF Saccharomyces cerevisiae IS RELATIVELY NON-SPECIFIC AND A SOURCE OF RIBOSOMAL HETEROGENEITY
David Cárdenas, Jesús Revuelta-Cervantes, Antonio Jiménez-Díaz, Hendricka Camargo, Miguel Remacha, and Juan P. G. Ballesta
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DNA robustly stimulates FANCD2 monoubiquitylation in the complex with FANCI
Koichi Sato, Kazue Toda, Masamichi Ishiai, Minoru Takata, and Hitoshi Kurumizaka
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Mechanism of strand displacement synthesis by DNA replicative polymerases
Manosas M, Spiering MM, Ding F, Bensimon D, Allemand JF, Benkovic SJ, Croquette V.
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Collaborative coupling between polymerase and helicase for leading-strand synthesis
Manosas M, Spiering MM, Ding F, Croquette V, Benkovic SJ.
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DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics
Laurens N, Rusling DA, Pernstich C, Brouwer I, Halford SE, Wuite GJ.
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DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations
Rusling DA, Laurens N, Pernstich C, Wuite GJ, Halford SE.
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Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences
Bao Ton-Hoang, Patricia Siguier, Yves Quentin, Séverine Onillon, Brigitte Marty, Gwennaele Fichant, and Mick Chandler
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Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation
Holub P, Lalakova J, Cerna H, Pasulka J, Sarazova M, Hrazdilova K, Arce MS, Hobor F, Stefl R, Vanacova S.
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Aberrant growth and lethality of Arabidopsis deficient in nonsense mediated RNA decay factors is caused by autoimmune-like response
Riehs-Kearnan N, Gloggnitzer J, Dekrout B, Jonak C, Riha K.
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Widespread occurrence of 5-methylcytosine in human coding and noncoding RNA
Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, Suter CM, Preiss T.
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Utp23p is required for dissociation of snR30 small nucleolar RNP from pre-ribosomal particles
Coralie Hoareau-Aveilla, Eléonore Fayet-Lebaron, Beáta E. Jády, Anthony K. Henras, and Tamás Kiss
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BC1-FMRP interaction is modulated by 2’-O Methylation: RNA binding activity of the Tudor domain and translational regulation at synapses
Caroline Lacoux, Daniele Di Marino, Pietro Pilo Boyl, Francesca Zalfa, Bing Yan, Maria Teresa Ciotti, Mattia Falconi, Henning Urlaub, Tilmann Achsel, Annie Mougin, Michèle Caizergues-Ferrer, and Claudia Bagni
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mRNA Knockdown by Single Strand RNA is Improved by Chemical Modifications
Henry J. Haringsma, Jenny J. Li, Ferdie Soriano, Denise M. Kenski, W. Michael Flanagan, and Aarron T. Willingham
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Biogenesis of mammalian microRNAs by a non-canonical processing pathway
Mallory A. Havens, Ashley A. Reich, Dominik M. Duelli, and Michelle L. Hastings
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Integration of DNA into bacterial chromosomes from plasmids without a counter-selection marker
John T. Heap, Muhammad Ehsaan, Clare M. Cooksley, Yen-Kuan Ng, Stephen T. Cartman, Klaus Winzer, and Nigel P. Minton
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Homologous recombination and its regulation
Krejci L, Altmannova V, Spirek M, Zhao X.
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Polbase : a repository of biochemical, genetic, and structural information about DNA polymerases
Langhorst BW, Jack WE, Reha-Krantz L, Nichols NM.
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ALFRED: an allele frequency resource for research and teaching
Rajeevan H, Soundararajan U, Kidd JR, Pakstis AJ, Kidd KK.
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SMART 7: Recent updates to the protein domain annotation resource
Letunic I, Doerks T, Bork P.
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Gene Expression Atlas update – a value-added database of microarray and sequencing-based functional genomics experiments
Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N et al.
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Ensembl Genomes: An Integrative Resource for Genome-Scale Data from non-Vertebrate Species
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G et al.
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WormBase 2012: More Genomes, More Data, New Website
Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R et al.
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The Mouse Genome Database (MGD): Comprehensive Resource for Genetics and Genomics of the Laboratory Mouse
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; the Mouse Genome Database Group.
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Pocketome: an encyclopedia of small-molecule binding sites in 4D
Kufareva I, Ilatovskiy AV, Abagyan R.
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MEROPS: the database of proteolytic enzymes, their substrates and inhibitors
Rawlings ND, Barrett AJ, Bateman A.
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doRiNA: a database of RNA interactions in post-transcriptional regulation
Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, Landthaler M, Dieterich C.
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IMG/M: the integrated metagenome data management and comparative analysis system
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M et al.
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PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update
Wang X, Spandidos A, Wang H, Seed B.
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InterPro in 2011: New developments in the family and domain prediction database
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al.
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eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T et al.
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Reorganizing the protein space at the Universal Protein Resource (UniProt)

The UniProt Consortium
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UniPathway: a resource for the exploration and annotation of metabolic pathways.
Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A.
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Mouse Phenome Database (MPD)
Maddatu TP, Grubb SC, Bult CJ, Bogue MA.
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Comparative interactomics with Funcoup 2.0
Alexeyenko A, Schmitt T, Tjärnberg A, Guala D, Frings O, Sonnhammer EL.
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ELM – the database of eukaryotic linear motifs.
Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A et al.
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The Genome Portal of the Department of Energy Joint Genome Institute
Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA et al.
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The IntAct molecular interaction database in 2012
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U et al.
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The UniProt-GO Annotation Database in 2011
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M et al.
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The Pfam Protein Families Database
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J et al.
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The DARC site: a Database of Aligned Ribosomal Complexes
Jarasch A, Dziuk P, Becker T, Armache JP, Hauser A, Wilson DN, Beckmann R.
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Tarbase 6.0: Capturing the Exponential Growth of miRNA Targets with Experimental Support
Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, and Hatzigeorgiou AG.
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The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M et al.
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PubChem’s BioAssay Database
Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Zhou Z, Han L, Karapetyan K, Dracheva S, Shoemaker BA et al.
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ScerTF: A comprehensive database of benchmarked position weight matrices for Saccharomyces species
Spivak AT, Stormo GD.
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