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1.

Research   Open Access

Evolution of clitellate phaosomes from rhabdomeric photoreceptor cells of polychaetes – a study in the leech Helobdella robusta (Annelida, Sedentaria, Clitellata)

Carmen Döring, Jasmin Gosda, Kristin Tessmar-Raible, Harald Hausen, Detlev Arendt, Günter Purschke Frontiers in Zoology 2013, 10:52 (5 September 2013)

Abstract | Full text | PDF | PubMed

2.

Research   Open Access Highly Accessed

Experimental characterization of the human non-sequence-specific nucleic acid interactome

Gerhard Dürnberger, Tilmann Bürckstümmer, Kilian Huber, Roberto Giambruno, Tobias Doerks, Evren Karayel, Thomas R Burkard, Ines Kaupe, André C Müller, Andreas Schönegger, Gerhard F Ecker, Hans Lohninger, Peer Bork, Keiryn L Bennett, Giulio Superti-Furga, Jacques Colinge Genome Biology 2013, 14:R81 (31 July 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A mass spectrometry and bioinformatics approach identifies human proteins that bind nucleic acids in a non-sequence-specific manner

3.

Poster presentation   Open Access

Synaptic boutons sizes are tuned to best fit their physiological performances

Markus M Knodel, Dan Bucher, Romina Geiger, Lihao Ge, Alfio Grillo, Gabriel Wittum, Christoph Schuster, Gillian Queisser BMC Neuroscience 2013, 14(Suppl 1):P138 (8 July 2013)

Full text | PDF

4.

Commentary   Open Access Highly Accessed

Somatic and visceral nervous systems - an ancient duality

Paola Bertucci, Detlev Arendt BMC Biology 2013, 11:54 (30 April 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The idea that vertebrates are composed of a ‘visceral’ and ‘somatic’ self, responding to internal and external stimuli, respectively, was first put forward in the 19th century. Now, molecular fingerprinting indicates a duality between the somatic and visceral nervous systems that appears to predate Bilataria.

5.

Database   Open Access Highly Accessed

TRACER: a resource to study the regulatory architecture of the mouse genome

Chao-Kung Chen, Orsolya Symmons, Veli Vural Uslu, Taro Tsujimura, Sandra Ruf, Damian Smedley, François Spitz BMC Genomics 2013, 14:215 (2 April 2013)

Abstract | Full text | PDF | PubMed

6.

Research   Open Access Highly Accessed

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes

James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendergast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells

7.

Methodology article   Open Access Highly Accessed

A new method to customize protein expression vectors for fast, efficient and background free parallel cloning

Judith Scholz, Hüseyin Besir, Claudia Strasser, Sabine Suppmann BMC Biotechnology 2013, 13:12 (14 February 2013)

Abstract | Full text | PDF | PubMed

8.

Review   Open Access Highly Accessed

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul JP Bonnal, Brad Chapman, Peter JA Cock, Tore Eriksson, Paul MK Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido et al. Journal of Biomedical Semantics 2013, 4:6 (11 February 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

This meeting report from the 3rd DBCLS BioHackathon examines how Semantic Web technologies can improve the quality and accessibility of life science research data on the Web.

9.

Methodology article   Open Access Highly Accessed

Genotyping 1000 yeast strains by next-generation sequencing

Stefan Wilkening, Manu M Tekkedil, Gen Lin, Emilie S Fritsch, Wu Wei, Julien Gagneur, David W Lazinski, Andrew Camilli, Lars M Steinmetz BMC Genomics 2013, 14:90 (9 February 2013)

Abstract | Full text | PDF | PubMed

10.

Research article   Open Access Highly Accessed

Consistent mutational paths predict eukaryotic thermostability

Vera van Noort, Bettina Bradatsch, Manimozhiyan Arumugam, Stefan Amlacher, Gert Bange, Chris Creevey, Sebastian Falk, Daniel R Mende, Irmgard Sinning, Ed Hurt, Peer Bork BMC Evolutionary Biology 2013, 13:7 (10 January 2013)

Abstract | Full text | PDF | PubMed

11.

Research article   Open Access

The protein interaction network of a taxis signal transduction system in a Halophilic Archaeon

Matthias Schlesner, Arthur Miller, Hüseyin Besir, Michalis Aivaliotis, Judith Streif, Beatrix Scheffer, Frank Siedler, Dieter Oesterhelt BMC Microbiology 2012, 12:272 (21 November 2012)

Abstract | Full text | PDF | PubMed | f1000

12.

Research   Open Access Highly Accessed

Analysis of variation at transcription factor binding sites in Drosophila and humans

Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, Ewan Birney Genome Biology 2012, 13:R49 (5 September 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Transcription factor binding site variability in fly and human provides evidence for a buffering phenomenon

13.

Research article   Open Access Highly Accessed

Personal receptor repertoires: olfaction as a model

Tsviya Olender, Sebastian M Waszak, Maya Viavant, Miriam Khen, Edna Ben-Asher, Alejandro Reyes, Noam Nativ, Charles J Wysocki, Dongliang Ge, Doron Lancet BMC Genomics 2012, 13:414 (21 August 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Data mining of the inventory of human olfactory receptor coding regions has revealed unusually high genetic diversity between individuals, suggesting humans have receptor repertoires that may result in a highly personalized perception of smell.

14.

Research article   Open Access

Side chain modified peptide nucleic acids (PNA) for knock-down of six3 in medaka embryos

Sebastian Dorn, Narges Aghaallaei, Gerlinde Jung, Baubak Bajoghli, Birgit Werner, Holger Bock, Thomas Lindhorst, Thomas Czerny BMC Biotechnology 2012, 12:50 (17 August 2012)

Abstract | Full text | PDF | PubMed

15.

Research article   Open Access Highly Accessed

Insertion of a myc-tag within α-dystroglycan domains improves its biochemical and microscopic detection

Simona Morlacchi, Francesca Sciandra, Maria Bigotti, Manuela Bozzi, Wolfgang Hübner, Antonio Galtieri, Bruno Giardina, Andrea Brancaccio BMC Biochemistry 2012, 13:14 (26 July 2012)

Abstract | Full text | PDF | PubMed

16.

Research article   Open Access

CalpB modulates border cell migration in Drosophila egg chambers

Endre Kókai, Ferencz Páldy, Kálmán Somogyi, Anil Chougule, Margit Pál, Éva Kerekes, Péter Deák, Péter Friedrich, Viktor Dombrádi, Géza Ádám BMC Developmental Biology 2012, 12:20 (24 July 2012)

Abstract | Full text | PDF | PubMed

17.

Method   Open Access

m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence

Jüri Reimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman, Nicholas M Luscombe Genome Biology 2012, 13:R55 (21 June 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A computational method that identifies process-specific regulators from high-throughput data. Its utility is shown in an analysis that identifies cell cycle regulators

18.

Review   Open Access Highly Accessed

A unified phylogeny-based nomenclature for histone variants

Paul B Talbert, Kami Ahmad, Geneviève Almouzni, Juan Ausió, Frederic Berger, Prem L Bhalla, William M Bonner, W Cande, Brian P Chadwick, Simon W L Chan, George A M Cross, Liwang Cui, Stefan I Dimitrov, Detlef Doenecke, José M Eirin-López, Martin A Gorovsky, Sandra B Hake, Barbara A Hamkalo, Sarah Holec, Steven E Jacobsen, Kinga Kamieniarz, Saadi Khochbin, Andreas G Ladurner, David Landsman, John A Latham, Benjamin Loppin, Harmit S Malik, William F Marzluff, John R Pehrson, Jan Postberg et al. Epigenetics & Chromatin 2012, 5:7 (31 May 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

In response to an urgent need to rationalize the current schemes for naming histone variants, researchers from over 30 institutions worldwide have developed consistent but flexible naming rules that are informative and database-searchable.

19.

Research article   Open Access

Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions

Cecilia Conaco, Pierre Neveu, Hongjun Zhou, Mary Arcila, Sandie M Degnan, Bernard M Degnan, Kenneth S Kosik BMC Genomics 2012, 13:209 (30 May 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

20.

Commentary   Open Access Highly Accessed

How Not to Be a Bioinformatician

Manuel Corpas, Segun Fatumo, Reinhard Schneider Source Code for Biology and Medicine 2012, 7:3 (28 May 2012)

Abstract | Full text | PDF | PubMed | 1 comment

21.

Research   Open Access

Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

Joachim Weischenfeldt, Johannes Waage, Geng Tian, Jing Zhao, Inge Damgaard, Janus Jakobsen, Karsten Kristiansen, Anders Krogh, Jun Wang, Bo T Porse Genome Biology 2012, 13:R35 (24 May 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

An extensive in vivo analysis of how nonsense mediated mRNA decay regulates alternative splicing in two mouse tissues

22.

Software   Open Access Highly Accessed

Arena3D: visualizing time-driven phenotypic differences in biological systems

Maria Secrier, Georgios A Pavlopoulos, Jan Aerts, Reinhard Schneider BMC Bioinformatics 2012, 13:45 (22 March 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

23.

Software article   Open Access Highly Accessed

Caipirini: using gene sets to rank literature

Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Wanderley-Nogueira, Nina Soares-Cavalcanti, Reinhard Schneider BioData Mining 2012, 5:1 (1 February 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

'Caipirini', a new software program, allows ranking of biomedical literature based on biological relevance to gene sets, thereby enabling data from these high-throughput experiments to be more easily accessed.

24.

Correction   Free

SpeCond: a method to detect condition-specific gene expression

Florence MG Cavalli, Richard Bourgon, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:413 (30 December 2011)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Correction: A method to detect condition-specific gene expression from microarray data

25.

Research article   Open Access

Which clustering algorithm is better for predicting protein complexes?

Charalampos N Moschopoulos, Georgios A Pavlopoulos, Ernesto Iacucci, Jan Aerts, Spiridon Likothanassis, Reinhard Schneider, Sophia Kossida BMC Research Notes 2011, 4:549 (20 December 2011)

Abstract | Full text | PDF | PubMed

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