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1.

Proceedings   Open Access

Combining heterogeneous data sources for accurate functional annotation of proteins

Artem Sokolov, Christopher Funk, Kiley Graim, Karin Verspoor, Asa Ben-Hur BMC Bioinformatics 2013, 14(Suppl 3):S10 (28 February 2013)

Abstract | Full text | PDF

2.

Research article   Open Access

Bayesian semiparametric regression models to characterize molecular evolution

Saheli Datta, Abel Rodriguez, Raquel Prado BMC Bioinformatics 2012, 13:278 (30 October 2012)

Abstract | Full text | PDF | PubMed

3.

Research article   Open Access Highly Accessed

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Danielle G Lemay, William F Martin, Angie S Hinrichs, Monique Rijnkels, J Bruce German, Ian Korf, Katherine S Pollard BMC Bioinformatics 2012, 13:253 (28 September 2012)

Abstract | Full text | PDF | PubMed

4.

Open letter   Free Highly Accessed

An encyclopedia of mouse DNA elements (Mouse ENCODE)

John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al. Genome Biology 2012, 13:418 (13 August 2012)

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

The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome

5.

Research article   Open Access

Composition and organization of active centromere sequences in complex genomes

Karen E Hayden, Huntington F Willard BMC Genomics 2012, 13:324 (20 July 2012)

Abstract | Full text | PDF | PubMed

6.

Review   Open Access

Tissue sampling methods and standards for vertebrate genomics

Pamela BY Wong, Edward O Wiley, Warren E Johnson, Oliver A Ryder, Stephen J O’Brien, David Haussler, Klaus-Peter Koepfli, Marlys L Houck, Polina Perelman, Gabriela Mastromonaco, Andrew C Bentley, Byrappa Venkatesh, Ya-ping Zhang, Robert W Murphy, GigaScience 2012, 1:8 (12 July 2012)

Abstract | Full text | PDF

7.

Research article   Open Access Highly Accessed

Molecular phylogeny of grunts (Teleostei, Haemulidae), with an emphasis on the ecology, evolution, and speciation history of New World species

José Tavera, Arturo P, Eduardo F Balart, Giacomo Bernardi BMC Evolutionary Biology 2012, 12:57 (26 April 2012)

Abstract | Full text | PDF | PubMed

8.

Methodology article   Open Access Highly Accessed

Molecular probe technology detects bacteria without culture

Richard W Hyman, Robert P St Onge, Hyunsung Kim, John S Tamaresis, Molly Miranda, Ana Aparicio, Marilyn Fukushima, Nader Pourmand, Linda C Giudice, Ronald W Davis BMC Microbiology 2012, 12:29 (9 March 2012)

Abstract | Full text | PDF | PubMed

9.

Open letter   Free Highly Accessed

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

John A St John, Edward L Braun, Sally R Isberg, Lee G Miles, Amanda Y Chong, Jaime Gongora, Pauline Dalzell, Christopher Moran, Bertrand Bed'Hom, Arkhat Abzhanov, Shane C Burgess, Amanda M Cooksey, Todd A Castoe, Nicholas G Crawford, Llewellyn D Densmore, Jennifer C Drew, Scott V Edwards, Brant C Faircloth, Matthew K Fujita, Matthew J Greenwold, Federico G Hoffmann, Jonathan M Howard, Taisen Iguchi, Daniel E Janes, Shahid Khan, Satomi Kohno, AP Jason de Koning, Stacey L Lance, Fiona M McCarthy, John E McCormack et al. Genome Biology 2012, 13:415 (31 January 2012)

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

An Open Letter describing the project to sequence the genomes of the saltwater crocodile, the American alligator and the Indian gharial

10.

Research   Open Access

Efficient in vitro RNA interference and immunofluorescence-based phenotype analysis in a human parasitic nematode, Brugia malayi

Frédéric Landmann, Jeremy M Foster, Barton E Slatko, William Sullivan Parasites & Vectors 2012, 5:16 (13 January 2012)

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

This manuscript demonstrates the efficient use of heterogeneous short interfering RNA mixes for performing RNAi in the parasitic nematode Brugia malayi and immunofluorescence-based analysis of cellular phenotypes. Image: Defective 2 cell embryo of Brugia malayi following RNAi targeting the polarity-determining gene, par-1.

11.

Research   Open Access

Robust flash denoising/deblurring by iterative guided filtering

Hae-Jong Seo, Peyman Milanfar EURASIP Journal on Advances in Signal Processing 2012, 2012:3 (6 January 2012)

Abstract | Full text | PDF

12.

Research   Open Access

OpenKnowledge for peer-to-peer experimentation in protein identification by MS/MS

Siu-wai Leung, Xueping Quan, Paolo Besana, Qian Li, Mark Collins, Dietlind Gerloff, Dave Robertson Automated Experimentation 2011, 3:3 (22 December 2011)

Abstract | Full text | PDF | PubMed

13.

Software   Open Access

NanoStriDE: normalization and differential expression analysis of NanoString nCounter data

Christopher D Brumbaugh, Hyunsung J Kim, Mario Giovacchini, Nader Pourmand BMC Bioinformatics 2011, 12:479 (16 December 2011)

Abstract | Full text | PDF | PubMed

14.

Proceedings   Open Access

Prioritizing single-nucleotide variations that potentially regulate alternative splicing

Mingxiang Teng, Yadong Wang, Guohua Wang, Jeesun Jung, Howard J Edenberg, Jeremy R Sanford, Yunlong Liu BMC Proceedings 2011, 5(Suppl 9):S40 (29 November 2011)

Abstract | Full text | PDF

15.

Research   Open Access Highly Accessed

Analysis of induced electrical currents from magnetic field coupling inside implantable neurostimulator leads

Oxana S Pantchenko, Seth J Seidman, Joshua W Guag BioMedical Engineering OnLine 2011, 10:94 (21 October 2011)

Abstract | Full text | PDF | PubMed

16.

Research   Open Access

Electromagnetic compatibility of implantable neurostimulators to RFID emitters

Oxana S Pantchenko, Seth J Seidman, Joshua W Guag, Donald M Witters, Curt L Sponberg BioMedical Engineering OnLine 2011, 10:50 (9 June 2011)

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

17.

Primary research   Open Access Highly Accessed

MHC class I-related chain A and B ligands are differentially expressed in human cervical cancer cell lines

Susana del Toro-Arreola, Naela Arreygue-Garcia, Adriana Aguilar-Lemarroy, Angel Cid-Arregui, Miriam Jimenez-Perez, Jesse Haramati, Patricio Barros-Nuñez, Oscar Gonzalez-Ramella, Alicia del Toro-Arreola, Pablo Ortiz-Lazareno, Georgina Hernandez-Flores, Alejandro Bravo-Cuellar, Adrian Daneri-Navarro, Luis F Jave-Suarez Cancer Cell International 2011, 11:15 (1 June 2011)

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

18.

Software   Open Access

Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization

Krishna M Roskin, Benedict Paten, David Haussler BMC Bioinformatics 2011, 12:144 (10 May 2011)

Abstract | Full text | PDF | PubMed

19.

Research   Open Access Highly Accessed

Discovery of permuted and recently split transfer RNAs in Archaea

Patricia P Chan, Aaron E Cozen, Todd M Lowe Genome Biology 2011, 12:R38 (13 April 2011)

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

Discovery of novel split and permuted archaeal tRNAs argues against a single, early origin in Archaea

20.

Research article   Open Access

Comparing the adaptive landscape across trait types: larger QTL effect size in traits under biotic selection

Allison M Louthan, Kathleen M Kay BMC Evolutionary Biology 2011, 11:60 (7 March 2011)

Abstract | Full text | PDF | PubMed | F1000 Biology

21.

Research   Open Access

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

Kohta Ikegami, Thea A Egelhofer, Susan Strome, Jason D Lieb Genome Biology 2010, 11:R120 (23 December 2010)

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

A modENCODE survey of chromosome interactions with the inner nuclear membrane finds interacting regions are distal and gene sparse

22.

Research   Open Access

Lineage divergence detected in the malaria vector Anopheles marajoara (Diptera: Culicidae) in Amazonian Brazil

Sascha N McKeon, Margaret A Lehr, Richard C Wilkerson, John F Ruiz, Maria A Sallum, Jose BP Lima, Marinete M Povoa, Jan E Conn Malaria Journal 2010, 9:271 (7 October 2010)

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

Genetic analysis plays an increasingly important role in identifying changes in population structure and elucidating taxonomic status and phylogenetic relationships. Anopheles marajoara, a local and regionally important vector in lowland rainforest: phylogenetic analysis detected paraphyly in the neotropical malaria vector Anopheles marajoara.

23.

Research Article   Open Access

CARNIVORE: A Disruption-Tolerant System for Studying Wildlife

Matthew Rutishauser, Vladislav Petkov, Jay Boice, Katia Obraczka, Patrick Mantey, TerrieM Williams, ChristopherC Wilmers EURASIP Journal on Wireless Communications and Networking 2011, 2011:968046 (30 September 2010)

Abstract | Full text | PDF

24.

Research   Open Access Highly Accessed

Trans-generational epigenetic regulation of C. elegans primordial germ cells

Hirofumi Furuhashi, Teruaki Takasaki, Andreas Rechtsteiner, Tengguo Li, Hiroshi Kimura, Paula M Checchi, Susan Strome, William G Kelly Epigenetics & Chromatin 2010, 3:15 (12 August 2010)

Abstract | Full text | PDF | PubMed

25.

Research   Open Access Highly Accessed

Prostate apoptosis response protein 4 sensitizes human colon cancer cells to chemotherapeutic 5-FU through mediation of an NFκB and microRNA network

Bi-Dar Wang, Christina Kline, Danielle M Pastor, Thomas L Olson, Bryan Frank, Truong Luu, Arun K Sharma, Gavin Robertson, Matthew T Weirauch, Steven R Patierno, Joshua M Stuart, Rosalyn B Irby, Norman H Lee Molecular Cancer 2010, 9:98 (30 April 2010)

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

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