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1.
3666 Accesses
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A comparison of methods for differential expression analysis of RNA-seq data
Charlotte Soneson, Mauro Delorenzi BMC Bioinformatics 2013, 14:91 (9 March 2013)
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2.
2317 Accesses
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4273π: Bioinformatics education on low cost ARM hardware
Daniel Barker, David EK Ferrier, Peter WH Holland, John BO Mitchell, Heleen Plaisier, Michael G Ritchie, Steven D Smart BMC Bioinformatics 2013, 14:243 (12 August 2013)
Abstract | Full text | PDF
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Editor’s summary
An open access, open learning method for teaching bioinformatics uses the Raspberry Pi computer and a custom operating system to teach early-career researchers key skills in systems administration and computational biology at low cost.
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3.
2168 Accesses
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Levenshtein error-correcting barcodes for multiplexed DNA sequencing
Tilo Buschmann, Leonid V Bystrykh BMC Bioinformatics 2013, 14:272 (11 September 2013)
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4.
2080 Accesses
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NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
Yingtao Bi, Ramana V Davuluri BMC Bioinformatics 2013, 14:262 (27 August 2013)
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5.
1747 Accesses
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Statistical analysis of real-time PCR data
Joshua S Yuan, Ann Reed, Feng Chen, C Neal Stewart BMC Bioinformatics 2006, 7:85 (22 February 2006)
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| PubMed | Cited on BioMed Central
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6.
1706 Accesses
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li, Colin N Dewey BMC Bioinformatics 2011, 12:323 (4 August 2011)
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Editor’s summary
RSEM is a new user-friendly software tool for quantifying transcript abundance from RNA-seq data that does not rely on a reference genome and is particularly useful for quantification with de novo transcriptome assemblies
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7.
1529 Accesses
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Comparing a few SNP calling algorithms using low-coverage sequencing data
Xiaoqing Yu, Shuying Sun BMC Bioinformatics 2013, 14:274 (17 September 2013)
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8.
1517 Accesses
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inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis
Patrícia Soares, Renato J Alves, Ana B Abecasis, Carlos Penha-Gonçalves, M Gabriela M Gomes, José B Pereira-Leal BMC Bioinformatics 2013, 14:264 (30 August 2013)
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9.
1492 Accesses
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Centroid based clustering of high throughput sequencing reads based on n-mer counts
Alexander Solovyov, W Lipkin BMC Bioinformatics 2013, 14:268 (8 September 2013)
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10.
1465 Accesses
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Ontology based molecular signatures for immune cell types via gene expression analysis
Terrence F Meehan, Nicole A Vasilevsky, Christopher J Mungall, David S Dougall, Melissa A Haendel, Judith A Blake, Alexander D Diehl BMC Bioinformatics 2013, 14:263 (30 August 2013)
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11.
1443 Accesses
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WGCNA: an R package for weighted correlation network analysis
Peter Langfelder, Steve Horvath BMC Bioinformatics 2008, 9:559 (29 December 2008)
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12.
1433 Accesses
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AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides
Oscar Conchillo-Solé, Natalia S de Groot, Francesc X Avilés, Josep Vendrell, Xavier Daura, Salvador Ventura BMC Bioinformatics 2007, 8:65 (27 February 2007)
Abstract | Full text | PDF
| PubMed | Cited on BioMed Central
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13.
1391 Accesses
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Efficient alignment of RNA secondary structures using sparse dynamic programming
Cuncong Zhong, Shaojie Zhang BMC Bioinformatics 2013, 14:269 (8 September 2013)
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14.
1266 Accesses
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A balanced iterative random forest for gene selection from microarray data
Ali Anaissi, Paul J Kennedy, Madhu Goyal, Daniel R Catchpoole BMC Bioinformatics 2013, 14:261 (27 August 2013)
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15.
1262 Accesses
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A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Mikel Esnaola, Pedro Puig, David Gonzalez, Robert Castelo, Juan R Gonzalez BMC Bioinformatics 2013, 14:254 (21 August 2013)
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16.
1253 Accesses
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Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
James H Bullard, Elizabeth Purdom, Kasper D Hansen, Sandrine Dudoit BMC Bioinformatics 2010, 11:94 (18 February 2010)
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17.
1160 Accesses
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Learning a Markov Logic network for supervised gene regulatory network inference
Céline Brouard, Christel Vrain, Julie Dubois, David Castel, Marie-Anne Debily, Florence d’Alché-Buc BMC Bioinformatics 2013, 14:273 (12 September 2013)
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18.
1113 Accesses
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The COG database: an updated version includes eukaryotes
Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale BMC Bioinformatics 2003, 4:41 (11 September 2003)
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19.
1096 Accesses
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Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing
Rong Xu, QuanQiu Wang BMC Bioinformatics 2013, 14:181 (6 June 2013)
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20.
1085 Accesses
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A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
Johanna Brodin, Mohan Krishnamoorthy, Gayathri Athreya, Will Fischer, Peter Hraber, Cheryl Gleasner, Lance Green, Bette Korber, Thomas Leitner BMC Bioinformatics 2013, 14:255 (21 August 2013)
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21.
1083 Accesses
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Benchmarking short sequence mapping tools
Ayat Hatem, Doruk Bozdağ, Amanda E Toland, Ümit V Çatalyürek BMC Bioinformatics 2013, 14:184 (7 June 2013)
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Editor’s summary
A benchmarking suite to analyze well-known next generation sequencing tools, mapping short reads to a reference genome, with respect to various technological and algorithmic perspectives and addressing issues using multiple approaches such as multiple simulators.
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22.
1074 Accesses
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Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
Jian Ye, George Coulouris, Irena Zaretskaya, Ioana Cutcutache, Steve Rozen, Thomas L Madden BMC Bioinformatics 2012, 13:134 (18 June 2012)
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23.
1070 Accesses
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μHEM for identification of differentially expressed miRNAs using hypercuboid equivalence partition matrix
Sushmita Paul, Pradipta Maji BMC Bioinformatics 2013, 14:266 (4 September 2013)
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24.
1027 Accesses
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Pathway-PDT: a flexible pathway analysis tool for nuclear families
Yo Park, Michael Schmidt, Eden R Martin, Margaret A Pericak-Vance, Ren-Hua Chung BMC Bioinformatics 2013, 14:267 (4 September 2013)
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25.
1010 Accesses
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RCircos: an R package for Circos 2D track plots
Hongen Zhang, Paul Meltzer, Sean Davis BMC Bioinformatics 2013, 14:244 (10 August 2013)
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