Volume 24,
Number 1,
1 January 2008
Genome Analysis
Genome Analysis
- Michael L. Tress, Jan-Jaap Wesselink, Adam Frankish, Gonzalo López, Nick Goldman, Ari Löytynoja, Tim Massingham, Fabio Pardi, Simon Whelan, Jennifer Harrow, Alfonso Valencia:
Determination and validation of principal gene products.
11-17
Electronic Edition (link) BibTeX
Sequence Analysis
- Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori:
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.
18-25
Electronic Edition (link) BibTeX
- Aalt D. J. van Dijk, Cajo J. F. ter Braak, R. G. Immink, G. C. Angenent, Roeland C. H. J. van Ham:
Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control.
26-33
Electronic Edition (link) BibTeX
- Koen Deforche, Ricardo Camacho, K. Van Laethem, P. Lemey, A. Rambaut, Yves Moreau, Anne-Mieke Vandamme:
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment.
34-41
Electronic Edition (link) BibTeX
- Aleksey V. Zimin, Douglas R. Smith, Granger G. Sutton, James A. Yorke:
Assembly reconciliation.
42-45
Electronic Edition (link) BibTeX
- Kuo-ching Liang, Xiaodong Wang, Dimitris Anastassiou:
A profile-based deterministic sequential Monte Carlo algorithm for motif discovery.
46-55
Electronic Edition (link) BibTeX
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
- Meng Wang, Xiaobo Zhou, Fuhai Li, Jeremy Huckins, Randall W. King, Stephen T. C. Wong:
Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy.
94-101
Electronic Edition (link) BibTeX
- Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng, Haixu Tang, Zhiyin Xun, Rong Zeng, Predrag Radivojac:
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics.
102-109
Electronic Edition (link) BibTeX
Data and Text Mining
Genome Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Data and Text Mining
Database and Ontologies
Erratum
Volume 24,
Number 2,
15 January 2008
Genome Analysis
Sequence Analysis
Gene Expression
Systems Biology
- Changyu Shen, Zhiping Wang, Ganesh Shankar, Xiang Zhang, Lang Li:
A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry.
202-208
Electronic Edition (link) BibTeX
- Simon Hardy, Pierre N. Robillard:
Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways.
209-217
Electronic Edition (link) BibTeX
- Denise Scholtens, Tony Chiang, Wolfgang Huber, Robert Gentleman:
Estimating node degree in bait-prey graphs.
218-224
Electronic Edition (link) BibTeX
- Jean-Loup Faulon, Milind Misra, Shawn Martin, Ken Sale, Rajat Sapra:
Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor.
225-233
Electronic Edition (link) BibTeX
Data and Text Mining
- Hanchuan Peng, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers:
Straightening Caenorhabditis elegans images.
234-242
Electronic Edition (link) BibTeX
- Mounir Errami, Justin M. Hicks, Wayne G. Fisher, David Trusty, Jonathan D. Wren, Tara C. Long, Harold R. Garner:
Déjà vu - A study of duplicate citations in Medline.
243-249
Electronic Edition (link) BibTeX
- Ichigaku Takigawa, Hiroshi Mamitsuka:
Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis.
250-257
Electronic Edition (link) BibTeX
- Giuseppe Jurman, Stefano Merler, Annalisa Barla, Silvano Paoli, Antonio Galea, Cesare Furlanello:
Algebraic stability indicators for ranked lists in molecular profiling.
258-264
Electronic Edition (link) BibTeX
Databases and Ontologies
- Da Yang, Yanhui Li, Hui Xiao, Qing Liu, Min Zhang, Jing Zhu, Wencai Ma, Chen Yao, Jing Wang, Dong Wang, Zheng Guo, Baofeng Yang:
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories.
265-271
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
- Yassen Assenov, Fidel Ramírez, Sven-Eric Schelhorn, Thomas Lengauer, Mario Albrecht:
Computing topological parameters of biological networks.
282-284
Electronic Edition (link) BibTeX
- Thomas W. Evans, Colin S. Gillespie, Darren J. Wilkinson:
The SBML discrete stochastic models test suite.
285-286
Electronic Edition (link) BibTeX
- Peter Li, Tom Oinn, Stian Soiland, Douglas B. Kell:
Automated manipulation of systems biology models using libSBML within Taverna workflows.
287-289
Electronic Edition (link) BibTeX
- Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott, Mark Gerstein:
An integrated system for studying residue coevolution in proteins.
290-292
Electronic Edition (link) BibTeX
- Sema Kachalo, Ranran Zhang, Eduardo D. Sontag, Réka Albert, Bhaskar DasGupta:
NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks.
293-295
Electronic Edition (link) BibTeX
Data and Text Mining
Databases and Ontologies
- Unitsa Sangket, Amornrat Phongdara, Wilaiwan Chotigeat, Darran Nathan, Woo-Yeon Kim, Jong Bhak, Chumpol Ngamphiw, Sissades Tongsima, Asif M. Khan, Honghuang Lin, Tin Wee Tan:
Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries.
299-301
Electronic Edition (link) BibTeX
Volume 24,
Number 3,
1 February 2008
Sequence Analysis
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Genome Analysis
Structural Bioinformatics
Gene Expression
- Daniele Masotti, Christine Nardini, Simona Rossi, Elena Bonora, Giovanni Romeo, Stefano Volinia, Luca Benini:
TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders.
428-429
Electronic Edition (link) BibTeX
- Paolo Magni, Fulvia Ferrazzi, Lucia Sacchi, Riccardo Bellazzi:
TimeClust: a clustering tool for gene expression time series.
430-432
Electronic Edition (link) BibTeX
- Rudi Alberts, Gonzalo Vera, Ritsert C. Jansen:
affyGG: computational protocols for genetical genomics with Affymetrix arrays.
433-434
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
- Julia Stoyanovich, Itsik Pe'er:
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data.
440-442
Electronic Edition (link) BibTeX
- J. Stuart Aitken, Yin Chen, Jonathan Bard:
OBO Explorer: an editor for open biomedical ontologies in OWL.
443-444
Electronic Edition (link) BibTeX
- Quentin Kaas, Jan-C. Westermann, Reena Halai, Conan K. L. Wang, David J. Craik:
ConoServer, a database for conopeptide sequences and structures.
445-446
Electronic Edition (link) BibTeX
- David Salgado, Gregory Gimenez, François Coulier, Christophe Marcelle:
COMPARE, a multi-organism system for cross-species data comparison and transfer of information.
447-449
Electronic Edition (link) BibTeX
- Gil Alterovitz, Adnaan Jiwaji, Marco Ramoni:
Automated programming for bioinformatics algorithm deployment.
450-451
Electronic Edition (link) BibTeX
Volume 24,
Number 4,
15 February 2008
Sequence Analysis
Genome Analysis
Sequence Analysis
- Xuehui Li, Tamer Kahveci, A. Mark Settles:
A novel genome-scale repeat finder geared towards transposons.
468-476
Electronic Edition (link) BibTeX
- Ido Ginodi, Tal Vider-Shalit, Lea Tsaban, Yoram Louzoun:
Precise score for the prediction of peptides cleaved by the proteasome.
477-483
Electronic Edition (link) BibTeX
- Sumedha Gunewardena, Zhaolei Zhang:
A hybrid model for robust detection of transcription factor binding sites.
484-491
Electronic Edition (link) BibTeX
- Walter Pirovano, K. Anton Feenstra, Jaap Heringa:
PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.
492-497
Electronic Edition (link) BibTeX
- Rotem Rubinstein, András Fiser:
Predicting disulfide bond connectivity in proteins by correlated mutations analysis.
498-504
Electronic Edition (link) BibTeX
- Yu-Chieh Liao, Min-Shi Lee, Chin-Yu Ko, Chao A. Hsiung:
Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus.
505-512
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Systems Biology
Volume 24,
Number 5,
1 March 2008
Genome Analysis
Sequence Analysis
- J. D. Fischer, C. E. Mayer, Johannes Söding:
Prediction of protein functional residues from sequence by probability density estimation.
613-620
Electronic Edition (link) BibTeX
- Igor V. Tetko, Igor V. Rodchenkov, Mathias C. Walter, Thomas Rattei, Hans-Werner Mewes:
Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information.
621-628
Electronic Edition (link) BibTeX
- Leping Li, Robert L. Bass, Yu Liang:
fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control.
629-636
Electronic Edition (link) BibTeX
- Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler:
Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
637-644
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Systems Biology
Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Data and Text Mining
Databases and Ontologies
Volume 24,
Number 6,
15 March 2008
Discovery Note:
Systems Biology
Original Papers:
Genome Analysis
- Jeong-Hyeon Choi, Sun Kim, Haixu Tang, Justen Andrews, Don G. Gilbert, John Colbourne:
A machine-learning approach to combined evidence validation of genome assemblies.
744-750
Electronic Edition (link) BibTeX
- Robin Andersson, Carl E. G. Bruder, Arkadiusz Piotrowski, Uwe Menzel, Helena Nord, Johanna Sandgren, Torgeir R. Hvidsten, Teresita Diaz de Ståhl, Jan P. Dumanski, Henryk Jan Komorowski:
A segmental maximum a posteriori approach to genome-wide copy number profiling.
751-758
Electronic Edition (link) BibTeX
- Henrik Bengtsson, Rafael A. Irizarry, Benilton Carvalho, Terence P. Speed:
Estimation and assessment of raw copy numbers at the single locus level.
759-767
Electronic Edition (link) BibTeX
- Guillem Rigaill, Philippe Hupé, Anna Almeida, Philippe La Rosa, Jean-Philippe Meyniel, Charles Decraene, Emmanuel Barillot:
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays.
768-774
Electronic Edition (link) BibTeX
Sequence Analysis
- Nanjiang Shu, Tuping Zhou, Sven Hovmöller:
Prediction of zinc-binding sites in proteins from sequence.
775-782
Electronic Edition (link) BibTeX
- Anuj R. Shah, Christopher S. Oehmen, Bobbie-Jo M. Webb-Robertson:
SVM-HUSTLE - an iterative semi-supervised machine learning approach for pairwise protein remote homology detection.
783-790
Electronic Edition (link) BibTeX
- Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Chi-Kwong Wong, Siu-Ming Yiu:
Compressed indexing and local alignment of DNA.
791-797
Electronic Edition (link) BibTeX
- Mark N. Wass, Michael J. E. Sternberg:
ConFunc - functional annotation in the twilight zone.
798-806
Electronic Edition (link) BibTeX
- Andreas Biegert, Johannes Söding:
De novo identification of highly diverged protein repeats by probabilistic consistency.
807-814
Electronic Edition (link) BibTeX
- Bruce R. Southey, Jonathan V. Sweedler, Sandra L. Rodriguez-Zas:
Prediction of neuropeptide cleavage sites in insects.
815-825
Electronic Edition (link) BibTeX
Phylogenetics
Systems Biology
- Vladislav Vyshemirsky, Mark Girolami:
Bayesian ranking of biochemical system models.
833-839
Electronic Edition (link) BibTeX
- Julio Saez-Rodriguez, Arthur Goldsipe, Jeremy Muhlich, Leonidas G. Alexopoulos, Bjorn Millard, Douglas A. Lauffenburger, Peter K. Sorger:
Flexible informatics for linking experimental data to mathematical models via DataRail.
840-847
Electronic Edition (link) BibTeX
- Henning Schmidt, Mads F. Madsen, Sune Danø, Gunnar Cedersund:
Complexity reduction of biochemical rate expressions.
848-854
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Notes:
Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Database and Ontologies
Volume 24,
Number 7,
1 April 2008
Original Papers:
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano:
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
932-942
Electronic Edition (link) BibTeX
- Yuan Ji, Yiling Lu, Gordon B. Mills:
Bayesian models based on test statistics for multiple hypothesis testing problems.
943-949
Electronic Edition (link) BibTeX
- Andrew W. Dowsey, Michael J. Dunn, Guang-Zhong Yang:
Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.
950-957
Electronic Edition (link) BibTeX
- Joshua N. Sampson, Steven G. Self:
Identifying trait clusters by linkage profiles: application in genetical genomics.
958-964
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Applications Notes:
Genome Analysis
Sequence Analysis
Phylogenetics
Data and Text Mining
Databases and Ontologies
- Jongsun Park, Jaejin Park, Suwang Jang, Seryun Kim, Sunghyung Kong, Jaeyoung Choi, Kyohun Ahn, Juhyeon Kim, Seungmin Lee, Sunggon Kim, Bongsoo Park, Kyongyong Jung, Soonok Kim, Seogchan Kang, Yong-Hwan Lee:
FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors.
1024-1025
Electronic Edition (link) BibTeX
- Bongshin Lee, Kristy Brown, Yetrib Hathout, Jinwook Seo:
GOTreePlus: an interactive gene ontology browser.
1026-1028
Electronic Edition (link) BibTeX
Letters to the Editor:
Gene Expression
Volume 24,
Number 8,
15 April 2008
Original Papers:
Genome Analysis:
Sequence Analysis
Gene Expression
Systems Biology
Applications Notes:
Genome Analysis
Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Volume 24,
Number 9,
1 May 2008
Sequence Analysis
Structural Bioinformatics
Gene Expression
