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, Kristel Van Laethem, Philippe Lemey, Andrew 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
- Andrey A. Shabalin, Håkon Tjelmeland, Cheng Fan, Charles M. Perou, Andrew B. Nobel:
Merging two gene-expression studies via cross-platform normalization.
1154-1160
Electronic Edition (link) BibTeX
- Reid F. Thompson, Mark Reimers, Batbayar Khulan, Mathieu Gissot, Todd A. Richmond, Quan Chen, Xin Zheng, Kami Kim, John M. Greally:
An analytical pipeline for genomic representations used for cytosine methylation studies.
1161-1167
Electronic Edition (link) BibTeX
- Meaza Demissie, Barbara Mascialino, Stefano Calza, Yudi Pawitan:
Unequal group variances in microarray data analyses.
1168-1174
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Applications Notes:
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Data and Text Mining
Databases and Ontologies
- Matthew P. Campbell, Louise Royle, Catherine M. Radcliffe, Raymond A. Dwek, Pauline M. Rudd:
GlycoBase and autoGU: tools for HPLC-based glycan analysis.
1214-1216
Electronic Edition (link) BibTeX
- Xiang Xu, Jinyu Wu, Jian Xiao, Yi Tan, Qiyu Bao, Fangqing Zhao, Xiaokun Li:
PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families.
1217-1220
Electronic Edition (link) BibTeX
- Hajo N. Krabbenhöft, Steffen Möller, Daniel Bayer:
Integrating ARC grid middleware with Taverna workflows.
1221-1222
Electronic Edition (link) BibTeX
Corrigendum
Volume 24,
Number 10,
15 May 2008
Discovery Note:
Data and Text Mining
Original Papers:
Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Databases and Ontologies
- Tiziana Castrignanò, M. D'Antonio, Anna Anselmo, Danilo Carrabino, A. D'Onorio De Meo, A. M. D'Erchia, Flavio Licciulli, M. Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, A. Riva, Raffaella Rizzi, Paola Bonizzoni, Graziano Pesole:
ASPicDB: A database resource for alternative splicing analysis.
1300-1304
Electronic Edition (link) BibTeX
Applications Notes:
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Databases and Ontologies
Corrigendum
Volume 24,
Number 11,
1 June 2008
Review:
Gene Expression
Original Papers:
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Databases and Ontologies
Applications Notes:
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Genetics and Population Analysis
Data and Text Mining
- Jung-jae Kim, Piotr Pezik, Dietrich Rebholz-Schuhmann:
MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline.
1410-1412
Electronic Edition (link) BibTeX
- Soyang Ha, Young-Ju Seo, Min-Seok Kwon, Byung-Ha Chang, Cheol Kyu Han, Jeong Hyeok Yoon:
IDMap: facilitating the detection of potential leads with therapeutic targets.
1413-1415
Electronic Edition (link) BibTeX
- Andreas Quandt, Patricia Hernandez, Alexandre Masselot, Céline Hernandez, Sergio Maffioletti, Cesare Pautasso, Ron D. Appel, Frédérique Lisacek:
swissPIT: a novel approach for pipelined analysis of mass spectrometry data.
1416-1417
Electronic Edition (link) BibTeX
Databases and Ontologies
Volume 24,
Number 12,
15 June 2008
Discovery Note:
Sequence Analysis
Original Papers:
Sequence Analysis
Systems Biology
Databases and Ontologies
Applications Notes:
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
- Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif R. Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca C. Wade, Ursula Kummer:
SYCAMORE - a systems biology computational analysis and modeling research environment.
1463-1464
Electronic Edition (link) BibTeX
- Maital Ashkenazi, Gary D. Bader, Allan Kuchinsky, Menachem Moshelion, David J. States:
Cytoscape ESP: simple search of complex biological networks.
1465-1466
Electronic Edition (link) BibTeX
- Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer:
jSquid: a Java applet for graphical on-line network exploration.
1467-1468
Electronic Edition (link) BibTeX
Databases and Ontologies
Volume 24,
Number 13,
1 July 2008
Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008.
2008
Contents BibTeX
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Systems Biology
- Bobbie-Jo M. Webb-Robertson, William R. Cannon, Christopher S. Oehmen, Anuj R. Shah, Vidhya Gurumoorthi, Mary S. Lipton, Katrina M. Waters:
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.
1503-1509
Electronic Edition (link) BibTeX
- Mattia Zampieri, Nicola Soranzo, Claudio Altafini:
Discerning static and causal interactions in genome-wide reverse engineering problems.
1510-1515
Electronic Edition (link) BibTeX
- Junil Kim, Tae-Geon Kim, Sung Hoon Jung, Jeong-Rae Kim, Taesung Park, Pat Heslop-Harrison, Kwang-Hyun Cho:
Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity.
1516-1522
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note - Sequence Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
- Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp II, Gordon A. Anderson, Richard D. Smith:
DAnTE: a statistical tool for quantitative analysis of -omics data.
1556-1558
Electronic Edition (link) BibTeX
- Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, Olga G. Troyanskaya:
The Sleipnir library for computational functional genomics.
1559-1561
Electronic Edition (link) BibTeX
Erratum
Volume 24,
Number 14,
15 July 2008
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
- Florian Centler, Christoph Kaleta, Pietro Speroni di Fenizio, Peter Dittrich:
Computing chemical organizations in biological networks.
1611-1618
Electronic Edition (link) BibTeX
- Jiguo Cao, Hongyu Zhao:
Estimating dynamic models for gene regulation networks.
1619-1624
Electronic Edition (link) BibTeX
- Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Franck Chauvat, Corinne Cassier-Chauvat, Jean-Christophe Aude, Pierre Legrain, Henning Hermjakob:
InteroPORC: automated inference of highly conserved protein interaction networks.
1625-1631
Electronic Edition (link) BibTeX
Data and Text Mining
Sequence Analysis
Phylogenetics
Genetics and Population Analysis
- Carlos Morcillo-Suarez, Josep Alegre, Ricardo Sangros, Elodie Gazave, Rafael de Cid, Roger Milne, Jorge Amigo, Anna Ferrer-Admetlla, Andrés Moreno-Estrada, Michelle Gardner, Ferran Casals, Anna Pérez-Lezaun, David Comas, Elena Bosch, Francesc Calafell, Jaume Bertranpetit, Arcadi Navarro:
SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data.
1643-1644
Electronic Edition (link) BibTeX
- Mamoru Kato, Yusuke Nakamura, Tatsuhiko Tsunoda:
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
1645-1646
Electronic Edition (link) BibTeX
Systems Biology
Databases and Ontologies
Systems Biology
Gene Expression
Volume 24,
Number 15,
1 August 2008
Genome Analysis
Sequence Analysis
Gene Expression
- Reinhard Schachtner, Dominik Lutter, P. Knollmüller, Ana Maria Tomé, Fabian J. Theis, Gerd Schmitz, Martin Stetter, Pedro Gómez Vilda, Elmar Wolfgang Lang:
Knowledge-based gene expression classification via matrix factorization.
1688-1697
Electronic Edition (link) BibTeX
- Anne-Laure Boulesteix, Christine Porzelius, Martin Daumer:
Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value.
1698-1706
Electronic Edition (link) BibTeX
- E. Purdom, Ken M. Simpson, M. D. Robinson, J. G. Conboy, A. V. Lapuk, Terence P. Speed:
FIRMA: a method for detection of alternative splicing from exon array data.
1707-1714
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Genome Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
Volume 24,
Number 16,
15 August 2008
ECCB'08 Proceedings, Seventh European Conference on Computational Biology, 22-26 September 2008, Cagliari, Italy.
2008
Contents BibTeX
Discovery Note:
Genome Analysis
Original Papers:
Genome Analysis
- Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai, Pan-Chyr Yang, Paul S. Meltzer, Eric Y. Chuang, Yidong Chen:
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.
1749-1756
Electronic Edition (link) BibTeX
- Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer:
Database indexing for production MegaBLAST searches.
1757-1764
Electronic Edition (link) BibTeX
Sequence Analysis
Structural Bioinformatics
Genetics and Population Analysis
Data and Text Mining
Applications Note:
Structural Bioinformatics
Genetics and Population Analysis
Databases and Ontologies
Volume 24,
Number 17,
1 September 2008
Review Paper:
Data and Text Mining
Original Papers:
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
- M. A. Marchisio, Jörg Stelling:
Computational design of synthetic gene circuits with composable parts.
1903-1910
Electronic Edition (link) BibTeX
- Heng Lian, William A. Thompson, Robert Thurman, John A. Stamatoyannopoulos, William Stafford Noble, Charles E. Lawrence:
Automated mapping of large-scale chromatin structure in ENCODE.
1911-1916
Electronic Edition (link) BibTeX
- Abhishek Garg, Alessandro Di Cara, Ioannis Xenarios, Luis Mendoza, Giovanni De Micheli:
Synchronous versus asynchronous modeling of gene regulatory networks.
1917-1925
Electronic Edition (link) BibTeX
- Yung-Keun Kwon, Kwang-Hyun Cho:
Coherent coupling of feedback loops: a design principle of cell signaling networks.
1926-1932
Electronic Edition (link) BibTeX
- Vladislav Vyshemirsky, Mark Girolami:
BioBayes: A software package for Bayesian inference in systems biology.
1933-1934
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note:
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Volume 24,
Number 18,
15 September 2008
Original Papers - Sequence Analysis
Structural Bioinformatics
Gene Expression
- Dhammika Amaratunga, Javier Cabrera, Yung-Seop Lee:
Enriched random forests.
2010-2014
Electronic Edition (link) BibTeX
- Liang Chen, Tiejun Tong, Hongyu Zhao:
Considering dependence among genes and markers for false discovery control in eQTL mapping.
2015-2022
Electronic Edition (link) BibTeX
- TaeHyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu, Jean-Pierre Kocher, Dennis A. Wigle, Vipin Kumar, Rui Kuang:
Robust and efficient identification of biomarkers by classifying features on graphs.
2023-2029
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
- Thomas Maiwald, Jens Timmer:
Dynamical modeling and multi-experiment fitting with PottersWheel.
2037-2043
Electronic Edition (link) BibTeX
- Markus W. Covert, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr:
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.
2044-2050
Electronic Edition (link) BibTeX
- Viviane Galvão, José Garcia Vivas Miranda, Ricardo Ribeiro-dos-Santos:
Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation.
2051-2056
Electronic Edition (link) BibTeX
- Min Zhang, Chen Yao, Zheng Guo, Jinfeng Zou, Lin Zhang, Hui Xiao, Dong Wang, Da Yang, Xue Gong, Jing Zhu, Yanhui Li, Xia Li:
Apparently low reproducibility of true differential expression discoveries in microarray studies.
2057-2063
Electronic Edition (link) BibTeX
- Mudassar Iqbal, Alex Alves Freitas, Colin G. Johnson, Massimo Vergassola:
Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data.
2064-2070
Electronic Edition (link) BibTeX
- Marco Grzegorczyk, Dirk Husmeier, Kieron D. Edwards, Peter Ghazal, Andrew J. Millar:
Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler.
2071-2078
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note- Sequence Analysis
- Marco Lippi, Andrea Passerini, Marco Punta, Burkhard Rost, Paolo Frasconi:
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
2094-2095
Electronic Edition (link) BibTeX
- Richard C. G. Holland, Thomas A. Down, Matthew R. Pocock, Andreas Prlic, David Huen, Keith James, Sylvain Foisy, Andreas Dräger, Andy Yates, Michael Heuer, Mark J. Schreiber:
BioJava: an open-source framework for bioinformatics.
2096-2097
Electronic Edition (link) BibTeX
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
- Torsten Blum, Oliver Kohlbacher:
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.
2108-2109
Electronic Edition (link) BibTeX
- H. Ramos, P. Shannon, Ruedi Aebersold:
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.
2110-2111
Electronic Edition (link) BibTeX
- Robert Kincaid, Allan Kuchinsky, Michael L. Creech:
VistaClara: an expression browser plug-in for Cytoscape.
2112-2114
Electronic Edition (link) BibTeX
- Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer:
ProCope - protein complex prediction and evaluation.
2115-2116
Electronic Edition (link) BibTeX
- Bing Xiong, Ke Liu, Jie Wu, David L. Burk, Hualiang Jiang, Jingkang Shen:
DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks.
2117-2118
Electronic Edition (link) BibTeX
Databases and Ontologies
- Rafael C. Jimenez, Antony F. Quinn, Alexander Garcia, Alberto Labarga, Kieran O'Neill, Fernando Martinez, Gustavo A. Salazar, Henning Hermjakob:
Dasty2, an Ajax protein DAS client.
2119-2121
Electronic Edition (link) BibTeX
- Catherine M. Lloyd, James R. Lawson, Peter J. Hunter, P. F. Nielsen:
The CellML Model Repository.
2122-2123
Electronic Edition (link) BibTeX
Letter to the Editor- Genome Analysis
Volume 24,
Number 19,
1 October 2008
Editorial
Original Papers - Genome Analysis
- Alejandro Cruz-Marcelo, Rudy Guerra, Marina Vannucci, Yiting Li, Ching C. Lau, Tsz-Kwong Man:
Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data.
2129-2136
Electronic Edition (link) BibTeX
- Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth:
Predicting pathway membership via domain signatures.
2137-2142
Electronic Edition (link) BibTeX
- Chandra Erdman, John W. Emerson:
A fast Bayesian change point analysis for the segmentation of microarray data.
2143-2148
Electronic Edition (link) BibTeX
- Laurent Jacob, Jean-Philippe Vert:
Protein-ligand interaction prediction: an improved chemogenomics approach.
2149-2156
Electronic Edition (link) BibTeX
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Applications Note - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Databases and Ontologies
Corrigenda
Erratum
Volume 24,
Number 20,
15 October 2008
Discovery Note - Sequence Analysis
Original Papers - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Vinay Pulim, Bonnie Berger, Jadwiga R. Bienkowska:
Optimal contact map alignment of protein-protein interfaces.
2324-2328
Electronic Edition (link) BibTeX
- Tuo Zhang, Hua Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, Lukasz A. Kurgan:
Accurate sequence-based prediction of catalytic residues.
2329-2338
Electronic Edition (link) BibTeX
- Ryan M. Bannen, Vanitha Suresh, George N. Phillips Jr, Stephen J. Wright, Julie C. Mitchell:
Optimal design of thermally stable proteins.
2339-2343
Electronic Edition (link) BibTeX
Gene Expression
Genetics and Population Analysis
Systems Biology
- Jaroslaw Smieja, Mohammad Jamaluddin, Allan R. Brasier, Marek Kimmel:
Model-based analysis of interferon-beta induced signaling pathway.
2363-2369
Electronic Edition (link) BibTeX
- Juan Cui, Qi Liu, David Puett, Ying Xu:
Computational prediction of human proteins that can be secreted into the bloodstream.
2370-2375
Electronic Edition (link) BibTeX
- Shuye Pu, Karen Ronen, James Vlasblom, Jack Greenblatt, Shoshana J. Wodak:
Local coherence in genetic interaction patterns reveals prevalent functional versatility.
2376-2383
Electronic Edition (link) BibTeX
- Kristen A. Wieghaus, Erwin P. Gianchandani, Mikell A. Paige, Milton L. Brown, Edward A. Botchwey, Jason A. Papin:
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule.
2384-2390
Electronic Edition (link) BibTeX
Applications Note - Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Databases and Ontologies
- Jing Zhang, Tao Ma, Yanda Li, Shao Li:
dbNEI2.0: building multilayer network for drug-NEI-disease.
2409-2411
Electronic Edition (link) BibTeX
- SiYuan Zheng, Jia Sheng, Chuan Wang, Xiaojing Wang, Yao Yu, Yun Li, Alex Michie, Jianliang Dai, Yang Zhong, Pei Hao, Lei Liu, Yixue Li:
MPSQ: a web tool for protein-state searching.
2412-2413
Electronic Edition (link) BibTeX
- Chaka Tang, Josephine F. Reyes, Fabio Luciani, Andrew R. Francis, Mark M. Tanaka:
spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex.
2414-2415
Electronic Edition (link) BibTeX
- Guangyong Zheng, Kang Tu, Qing Yang, Yun Xiong, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li:
ITFP: an integrated platform of mammalian transcription factors.
2416-2417
Electronic Edition (link) BibTeX
- Jason Persampieri, Deborah I. Ritter, Daniel Lees, Jessica Lehoczky, Qiang Li, Su Guo, Jeffrey H. Chuang:
cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation.
2418-2419
Electronic Edition (link) BibTeX
Letter to the Editor - Genome Analysis
Erratum
Volume 24,
Number 21,
1 November 2008
Discovery Notes - Sequence Analysis
Original Papers - Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Applications Note - Genome Analysis
Phylogenetics
Gene Expression
Systems Biology
- Dorothea Emig, Melissa S. Cline, Thomas Lengauer, Mario Albrecht:
Integrating expression data with domain interaction networks.
2546-2548
Electronic Edition (link) BibTeX
- Holger Fröhlich, Tim Beißbarth, Achim Tresch, Dennis Kostka, Juby Jacob, Rainer Spang, Florian Markowetz:
Analyzing gene perturbation screens with nested effects models in R and bioconductor.
2549-2550
Electronic Edition (link) BibTeX
- Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios Sotiropoulos, Yiannis N. Kaznessis:
SynBioSS: the synthetic biology modeling suite.
2551-2553
Electronic Edition (link) BibTeX
- Guillermo Rodrigo, Javier Carrera, Kristala Jones Prather, Alfonso Jaramillo:
DESHARKY: automatic design of metabolic pathways for optimal cell growth.
2554-2556
Electronic Edition (link) BibTeX
- Tian Xia, Julie A. Dickerson:
OmicsViz: Cytoscape plug-in for visualizing omics data across species.
2557-2558
Electronic Edition (link) BibTeX
Data and Text Mining
Databases and Ontologies
- Mehdi Pirooznia, Tanwir Habib, Edward J. Perkins, Youping Deng:
GOfetcher: a database with complex searching facility for gene ontology.
2561-2563
Electronic Edition (link) BibTeX
- C. Nelson Hayes, Diego Diez, Nicolas Joannin, Wataru Honda, Minoru Kanehisa, Mats Wahlgren, Craig E. Wheelock, Susumu Goto:
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation.
2564-2565
Electronic Edition (link) BibTeX
Letters to the Editor - Gene Expression
Systems Biology
Volume 24,
Number 22,
15 November 2008
Original Papers - Genome Analysis
Phylogenetics
Gene Expression
Systems Biology
- Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi:
Bayesian learning of biological pathways on genomic data assimilation.
2592-2601
Electronic Edition (link) BibTeX
- Katrin Sameith, Philipp Antczak, Elliot Marston, Nil Turan, Dieter Maier, Tanja Stankovic, Francesco Falciani:
Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage.
2602-2607
Electronic Edition (link) BibTeX
- Ta-tsen Soong, Kazimierz O. Wrzeszczynski, Burkhard Rost:
Physical protein-protein interactions predicted from microarrays.
2608-2614
Electronic Edition (link) BibTeX
- Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, David A. Fell:
Can sugars be produced from fatty acids? A test case for pathway analysis tools.
2615-2621
Electronic Edition (link) BibTeX
Data and Text Mining
- Seesandra V. Rajagopala, Johannes Goll, N. D. Deve Gowda, Kumar C. Sunil, Björn Titz, Arnab Mukherjee, Sharmila S. Mary, Naresh Raviswaran, Chetan S. Poojari, Srinivas Ramachandra, Svetlana Shtivelband, Stephen M. Blazie, Julia Hofmann, Peter Uetz:
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions.
2622-2627
Electronic Edition (link) BibTeX
Applications Note - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Databases and Ontologies
German Conference on Bioinformatics:
Systems Biology
Sequence Analysis
Copyright © Sat May 16 23:51:34 2009
by Michael Ley (ley@uni-trier.de)
