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
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
- 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
- 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
- Aleksey V. Zimin, Douglas R. Smith, Granger G. Sutton, James A. Yorke:
Assembly reconciliation.
42-45
- Kuo-ching Liang, Xiaodong Wang, Dimitris Anastassiou:
A profile-based deterministic sequential Monte Carlo algorithm for motif discovery.
46-55
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
- 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
Data and Text Mining
Genome Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Data and Text Mining
Database and Ontologies
Erratum
- Peng Liu, J. T. Gene Hwang:
Gene expression: Quick calculation for sample size while controlling false discovery rate with application to microarray analysis.
149
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
- Simon Hardy, Pierre N. Robillard:
Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways.
209-217
- Denise Scholtens, Tony Chiang, Wolfgang Huber, Robert Gentleman:
Estimating node degree in bait-prey graphs.
218-224
- 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
Data and Text Mining
- Hanchuan Peng, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers:
Straightening Caenorhabditis elegans images.
234-242
- 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
- Ichigaku Takigawa, Hiroshi Mamitsuka:
Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis.
250-257
- Giuseppe Jurman, Stefano Merler, Annalisa Barla, Silvano Paoli, Antonio Galea, Cesare Furlanello:
Algebraic stability indicators for ranked lists in molecular profiling.
258-264
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
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
- Thomas W. Evans, Colin S. Gillespie, Darren J. Wilkinson:
The SBML discrete stochastic models test suite.
285-286
- Peter Li, Tom Oinn, Stian Soiland, Douglas B. Kell:
Automated manipulation of systems biology models using libSBML within Taverna workflows.
287-289
- 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
- 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
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
Volume 24,
Number 3,
1 February 2008
Sequence Analysis
- Shuji Fujita, Hideo Iba:
Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates.
303-308
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Fangxin Hong, Rainer Breitling:
A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments.
374-382
Genetics and Population Analysis
Systems Biology
Data and Text Mining
- Li Wang, Ji Zhu, Hui Zou:
Hybrid huberized support vector machines for microarray classification and gene selection.
412-419
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
- Paolo Magni, Fulvia Ferrazzi, Lucia Sacchi, Riccardo Bellazzi:
TimeClust: a clustering tool for gene expression time series.
430-432
- Rudi Alberts, Gonzalo Vera, Ritsert C. Jansen:
affyGG: computational protocols for genetical genomics with Affymetrix arrays.
433-434
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
- J. Stuart Aitken, Yin Chen, Jonathan Bard:
OBO Explorer: an editor for open biomedical ontologies in OWL.
443-444
- Quentin Kaas, Jan-C. Westermann, Reena Halai, Conan K. L. Wang, David J. Craik:
ConoServer, a database for conopeptide sequences and structures.
445-446
- David Salgado, Gregory Gimenez, François Coulier, Christophe Marcelle:
COMPARE, a multi-organism system for cross-species data comparison and transfer of information.
447-449
- Gil Alterovitz, Adnaan Jiwaji, Marco Ramoni:
Automated programming for bioinformatics algorithm deployment.
450-451
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
- Ido Ginodi, Tal Vider-Shalit, Lea Tsaban, Yoram Louzoun:
Precise score for the prediction of peptides cleaved by the proteasome.
477-483
- Sumedha Gunewardena, Zhaolei Zhang:
A hybrid model for robust detection of transcription factor binding sites.
484-491
- Walter Pirovano, K. Anton Feenstra, Jaap Heringa:
PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.
492-497
- Rotem Rubinstein, András Fiser:
Predicting disulfide bond connectivity in proteins by correlated mutations analysis.
498-504
- 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
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
- Yuntao Qian, Robert F. Murphy:
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models.
569-576
Genome Analysis
- Niranjan Nagarajan, Uri Keich:
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.
577-578
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
- 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
- Leping Li, Robert L. Bass, Yu Liang:
fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control.
629-636
- Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler:
Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
637-644
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
- 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
- Henrik Bengtsson, Rafael A. Irizarry, Benilton Carvalho, Terence P. Speed:
Estimation and assessment of raw copy numbers at the single locus level.
759-767
- 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
Sequence Analysis
- Nanjiang Shu, Tuping Zhou, Sven Hovmöller:
Prediction of zinc-binding sites in proteins from sequence.
775-782
- 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
- Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Chi-Kwong Wong, Siu-Ming Yiu:
Compressed indexing and local alignment of DNA.
791-797
- Mark N. Wass, Michael J. E. Sternberg:
ConFunc - functional annotation in the twilight zone.
798-806
- Andreas Biegert, Johannes Söding:
De novo identification of highly diverged protein repeats by probabilistic consistency.
807-814
- Bruce R. Southey, Jonathan V. Sweedler, Sandra L. Rodriguez-Zas:
Prediction of neuropeptide cleavage sites in insects.
815-825
Phylogenetics
Systems Biology
- Vladislav Vyshemirsky, Mark Girolami:
Bayesian ranking of biochemical system models.
833-839
- 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
- Henning Schmidt, Mads F. Madsen, Sune Danø, Gunnar Cedersund:
Complexity reduction of biochemical rate expressions.
848-854
Data and Text Mining
Applications Notes:
Genome Analysis
Sequence Analysis
Phylogenetics
- Mark Derthick:
Interactive visualization software for exploring phylogenetic trees and clades.
868-869
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Database and Ontologies
Volume 24,
Number 7,
1 April 2008
Original Papers:
Genome Analysis
- Hyunju Lee, Sek Won Kong, Peter J. Park:
Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes.
889-896
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
- Yuan Ji, Yiling Lu, Gordon B. Mills:
Bayesian models based on test statistics for multiple hypothesis testing problems.
943-949
- Andrew W. Dowsey, Michael J. Dunn, Guang-Zhong Yang:
Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.
950-957
- Joshua N. Sampson, Steven G. Self:
Identifying trait clusters by linkage profiles: application in genetical genomics.
958-964
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Applications Notes:
Genome Analysis
Sequence Analysis
- David He, John Parkinson:
SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences.
1016-1017
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
- Bongshin Lee, Kristy Brown, Yetrib Hathout, Jinwook Seo:
GOTreePlus: an interactive gene ontology browser.
1026-1028
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
- Anders Lanzén, Tom Oinn:
The Taverna Interaction Service: enabling manual interaction in workflows.
1118-1120
Volume 24,
Number 9,
1 May 2008
Sequence Analysis
Structural Bioinformatics
- Victor I. Lesk, Michael J. E. Sternberg:
3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm.
1137-1144
- Aleksandar Poleksic, Mark A. Fienup:
Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms.
1145-1153
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
- 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
- Meaza Demissie, Barbara Mascialino, Stefano Calza, Yudi Pawitan:
Unequal group variances in microarray data analyses.
1168-1174
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
- 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
- Hajo N. Krabbenhöft, Steffen Möller, Daniel Bayer:
Integrating ARC grid middleware with Taverna workflows.
1221-1222
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, Anna Maria 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
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
- Sridhar Hannenhalli:
Eukaryotic transcription factor binding sites - modeling and integrative search methods.
1325-1331
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
- Thibaut Jombart:
adegenet: a R package for the multivariate analysis of genetic markers.
1403-1405
- Gilles Guillot, Filipe Santos, Arnaud Estoup:
Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface.
1406-1407
- Bo Peng, Christopher I. Amos:
Forward-time simulations of non-random mating populations using simuPOP.
1408-1409
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
- 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
- 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
Databases and Ontologies
Volume 24,
Number 12,
15 June 2008
Discovery Note:
Sequence Analysis
- Jacob A. Tennessen:
Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence.
1421-1425
Original Papers:
Sequence Analysis
Systems Biology
Databases and Ontologies
Applications Notes:
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Korbinian Strimmer:
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates.
1461-1462
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
- Maital Ashkenazi, Gary D. Bader, Allan Kuchinsky, Menachem Moshelion, David J. States:
Cytoscape ESP: simple search of complex biological networks.
1465-1466
- Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer:
jSquid: a Java applet for graphical on-line network exploration.
1467-1468
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
Sequence Analysis
- John A. Capra, Mona Singh:
Characterization and prediction of residues determining protein functional specificity.
1473-1480
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
- Mattia Zampieri, Nicola Soranzo, Claudio Altafini:
Discerning static and causal interactions in genome-wide reverse engineering problems.
1510-1515
- 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
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
- Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, Olga G. Troyanskaya:
The Sleipnir library for computational functional genomics.
1559-1561
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
- Jiguo Cao, Hongyu Zhao:
Estimating dynamic models for gene regulation networks.
1619-1624
- 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
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
- 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
Systems Biology
Databases and Ontologies
Systems Biology
- Mark R. Segal:
On E-values for tandem MS scoring schemes.
1652-1653
Gene Expression
Volume 24,
Number 15,
1 August 2008
Genome Analysis
- Shuo Jiao, Shunpu Zhang:
On correcting the overestimation of the permutation-based false discovery rate estimator.
1655-1661
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
- Anne-Laure Boulesteix, Christine Porzelius, Martin Daumer:
Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value.
1698-1706
- E. Purdom, Ken M. Simpson, Mark 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
Systems Biology
Data and Text Mining
Genome Analysis
Structural Bioinformatics
Gene Expression
- Carl Murie, Robert Nadon:
A correction for estimating error when using the Local Pooled Error Statistical Test.
1735-1736
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
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
- Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer:
Database indexing for production MegaBLAST searches.
1757-1764
Sequence Analysis
Structural Bioinformatics
- Liam J. McGuffin:
Intrinsic disorder prediction from the analysis of multiple protein fold recognition models.
1798-1804
Genetics and Population Analysis
Data and Text Mining
Applications Note:
Structural Bioinformatics
- Yungki Park, Volkhard Helms:
MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon.
1819-1820
Genetics and Population Analysis
