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Computational Biology and Chemistry

Short Title: Comput. Biol. Chem.
Publisher: Elsevier (Pergamon), Oxford
ISSN: 1476-9271
Online: http://www.sciencedirect.com/science/journal/14769271
Predecessor: Computers and Chemistry
Documents Indexed: 370 Publications (since 2003)
References Indexed: 366 Publications with 11,423 References.
all top 5

Authors

8 Michel, Christian J.
7 Taylor, William R.
7 Viljoen, Hendrik J.
6 Crabbe, M. James C.
5 Cho, Kwang-Hyun
5 Pienaar, Elsje
4 Błażewicz, Jacek
4 Du, Zhihua
4 Gromiha, M. Michael
4 Li, Yixue
4 Mewes, Hans-Werner
4 Sadeghi, Mehdi
4 Zhang, Yuan
3 Albrecht, Andreas A.
3 Almeida, Antônio-Carlos G.
3 Axenovich, Tatiana I.
3 Bolshoy, Alexander
3 Cai, Yudong
3 Colonna, Giovanni
3 Costantini, Susan
3 Duarte, Mário A.
3 Facchiano, Angelo M.
3 Feng, Enmin
3 Formanowicz, Piotr
3 Gorodkin, Jan
3 Hénaut, Alain
3 Infantosi, Antonio Fernando C.
3 Lai, Yinglei
3 Levtsova, O. V.
3 Li, Menglong
3 Li, Wentian
3 Lin, Feng
3 Nasibov, Efendi N.
3 Oehmen, Christopher S.
3 Riva, Alessandra
3 Rodrigues, Antônio M.
3 Schnell, Santiago
3 Seligmann, Hervé
3 Shaitan, K. V.
3 Shimizu, Toshio
3 Song, Joon Jin
3 Takasaki, Shigeru
3 Teixeira, Hewerson Z.
3 Tetko, Igor V.
3 Toropov, Andrey A.
3 Ulanowicz, Robert E.
3 Utkin, Yu. N.
3 Wang, Ruisheng
3 Webb-Robertson, Bobbie-Jo M.
3 Whitney, Scott E.
3 Wu, Baolin
3 Xiao, Yi
3 Yang, Yaning
3 Yu, Weichuan
3 Zhao, Hongyu
3 Zheng, Nan
3 Zhong, Yang
2 Ahmad, Shandar
2 Antonov, Alexey V.
2 Bonatto, Diego
2 Britz, Dieter
2 Brojen Singh, R. K.
2 Çakır, Tunahan
2 Cao, Ying
2 Carpentier, Anne-Sophie
2 Chang, Hsueh-Wei
2 Chen, Hanlin
2 Chou, Kuochen
2 Chuang, Li-Yeh
2 Eslahchi, Changiz
2 Estrada, Ernesto
2 Fang, Weiwu
2 Fluitt, Aaron M.
2 Frey, Gabriel
2 Galat, Andrzej
2 Gong, Xi
2 Gribskov, Michael
2 Guo, Yanzhi
2 Han, Kyungsook
2 Hu, Zhangzhi
2 Ikeda, Masami
2 Jonassen, Inge
2 Kandemir-Cavas, Cagin
2 Kasprzak, Marta
2 Kim, Shinuk
2 Komeiji, Yuto
2 Korol, Abraham B.
2 Kumar, Vanaja
2 Lattimore, B. Samuel
2 Lee, Hojin
2 Leszczynski, Jerzy
2 Li, Siguangc
2 Lin, Lei
2 Llabrés, Mercè
2 Luo, Yuping
2 Madhavi Sastry, G.
2 Markiewicz, Wojciech T.
2 Mester, D. I.
2 Mordvintsev, D. Yu.
2 Moshiri, Behzad
...and 888 more Authors

Publications by Year

Citations contained in zbMATH Open

164 Publications have been cited 486 times in 429 Documents Cited by Year
Stochastic approaches for modelling in vivo reactions. Zbl 1087.92035
Turner, T. E.; Schnell, S.; Burrage, K.
39
2004
A novel feature representation method based on Chou’s pseudo amino acid composition for protein structural class prediction. Zbl 1403.92221
Sahu, Sitanshu Sekhar; Panda, Ganapati
22
2010
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Zbl 1086.92018
McCollum, James M.; Peterson, Gregory D.; Cox, Chris D.; Simpson, Michael L.; Samatova, Nagiza F.
15
2006
Circular code motifs in transfer and 16S ribosomal RNAs: a possible translation code in genes. Zbl 1365.92036
Michel, Christian J.
13
2012
Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes. Zbl 1102.92019
Frey, Gabriel; Michel, Christian J.
13
2006
Damping of Crank-Nicolson error oscillations. Zbl 1039.92047
Britz, D.; Østerby, O.; Strutwolf, J.
11
2003
Improved binary PSO for feature selection using gene expression data. Zbl 1142.92319
Chuang, Li-Yeh; Chang, Hsueh-Wei; Tu, Chung-Jui; Yang, Cheng-Hong
11
2008
Quantitative methods for ecological network analysis. Zbl 1088.92061
Ulanowicz, Robert E.
11
2004
Identification of all trinucleotide circular codes. Zbl 1366.92047
Michel, Christian J.; Pirillo, Giuseppe
11
2010
Optimal classification for time-course gene expression data using functional data analysis. Zbl 1158.62085
Song, Joon Jin; Deng, Weiguo; Lee, Ho-Jin; Kwon, Deukwoo
8
2008
Structural information content of networks: graph entropy based on local vertex functionals. Zbl 1141.92043
Dehmer, Matthias; Emmert-Streib, Frank
7
2008
Haplotype assembly from aligned weighted SNP fragments. Zbl 1102.92031
Zhao, Yuying; Wu, Lingyun; Zhang, Jihong; Wang, Ruisheng; Zhang, Xiangsun
7
2005
Clustering of time-course gene expression data using functional data analysis. Zbl 1122.92029
Song, Joon Jin; Lee, Ho-Jin; Morris, Jeffrey S.; Kang, Sanghoon
6
2007
An analytical model of gene evolution with six mutation parameters: An application to archaeal circular codes. Zbl 1086.92038
Frey, Gabriel; Michel, Christian J.
6
2006
Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques. Zbl 1088.92024
Mohseni-Zadeh, S.; Brézellec, P.; Risler, J.-L.
6
2004
Gene selection from microarray data for cancer classification – a machine learning approach. Zbl 1095.92040
Wang, Yu.; Tetko, Igor V.; Hall, Mark A.; Frank, Eibe; Facius, Axel; Mayer, Klaus F. X.; Mewes, Hans W.
6
2005
Developing Itô stochastic differential equation models for neuronal signal transduction pathways. Zbl 1098.92035
Manninen, Tiina; Linne, Marja-Leena; Ruohonen, Keijo
6
2006
High order accurate, one-sided finite-difference approximations to concentration gradients at the boundaries, for the simulation of electrochemical reaction-diffusion problems in one-dimensional space geometry. Zbl 1048.92037
Bieniasz, L. K.
5
2003
Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Zbl 1141.92312
Fluitt, Aaron; Pienaar, Elsje; Viljoen, Hendrik
5
2007
Hybrid particle swarm optimization and tabu search approach for selecting genes for tumor classification using gene expression data. Zbl 1142.92020
Shen, Qi; Shi, Weimin; Kong, Wei
5
2008
Sparse optimal scoring for multiclass cancer diagnosis and biomarker detection using microarray data. Zbl 1158.92316
Leng, Chenlei
5
2008
Dealing with repetitions in sequencing by hybridization. Zbl 1118.92028
Blazewicz, Jacek; Glover, Fred; Kasprzak, Marta; Markiewicz, Wojciech T.; Oğuz, Ceyda; Rebholz-Schuhmann, Dietrich; Swiercz, Aleksandra
5
2006
A mathematical analysis of SELEX. Zbl 1124.92015
Levine, Howard A.; Nilsen-Hamilton, Marit
5
2007
Stable feature selection for biomarker discovery. Zbl 1403.92068
He, Zengyou; Yu, Weichuan
5
2010
Integer linear programming as a tool for constructing trees from quartet data. Zbl 1102.92042
Weyer-Menkhoff, Jan; Devauchelle, Claudine; Grossmann, Alex; Grünewald, Stefan
5
2005
Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case. Zbl 1365.92038
Seligmann, Hervé
4
2012
HELFIT: Helix fitting by a total least squares method. Zbl 1158.62076
Enkhbayar, Purevjav; Damdinsuren, Sodov; Osaki, Mitsuru; Matsushima, Norio
4
2008
Computational method for inferring objective function of glycerol metabolism in Klebsiella pneumoniae. Zbl 1158.92013
Gong, Zhaohua; Liu, Chongyang; Feng, Enmin; Zhang, Qingrui
4
2009
Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence. Zbl 1119.92033
Zhang, Tongliang; Ding, Yongsheng; Chou, Kuo-Chen
4
2006
An analysis of the Petri net based model of the human body iron homeostasis process. Zbl 1124.92007
Sackmann, Andrea; Formanowicz, Dorota; Formanowicz, Piotr; Koch, Ina; Blazewicz, Jacek
4
2007
Protein knots and fold complexity: some new twists. Zbl 1125.92028
Taylor, William R.
4
2007
Comparing two \(K\)-category assignments by a \(K\)-category correlation coefficient. Zbl 1088.92017
Gorodkin, J.
4
2004
Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Zbl 1088.92042
Tan, Yongxi; Shi, Leming; Tong, Weida; Hwang, G. T. Gene; Wang, Charles
4
2004
Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries. Zbl 1088.92014
Błażewicz, Jacek; Formanowicz, Piotr; Kasprzak, Marta; Markiewicz, Wojciech T.; Świercz, Aleksandra
4
2004
A new family of metrics for biopolymer contact structures. Zbl 1088.92022
Llabrés, M.; Rosselló, F.
4
2004
Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms. Zbl 1087.92019
Berry, Emily A.; Dalby, Andrew R.; Yang, Zheng Rong
4
2004
A common sequence-associated physicochemical feature for proteins of beta-trefoil family. Zbl 1095.92043
Xu, Ruizhen; Xiao, Yi
4
2005
Application of residue distribution along the sequence for discriminating outer membrane proteins. Zbl 1096.92015
Gromiha, M. Michael; Ahmad, Shandar; Suwa, Makiko
4
2005
A local average connectivity-based method for identifying essential proteins from the network level. Zbl 1366.92046
Li, Min; Wang, Jianxin; Chen, Xiang; Wang, Huan; Pan, Yi
4
2011
Photosynthetic models with maximum entropy production in irreversible charge transfer steps. Zbl 1035.92014
Juretić, Davor; Županović, Paško
3
2003
Rival penalized competitive learning (RPCL): A topology-determining algorithm for analyzing gene expression data. Zbl 1034.92011
Nair, T. Murlidharan; Zheng, Christina L.; Fink, J. Lynn; Stuart, Robert O.; Gribskov, Michael
3
2003
A hybrid Bayesian network learning method for constructing gene networks. Zbl 1141.92319
Wang, Mingyi; Chen, Zuozhou; Cloutier, Sylvie
3
2007
Stochastic protein folding simulation in the three-dimensional HP-model. Zbl 1159.92016
Albrecht, A. A.; Skaliotis, A.; Steinhöfel, K.
3
2008
Discrete-time stochastic modeling and simulation of biochemical networks. Zbl 1158.92018
Sandmann, Werner
3
2008
The haplotype assembly model with genotype information and iterative local-exhaustive search algorithm. Zbl 1122.92051
Wang, Ying; Feng, Enmin; Wang, Ruisheng; Zhang, Dan
3
2007
Predicting deleterious non-synonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes. Zbl 1244.92019
Qin, Wenli; Li, Yizhou; Li, Juan; Yu, Lezheng; Wu, Di; Jing, Runyu; Pu, Xuemei; Guo, Yanzhi; Li, Menglong
3
2012
Directional persistence and the optimality of run-and-tumble chemotaxis. Zbl 1403.92038
Nicolau, Dan V. jun.; Armitage, Judith P.; Maini, Philip K.
3
2009
A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM. Zbl 1403.92209
Kavousi, Kaveh; Moshiri, Behzad; Sadeghi, Mehdi; Araabi, Babak N.; Moosavi-Movahedi, Ali Akbar
3
2011
Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis. Zbl 1088.92013
Anishetty, Sharmila; Pulimi, Mrudula; Pennathur, Gautam
3
2005
Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Zbl 1087.92047
Yu, Weichuan; Wu, Baolin; Lin, Ning; Stone, Kathy; Williams, Kenneth; Zhao, Hongyu
3
2006
Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification. Zbl 1088.92027
Whitney, Scott E.; Sudhir, Alugupally; Nelson, R. Michael; Viljoen, Hendrik J.
3
2004
Hydrophobic collapse in (in silico) protein folding. Zbl 1098.92024
Brylinski, Michal; Konieczny, Leszek; Roterman, Irena
3
2006
The ambush hypothesis at the whole-organism level: off frame, ‘hidden’ stops in vertebrate mitochondrial genes increase developmental stability. Zbl 1366.92050
Seligmann, Hervé
3
2010
Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. Zbl 1365.92042
Damiani, Chiara; Filisetti, Alessandro; Graudenzi, Alex; Lecca, Paola
2
2013
Finite difference method of simulation of non-steady-state ion transfer in electrochemical systems with allowance for migration. Zbl 1025.92016
Volgin, V. M.; Volgina, O. V.; Davydov, A. D.
2
2003
A central partition of molecular conformational space. I: Basic structures. Zbl 1025.92006
Gabarro-Arpa, Jacques
2
2003
Simulating cellular dynamics through a coupled transcription, translation, metabolic model. Zbl 1035.92012
Weitzke, Elizabeth L.; Ortoleva, Peter J.
2
2003
Some steps toward a central theory of ecosystem dynamics. Zbl 1035.92047
Ulanowicz, Robert E.
2
2003
Sequential imputation for missing values. Zbl 1142.62103
Verboven, Sabine; Vanden Branden, Karlien; Goos, Peter
2
2007
Model and simulation of \(\mathrm{Na}^+/\mathrm{K}^+\) pump phosphorylation in the presence of palytoxin. Zbl 1142.92325
Rodrigues, Antônio M.; Almeida, Antônio-Carlos G.; Infantosi, Antonio F. C.; Teixeira, Hewerson Z.; Duarte, Mario A.
2
2008
Exploring case-control genetic association tests using phase diagrams. Zbl 1158.62080
Li, Wentian; Suh, Young Ju; Yang, Yaning
2
2008
Plant microRNA detection using the circular code information. Zbl 1158.92009
Ahmed, Ahmed; Michel, Christian J.
2
2008
Protein subcellular location prediction using optimally weighted fuzzy \(k\)-NN algorithm. Zbl 1158.92310
Nasibov, Efendi; Kandemir-Cavas, Cagin
2
2008
Robust data imputation. Zbl 1158.62074
Branden, Karlien Vanden; Verboven, Sabine
2
2009
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. Zbl 1158.92016
Kielbassa, J.; Bortfeldt, R.; Schuster, S.; Koch, I.
2
2009
The multi-step phosphorelay mechanism of unorthodox two-component systems in E. coli realizes ultrasensitivity to stimuli while maintaining robustness to noises. Zbl 1112.92022
Kim, Jeong-Rae; Cho, Kwang-Hyun
2
2006
Identification of functional modules in a PPI network by clique percolation clustering. Zbl 1112.92028
Zhang, Shihua; Ning, Xuemei; Zhang, Xiangsun
2
2006
Codon phylogenetic distance. Zbl 1124.92035
Michel, Christian J.
2
2007
A new expertness index for assessment of secondary structure prediction engines. Zbl 1124.92014
Kazemian, M.; Moshiri, B.; Nikbakht, H.; Lucas, C.
2
2007
Hidden symmetries in the primary sequences of beta-barrel family. Zbl 1124.92012
Ji, Xiaofeng; Chen, Hanlin; Xiao, Yi
2
2007
Effect of internal viscosity on Brownian dynamics of DNA molecules in shear flow. Zbl 1124.92004
Yang, Xiao-Dong; Melnik, Roderick V. N.
2
2007
Predicting water solubility and octanol water partition coefficient for carbon nanotubes based on the chiral vector. Zbl 1124.92062
Toropov, Andrey A.; Leszczynska, Danuta; Leszczynski, Jerzy
2
2007
ECS: an automatic enzyme classifier based on functional domain composition. Zbl 1125.92027
Lu, Lingyi; Qian, Ziliang; Cai, Yu-Dong; Li, Yixue
2
2007
Inferring gene regulatory networks from temporal expression profiles under time-delay and noise. Zbl 1122.92026
Kim, Shinuk; Kim, Junil; Cho, Kwang-Hyun
2
2007
Computation of direct and inverse mutations with the SEGM web server (stochastic evolution of genetic motifs): an application to splice sites of human genome introns. Zbl 1403.92129
Benard, Emmanuel; Michel, Christian J.
2
2009
Algebraic methods for inferring biochemical networks: a maximum likelihood approach. Zbl 1403.92090
Craciun, Gheorghe; Pantea, Casian; Rempala, Grzegorz A.
2
2009
Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential. Zbl 1403.92197
Aita, Takuyo; Nishigaki, Koichi; Husimi, Yuzuru
2
2010
A stochastic evolution model for residue insertion-deletion independent from substitution. Zbl 1403.92141
Lèbre, Sophie; Michel, Christian J.
2
2010
Parameter estimation in modulated, unbranched reaction chains within biochemical systems. Zbl 1087.92027
Lall, Raman; Voit, Eberhard O.
2
2005
Using nearest feature line and tunable nearest neighbor methods for prediction of protein subcellular locations. Zbl 1087.92024
Gao, Qing-Bin; Wang, Zheng-Zhi
2
2005
Classifying G-protein coupled receptors with bagging classification tree. Zbl 1089.92009
Huang, Ying; Cai, Jun; Ji, Liang; Li, Yanda
2
2004
Fast and high precision algorithms for optimization in large-scale genomic problems. Zbl 1089.92013
Mester, D. I.; Ronin, Y. I.; Nevo, E.; Korol, A. B.
2
2004
A molecular model for transcription in the RNA world based on the ribosome large subunit. Zbl 1089.92018
Taylor, William R.
2
2004
PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules. Zbl 1089.92010
Komeiji, Yuto; Inadomi, Yuichi; Nakano, Tatsuya
2
2004
Cycling in ecological networks: Finn’s index revisited. Zbl 1088.92052
Allesina, Stefano; Ulanowicz, Robert E.
2
2004
A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data. Zbl 1095.92054
Lai, Yinglei; Zhao, Hongyu
2
2005
Analyzing functional similarity of protein sequences with discrete wavelet transform. Zbl 1097.92024
Wen, Zhining; Wang, Kelong; Li, Menglong; Nie, Fusheng; Yang, Yi
2
2005
Reconstruction of large phylogenetic trees: a parallel approach. Zbl 1102.92039
Du, Zhihua; Lin, Feng; Roshan, Usman W.
2
2005
SVM-BALSA: Remote homology detection based on Bayesian sequence alignment. Zbl 1102.92029
Webb-Robertson, Bobbie-Jo; Oehmen, Christopher; Matzke, Melissa
2
2005
CE-PLoc: An ensemble classifier for predicting protein subcellular locations by fusing different modes of pseudo amino acid composition. Zbl 1226.92020
Khan, Asifullah; Majid, Abdul; Hayat, Maqsood
2
2011
A model of tuberculosis transmission and intervention strategies in an urban residential area. Zbl 1366.92129
Pienaar, Elsje; Fluitt, Aaron M.; Whitney, Scott E.; Freifeld, Alison G.; Viljoen, Hendrik J.
2
2010
Abstract next subvolume method: a logical process-based approach for spatial stochastic simulation of chemical reactions. Zbl 1366.92051
Wang, Bing; Hou, Bonan; Xing, Fei; Yao, Yiping
2
2011
Deposition and extension approach to find longest common subsequence for thousands of long sequences. Zbl 1365.92004
Ning, Kang
1
2010
Angle dependent total cross sections and the optical theorem. Zbl 1134.33323
Levitina, T. V.; Brändas, E. J.
1
2003
Expression profiles in the progression of ductal carcinoma in the breast. Zbl 1024.92011
Lattimore, B. Samuel; Crabbe, M. James C.
1
2003
Dynamical characteristics of bacteria clustering by self-generated attractants. Zbl 1141.92307
Kim, Munju; Baek, Songjoon; Jung, Sung Hoon; Cho, Kwang-Hyun
1
2007
Inferring biomolecular interaction networks based on convex optimization. Zbl 1141.92015
Han, Soohee; Yoon, Yeoin; Cho, Kwang-Hyun
1
2007
Revisiting the relationship between compositional sequence complexity and periodicity. Zbl 1144.92014
Bolshoy, Alexander
1
2008
Meta-analysis for ranked discovery datasets: theoretical framework and empirical demonstration for microarrays. Zbl 1144.62363
Zintzaras, Elias; Ioannidis, John P. A.
1
2008
Oscillations of Hes7 caused by negative autoregulation and ubiquitination. Zbl 1274.92043
Zeiser, S.; Rivera, O.; Kuttler, C.; Hense, B.; Lasser, R.; Winkler, G.
1
2008
Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. Zbl 1365.92042
Damiani, Chiara; Filisetti, Alessandro; Graudenzi, Alex; Lecca, Paola
2
2013
Circular code motifs in transfer and 16S ribosomal RNAs: a possible translation code in genes. Zbl 1365.92036
Michel, Christian J.
13
2012
Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case. Zbl 1365.92038
Seligmann, Hervé
4
2012
Predicting deleterious non-synonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes. Zbl 1244.92019
Qin, Wenli; Li, Yizhou; Li, Juan; Yu, Lezheng; Wu, Di; Jing, Runyu; Pu, Xuemei; Guo, Yanzhi; Li, Menglong
3
2012
Derivation of an artificial gene to improve classification accuracy upon gene selection. Zbl 1244.92044
Seo, Minseok; Oh, Sejong
1
2012
A hyper-heuristic for the longest common subsequence problem. Zbl 1244.92021
Tabataba, Farzaneh Sadat; Mousavi, Sayyed Rasoul
1
2012
A local average connectivity-based method for identifying essential proteins from the network level. Zbl 1366.92046
Li, Min; Wang, Jianxin; Chen, Xiang; Wang, Huan; Pan, Yi
4
2011
A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM. Zbl 1403.92209
Kavousi, Kaveh; Moshiri, Behzad; Sadeghi, Mehdi; Araabi, Babak N.; Moosavi-Movahedi, Ali Akbar
3
2011
CE-PLoc: An ensemble classifier for predicting protein subcellular locations by fusing different modes of pseudo amino acid composition. Zbl 1226.92020
Khan, Asifullah; Majid, Abdul; Hayat, Maqsood
2
2011
Abstract next subvolume method: a logical process-based approach for spatial stochastic simulation of chemical reactions. Zbl 1366.92051
Wang, Bing; Hou, Bonan; Xing, Fei; Yao, Yiping
2
2011
Effective sample size: quick estimation of the effect of related samples in genetic case-control association analyses. Zbl 1403.92160
Yang, Yaning; Remmers, Elaine F.; Ogunwole, Chukwuma B.; Kastner, Daniel L.; Gregersen, Peter K.; Li, Wentian
1
2011
Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion. Zbl 1403.92081
Seligmann, Hervé
1
2011
A novel feature representation method based on Chou’s pseudo amino acid composition for protein structural class prediction. Zbl 1403.92221
Sahu, Sitanshu Sekhar; Panda, Ganapati
22
2010
Identification of all trinucleotide circular codes. Zbl 1366.92047
Michel, Christian J.; Pirillo, Giuseppe
11
2010
Stable feature selection for biomarker discovery. Zbl 1403.92068
He, Zengyou; Yu, Weichuan
5
2010
The ambush hypothesis at the whole-organism level: off frame, ‘hidden’ stops in vertebrate mitochondrial genes increase developmental stability. Zbl 1366.92050
Seligmann, Hervé
3
2010
Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential. Zbl 1403.92197
Aita, Takuyo; Nishigaki, Koichi; Husimi, Yuzuru
2
2010
A stochastic evolution model for residue insertion-deletion independent from substitution. Zbl 1403.92141
Lèbre, Sophie; Michel, Christian J.
2
2010
A model of tuberculosis transmission and intervention strategies in an urban residential area. Zbl 1366.92129
Pienaar, Elsje; Fluitt, Aaron M.; Whitney, Scott E.; Freifeld, Alison G.; Viljoen, Hendrik J.
2
2010
Deposition and extension approach to find longest common subsequence for thousands of long sequences. Zbl 1365.92004
Ning, Kang
1
2010
A Poisson-based adaptive affinity propagation clustering for SAGE data. Zbl 1403.92084
Tang, DongMing; Zhu, QingXin; Yang, Fan
1
2010
A hierarchic collision detection algorithm for simple Brownian dynamics. Zbl 1366.92005
Katsimitsoulia, Zoe; Taylor, William R.
1
2010
Computational method for inferring objective function of glycerol metabolism in Klebsiella pneumoniae. Zbl 1158.92013
Gong, Zhaohua; Liu, Chongyang; Feng, Enmin; Zhang, Qingrui
4
2009
Directional persistence and the optimality of run-and-tumble chemotaxis. Zbl 1403.92038
Nicolau, Dan V. jun.; Armitage, Judith P.; Maini, Philip K.
3
2009
Robust data imputation. Zbl 1158.62074
Branden, Karlien Vanden; Verboven, Sabine
2
2009
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. Zbl 1158.92016
Kielbassa, J.; Bortfeldt, R.; Schuster, S.; Koch, I.
2
2009
Computation of direct and inverse mutations with the SEGM web server (stochastic evolution of genetic motifs): an application to splice sites of human genome introns. Zbl 1403.92129
Benard, Emmanuel; Michel, Christian J.
2
2009
Algebraic methods for inferring biochemical networks: a maximum likelihood approach. Zbl 1403.92090
Craciun, Gheorghe; Pantea, Casian; Rempala, Grzegorz A.
2
2009
Computational identification of novel microRNA homologs in the chimpanzee genome. Zbl 1156.92014
Baev, Vesselin; Daskalova, Evelina; Minkov, Ivan
1
2009
Identifying the target mRNAs of microRNAs in colorectal cancer. Zbl 1156.92024
Kim, Shinuk; Choi, Minsoo; Cho, Kwang-Hyun
1
2009
A simple method of identifying symmetric substructures of proteins. Zbl 1156.92016
Chen, Hanlin; Huang, Yanzhao; Xiao, Yi
1
2009
Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm optimization. Zbl 1156.92022
Chang, Hsueh-Wei; Yang, Cheng-Hong; Ho, Chang-Hsuan; Wen, Cheng-Hao; Chuang, Li-Yeh
1
2009
Hybrid stochastic simulations of intracellular reaction-diffusion systems. Zbl 1403.92098
Kalantzis, Georgios
1
2009
Upstream curved sequences in E. coli are related to the regulation of transcription initiation. Zbl 1403.92078
Nov Klaiman, Tamar; Hosid, Sergey; Bolshoy, Alexander
1
2009
A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. Zbl 1403.92027
Lai, Xin; Nikolov, Svetoslav; Wolkenhauer, Olaf; Vera, Julio
1
2009
Efficiency analysis of KNN and minimum distance-based classifiers in enzyme family prediction. Zbl 1403.92215
Nasibov, Efendi; Kandemir-Cavas, Cagin
1
2009
Improved binary PSO for feature selection using gene expression data. Zbl 1142.92319
Chuang, Li-Yeh; Chang, Hsueh-Wei; Tu, Chung-Jui; Yang, Cheng-Hong
11
2008
Optimal classification for time-course gene expression data using functional data analysis. Zbl 1158.62085
Song, Joon Jin; Deng, Weiguo; Lee, Ho-Jin; Kwon, Deukwoo
8
2008
Structural information content of networks: graph entropy based on local vertex functionals. Zbl 1141.92043
Dehmer, Matthias; Emmert-Streib, Frank
7
2008
Hybrid particle swarm optimization and tabu search approach for selecting genes for tumor classification using gene expression data. Zbl 1142.92020
Shen, Qi; Shi, Weimin; Kong, Wei
5
2008
Sparse optimal scoring for multiclass cancer diagnosis and biomarker detection using microarray data. Zbl 1158.92316
Leng, Chenlei
5
2008
HELFIT: Helix fitting by a total least squares method. Zbl 1158.62076
Enkhbayar, Purevjav; Damdinsuren, Sodov; Osaki, Mitsuru; Matsushima, Norio
4
2008
Stochastic protein folding simulation in the three-dimensional HP-model. Zbl 1159.92016
Albrecht, A. A.; Skaliotis, A.; Steinhöfel, K.
3
2008
Discrete-time stochastic modeling and simulation of biochemical networks. Zbl 1158.92018
Sandmann, Werner
3
2008
Model and simulation of \(\mathrm{Na}^+/\mathrm{K}^+\) pump phosphorylation in the presence of palytoxin. Zbl 1142.92325
Rodrigues, Antônio M.; Almeida, Antônio-Carlos G.; Infantosi, Antonio F. C.; Teixeira, Hewerson Z.; Duarte, Mario A.
2
2008
Exploring case-control genetic association tests using phase diagrams. Zbl 1158.62080
Li, Wentian; Suh, Young Ju; Yang, Yaning
2
2008
Plant microRNA detection using the circular code information. Zbl 1158.92009
Ahmed, Ahmed; Michel, Christian J.
2
2008
Protein subcellular location prediction using optimally weighted fuzzy \(k\)-NN algorithm. Zbl 1158.92310
Nasibov, Efendi; Kandemir-Cavas, Cagin
2
2008
Revisiting the relationship between compositional sequence complexity and periodicity. Zbl 1144.92014
Bolshoy, Alexander
1
2008
Meta-analysis for ranked discovery datasets: theoretical framework and empirical demonstration for microarrays. Zbl 1144.62363
Zintzaras, Elias; Ioannidis, John P. A.
1
2008
Oscillations of Hes7 caused by negative autoregulation and ubiquitination. Zbl 1274.92043
Zeiser, S.; Rivera, O.; Kuttler, C.; Hense, B.; Lasser, R.; Winkler, G.
1
2008
Subsequence-based feature map for protein function classification. Zbl 1141.92018
Sarac, Omer Sinan; Gürsoy-Yüzügüllü, Özge; Cetin-Atalay, Rengul; Atalay, Volkan
1
2008
PK-means: A new algorithm for gene clustering. Zbl 1159.92018
Du, Zhihua; Wang, Yiwei; Ji, Zhen
1
2008
Identifying essential conditions for refractoriness of Leão’s spreading depression – computational modeling. Zbl 1161.92015
Teixeira, Hewerson Z.; Almeida, Antônio-Carlos G.; Infantosi, Antonio F. C.; Rodrigues, Antônio M.; Costa, Natália L.; Duarte, Mário A.
1
2008
Variable predictive model based classification algorithm for effective separation of protein structural classes. Zbl 1158.62081
Raghuraj, Rao; Lakshminarayanan, S.
1
2008
A feature vector integration approach for a generalized support vector machine pairwise homology algorithm. Zbl 1158.92021
Webb-Robertson, Bobbie-Jo M.; Oehmen, Christopher S.; Shah, Anuj R.
1
2008
Clustering of time-course gene expression data using functional data analysis. Zbl 1122.92029
Song, Joon Jin; Lee, Ho-Jin; Morris, Jeffrey S.; Kang, Sanghoon
6
2007
Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Zbl 1141.92312
Fluitt, Aaron; Pienaar, Elsje; Viljoen, Hendrik
5
2007
A mathematical analysis of SELEX. Zbl 1124.92015
Levine, Howard A.; Nilsen-Hamilton, Marit
5
2007
An analysis of the Petri net based model of the human body iron homeostasis process. Zbl 1124.92007
Sackmann, Andrea; Formanowicz, Dorota; Formanowicz, Piotr; Koch, Ina; Blazewicz, Jacek
4
2007
Protein knots and fold complexity: some new twists. Zbl 1125.92028
Taylor, William R.
4
2007
A hybrid Bayesian network learning method for constructing gene networks. Zbl 1141.92319
Wang, Mingyi; Chen, Zuozhou; Cloutier, Sylvie
3
2007
The haplotype assembly model with genotype information and iterative local-exhaustive search algorithm. Zbl 1122.92051
Wang, Ying; Feng, Enmin; Wang, Ruisheng; Zhang, Dan
3
2007
Sequential imputation for missing values. Zbl 1142.62103
Verboven, Sabine; Vanden Branden, Karlien; Goos, Peter
2
2007
Codon phylogenetic distance. Zbl 1124.92035
Michel, Christian J.
2
2007
A new expertness index for assessment of secondary structure prediction engines. Zbl 1124.92014
Kazemian, M.; Moshiri, B.; Nikbakht, H.; Lucas, C.
2
2007
Hidden symmetries in the primary sequences of beta-barrel family. Zbl 1124.92012
Ji, Xiaofeng; Chen, Hanlin; Xiao, Yi
2
2007
Effect of internal viscosity on Brownian dynamics of DNA molecules in shear flow. Zbl 1124.92004
Yang, Xiao-Dong; Melnik, Roderick V. N.
2
2007
Predicting water solubility and octanol water partition coefficient for carbon nanotubes based on the chiral vector. Zbl 1124.92062
Toropov, Andrey A.; Leszczynska, Danuta; Leszczynski, Jerzy
2
2007
ECS: an automatic enzyme classifier based on functional domain composition. Zbl 1125.92027
Lu, Lingyi; Qian, Ziliang; Cai, Yu-Dong; Li, Yixue
2
2007
Inferring gene regulatory networks from temporal expression profiles under time-delay and noise. Zbl 1122.92026
Kim, Shinuk; Kim, Junil; Cho, Kwang-Hyun
2
2007
Dynamical characteristics of bacteria clustering by self-generated attractants. Zbl 1141.92307
Kim, Munju; Baek, Songjoon; Jung, Sung Hoon; Cho, Kwang-Hyun
1
2007
Inferring biomolecular interaction networks based on convex optimization. Zbl 1141.92015
Han, Soohee; Yoon, Yeoin; Cho, Kwang-Hyun
1
2007
SMILES as an alternative to the graph in QSAR modelling of bee toxicity. Zbl 1124.62086
Toropov, Andrey A.; Benfenati, Emilio
1
2007
A clustering algorithm based on two distance functions for MEC model. Zbl 1124.92019
Wang, Ying; Feng, Enmin; Wang, Ruisheng
1
2007
Sequence comparison and environmental adaptation of a bacterial endonuclease. Zbl 1125.92050
Altermark, Bjørn; Thorvaldsen, Steinar; Moe, Elin; Smalås, Arne O.; Willassen, Nils P.
1
2007
Simulation of conformational changes occurring when a protein interacts with its receptor. Zbl 1122.92024
Costantini, S.; Colonna, G.; Facchiano, A. M.
1
2007
Chromosome segregation in Escherichia coli division: a free energy-driven string model. Zbl 1122.92023
Fan, J.; Tuncay, K.; Ortoleva, P. J.
1
2007
Global warming and coral reefs: modelling the effect of temperature on Acropora palmata colony growth. Zbl 1122.92063
Crabbe, M. James C.
1
2007
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Zbl 1086.92018
McCollum, James M.; Peterson, Gregory D.; Cox, Chris D.; Simpson, Michael L.; Samatova, Nagiza F.
15
2006
Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes. Zbl 1102.92019
Frey, Gabriel; Michel, Christian J.
13
2006
An analytical model of gene evolution with six mutation parameters: An application to archaeal circular codes. Zbl 1086.92038
Frey, Gabriel; Michel, Christian J.
6
2006
Developing Itô stochastic differential equation models for neuronal signal transduction pathways. Zbl 1098.92035
Manninen, Tiina; Linne, Marja-Leena; Ruohonen, Keijo
6
2006
Dealing with repetitions in sequencing by hybridization. Zbl 1118.92028
Blazewicz, Jacek; Glover, Fred; Kasprzak, Marta; Markiewicz, Wojciech T.; Oğuz, Ceyda; Rebholz-Schuhmann, Dietrich; Swiercz, Aleksandra
5
2006
Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence. Zbl 1119.92033
Zhang, Tongliang; Ding, Yongsheng; Chou, Kuo-Chen
4
2006
Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Zbl 1087.92047
Yu, Weichuan; Wu, Baolin; Lin, Ning; Stone, Kathy; Williams, Kenneth; Zhao, Hongyu
3
2006
Hydrophobic collapse in (in silico) protein folding. Zbl 1098.92024
Brylinski, Michal; Konieczny, Leszek; Roterman, Irena
3
2006
The multi-step phosphorelay mechanism of unorthodox two-component systems in E. coli realizes ultrasensitivity to stimuli while maintaining robustness to noises. Zbl 1112.92022
Kim, Jeong-Rae; Cho, Kwang-Hyun
2
2006
Identification of functional modules in a PPI network by clique percolation clustering. Zbl 1112.92028
Zhang, Shihua; Ning, Xuemei; Zhang, Xiangsun
2
2006
A comment on “Prediction of protein structural classes by a new measure of information discrepancy”. Zbl 1120.92019
Kedarisetti, Kanaka Durga; Kurgan, Lukasz; Dick, Scott
1
2006
Computational identification of microRNAs and their targets. Zbl 1112.92027
Zhang, Baohong; Pan, Xiaoping; Wang, Qinglian; Cobb, George P.; Anderson, Todd A.
1
2006
\(\beta\)-barrel transmembrane proteins: geometric modelling, detection of transmembrane region, and structural properties. Zbl 1112.92025
Valavanis, Ioannis K.; Bagos, Pantelis G.; Emiris, Ioannis Z.
1
2006
QSPR modeling of the half-wave potentials of benzoxazines by optimal descriptors calculated with the SMILES. Zbl 1118.92072
Toropov, Andrey; Nesmerak, Karel; Raska, Ivan jun.; Waisser, Karel; Palat, Karel
1
2006
Multilocus consensus genetic maps (MCGM): Formulation, algorithms, and results. Zbl 1087.92030
Mester, D. I.; Ronin, Y. I.; Korostishevsky, M. A.; Pikus, V. L.; Glazman, A. E.; Korol, A. B.
1
2006
Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks. Zbl 1088.92023
Marashi, Sayed-Amir; Goodarzi, Hani; Sadeghi, Mehdi; Eslahchi, Changiz; Pezeshk, Hamid
1
2006
Construction and characterization of a rock-cluster-based EST analysis pipeline. Zbl 1088.92033
Zhu, Tao; Zhou, Jianfeng; An, Yuming; Zhou, Jinhua; Li, Hongyu; Xu, Gang; Ma, Ding
1
2006
Modelling variations in corallite morphology of Galaxea fascicularis coral colonies with depth and light on coastal fringing reefs in the Wakatobi Marine National Park (S. E. Sulawesi, Indonesia). Zbl 1108.92041
Crabbe, M. James C.; Smith, David J.
1
2006
Selecting effective siRNA sequences based on the self-organizing map and statistical techniques. Zbl 1102.92027
Takasaki, Shigeru; Kawamura, Yoshihiro; Konagaya, Akihiko
1
2006
Predicting \(O\)-glycosylation sites in mammalian proteins by using SVMs. Zbl 1102.92022
Li, Sujun; Liu, Boshu; Zeng, Rong; Cai, Yudong; Li, Yixue
1
2006
Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides. Zbl 1102.92024
Marchut, Alexander J.; Hall, Carol K.
1
2006
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Cited by 1,042 Authors

25 Michel, Christian J.
8 Błażewicz, Jacek
8 Dehmer, Matthias
8 Fimmel, Elena
8 Strüngmann, Lutz H.
6 Pirillo, Giuseppe
5 Chou, Kuochen
5 Formanowicz, Piotr
5 Wolf, Verena
4 Albrecht, Andreas A.
4 Świercz, Aleksandra
4 Thanh, Vo Hong
4 Viljoen, Hendrik J.
4 Xiao, Xuan
3 Aita, Takuyo
3 Almeida, Antônio-Carlos G.
3 Benfenati, Emilio
3 Burrage, Kevin
3 Crabbe, M. James C.
3 Feng, Enmin
3 Formanowicz, Dorota
3 Giannerini, Simone
3 Grünewald, Stefan
3 Henzinger, Thomas A.
3 Husimi, Yuzuru
3 Khan, Asifullah
3 Leszczynska, Danuta
3 Leszczynski, Jerzy
3 Levine, Howard Allen
3 Lin, Hao
3 Moshiri, Behzad
3 Moulton, Vincent L.
3 Mousavi, Sayyed Rasoul
3 Nasibov, Efendi N.
3 Pan, Wei
3 Peng, Xinjun
3 Pienaar, Elsje
3 Sadeghi, Mehdi
3 Seligmann, Hervé
3 Seo, Yeon-Jung
3 Steinhöfel, Kathleen K.
3 Toropov, Andrey A.
3 Toropova, Alla P.
3 Voit, Eberhard Otto
3 Wang, Yifei
3 Wu, Lingyun
2 Araabi, Babak Nadjar
2 Bahi, Jacques Mohcine
2 Benard, Emmanuel
2 Bersani, Alberto Maria
2 Bersani, Enrico
2 Bieniasz, Lesław K.
2 Burke, Edmund Kieran
2 Cao, Shujuan
2 Chen, Hanlin
2 Cho, Kwang-Hyun
2 Cox, Chris D.
2 Dehzangi, Abdollah
2 Ding, Hui
2 Duarte, Mário A.
2 Emmert-Streib, Frank
2 Frey, Gabriel
2 Gabarro-Arpa, Jacques
2 Georgiou, Dimitrios N.
2 Gonzalez, Diego Luis
2 Grima, Ramon
2 Gromiha, M. Michael
2 Hayat, Maqsood
2 Higham, Desmond J.
2 Huber, Katharina T.
2 Infantosi, Antonio Fernando C.
2 Ji, Xiaofeng
2 Jia, Jiteng
2 Jobstmann, Barbara
2 Kandemir-Cavas, Cagin
2 Kang, Hye-Won
2 Karakasidis, Theodoros E.
2 Kasprzak, Marta
2 Kavousi, Kaveh
2 Khaliq, Abdul Q. M.
2 Konieczny, Leszek
2 Li, Dongfen
2 Li, Wentian
2 Liao, Xiaofeng
2 Lyons, James E.
2 McCollum, James M.
2 Moosavi-Movahedi, Ali Akbar
2 Mowshowitz, Abbe
2 Nelson, Michael J.
2 Nieto Roig, Juan Jose
2 Nilsen-Hamilton, Marit
2 Nishigaki, Koichi
2 Oehmen, Christopher S.
2 Oğuz, Ceyda
2 Paliwal, Kuldip K.
2 Pirillo, Mario A.
2 Priami, Corrado
2 Rakkiyappan, Rajan
2 Ramos, Juan I.
2 Rodrigues, Antônio M.
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Cited in 117 Journals

80 Journal of Theoretical Biology
79 Computational Biology and Chemistry
23 Bulletin of Mathematical Biology
14 Mathematical Biosciences
12 Journal of Mathematical Chemistry
11 Applied Mathematics and Computation
9 Computational & Mathematical Methods in Medicine
7 Journal of Mathematical Biology
6 Computers & Mathematics with Applications
6 Theoretical Computer Science
6 Computational Statistics and Data Analysis
6 Mathematical Problems in Engineering
5 Information Sciences
5 Journal of Computational and Applied Mathematics
5 Pattern Recognition
4 Annals of Operations Research
4 Electronic Journal of Statistics
3 Discrete Applied Mathematics
3 International Journal of Theoretical Physics
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3 Physica A
3 Journal of Classification
3 Computers & Operations Research
3 European Journal of Operational Research
3 International Journal of Computer Mathematics
3 Entropy
3 Mathematical Biosciences and Engineering
2 Journal of Multivariate Analysis
2 Applied Mathematics and Mechanics. (English Edition)
2 Computer Aided Geometric Design
2 Applied Mathematics Letters
2 Mathematical and Computer Modelling
2 Neural Networks
2 Journal of Global Optimization
2 Applied Mathematical Modelling
2 Foundations of Computing and Decision Sciences
2 Chaos
2 Natural Computing
2 Statistical Applications in Genetics and Molecular Biology
2 International Journal of Computational Methods
2 Nonlinear Analysis. Hybrid Systems
2 The Annals of Applied Statistics
2
2 Symmetry
2 Statistics and Computing
2 ISRN Biomathematics
2 Philosophical Transactions of the Royal Society of London. A. Mathematical, Physical and Engineering Sciences
1 International Journal of Control
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1 International Journal of Approximate Reasoning
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1 Machine Learning
1 MSCS. Mathematical Structures in Computer Science
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1 Communications in Statistics. Simulation and Computation
1 Proceedings of the National Academy of Sciences of the United States of America
1 SIAM Journal on Applied Mathematics
1 International Journal of Bifurcation and Chaos in Applied Sciences and Engineering
1 Test
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1 Russian Journal of Mathematical Physics
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1 ACM Transactions on Modeling and Computer Simulation
1 Science in China. Series E
1 Differential Equations and Dynamical Systems
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1 Journal of Shanghai University
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1 Mathematical and Computer Modelling of Dynamical Systems
1 Journal of the Royal Statistical Society. Series B. Statistical Methodology
1 Discrete Dynamics in Nature and Society
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1 CEJOR. Central European Journal of Operations Research
1 Biostatistics
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1 Journal of Machine Learning Research (JMLR)
1 Advances in Complex Systems
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