20.4.3 Extraction and Analysis of Proteins

Thompson, R.[Richard],
A measure of shared information in classes of patterns,
PR(12), No. 6, 1980, pp. 369-379.
WWW Version. 0309
Insight into the patterns of variation in the amino acid sequences of proteins. BibRef

Leherte, L., Glasgow, J., Baxter, K., Steeg, E., and Fortier, S.,
Analysis of Three-Dimensional Protein Images,
JAIR(7), 1997, pp. 125-159.
HTML Version. BibRef 9700

Zaki, M.J., Jin, S.[Shan], Bystroff, C.,
Mining residue contacts in proteins using local structure predictions,
SMC-B(33), No. 5, October 2003, pp. 789-801.
IEEE Abstract. 0310
BibRef

Yang, Z.R.[Zheng Rong],
Orthogonal kernel Machine for the prediction of functional sites in proteins,
SMC-B(35), No. 1, February 2005, pp. 100-106.
IEEE Abstract. 0501
BibRef

Zhang, G.Z.[Guang-Zheng], Huang, D.S., Quan, Z.H.,
Combining a binary input encoding scheme with RBFNN for globulin protein inter-residue contact map prediction,
PRL(26), No. 10, 15 July 2005, pp. 1543-1553.
WWW Version. 0506
BibRef

Zhang, G.Z.[Guang-Zheng], Huang, D.S., Zhu, Y.P., Li, Y.X.,
Improving protein secondary structure prediction by using the residue conformational classes,
PRL(26), No. 15, November 2005, pp. 2346-2352.
WWW Version. 0510
BibRef

Zhao, T., Velliste, M., Boland, M.V., Murphy, R.F.,
Object Type Recognition for Automated Analysis of Protein Subcellular Location,
IP(14), No. 9, September 2005, pp. 1351-1359.
IEEE DOI Link 0508
BibRef

Zacharakis, G., Ripoll, J., Weissleder, R., Ntziachristos, V.,
Fluorescent protein tomography scanner for small animal imaging,
MedImg(24), No. 7, July 2005, pp. 878-885.
IEEE DOI Link 0508
BibRef

Lozano, M.A., Escolano, F.,
Protein classification by matching and clustering surface graphs,
PR(39), No. 4, April 2006, pp. 539-551.
WWW Version. Protein classification; Graph matching; Energy minimization; Graph clustering; EM algorithms 0604
BibRef

Kim, J.K.[Jong Kyoung], Raghava, G.P.S., Bang, S.Y.[Sung-Yang], Choi, S.[Seungjin],
Prediction of subcellular localization of proteins using pairwise sequence alignment and support vector machine,
PRL(27), No. 9, July 2006, pp. 996-1001.
WWW Version. 0605
BibRef

Kim, J.K.[Jong Kyoung], Bang, S.Y.[Sung-Yang], Choi, S.[Seungjin],
Sequence-driven features for prediction of subcellular localization of proteins,
PR(39), No. 12, December 2006, pp. 2301-2311.
WWW Version. 0609
Protein sequence feature extraction; Subcellular localization prediction; Support vector machine BibRef

Vijaya, P.A., Murty, M.N.[M. Narasimha], Subramanian, D.K.,
Efficient bottom-up hybrid hierarchical clustering techniques for protein sequence classification,
PR(39), No. 12, December 2006, pp. 2344-2355.
WWW Version. 0609
BibRef
Earlier:
An efficient technique for protein sequence clustering and classification,
ICPR04(II: 447-450).
IEEE DOI Link 0409
Hybrid clustering; Hierarchical structure; Protein sequences; Median strings/sequences; Prototypes; Feature selection; Classification accuracy BibRef

Khoja, R.[Rahim], Marolia, M.[Mehul], Acharya, T.[Tinku], Chakrabarti, C.[Chaitali],
A coprocessor architecture for fast protein structure prediction,
PR(39), No. 12, December 2006, pp. 2494-2505.
WWW Version. 0609
Protein structure prediction; PSIPRED; PSI BLAST; Neural network; VLSI architecture BibRef

Plötz, T.[Thomas], Fink, G.A.[Gernot A.],
Pattern Recognition methods for advanced stochastic protein sequence analysis using HMMs,
PR(39), No. 12, December 2006, pp. 2267-2280.
WWW Version. 0609
BibRef
Earlier:
Feature Extraction for Improved Profile HMM Based Biological Sequence Analysis,
ICPR04(II: 315-318).
IEEE DOI Link 0409
DNA sequencing. Protein sequence analysis; Probabilistic protein family modeling; HMM BibRef

Bergkvist, A.[Anders], Damaschke, P.[Peter],
Fast algorithms for finding disjoint subsequences with extremal densities,
PR(39), No. 12, December 2006, pp. 2281-2292.
WWW Version. 0609
Holes in data; Range prediction; Protein torsion angle; Protein structure prediction; Dynamic programming; Selection algorithms; Time complexity BibRef

Huang, D.S.A.[De-Shu-Ang], Zhao, X.M.[Xing-Ming], Huang, G.B.[Guang-Bin], Cheung, Y.M.[Yiu-Ming],
Classifying protein sequences using hydropathy blocks,
PR(39), No. 12, December 2006, pp. 2293-2300.
WWW Version. 0609
Hydropathy blocks; Protein sequence classification; Support vector machine BibRef

Kurgan, L.A.[Lukasz A.], Homaeian, L.[Leila],
Prediction of structural classes for protein sequences and domains--Impact of prediction algorithms, sequence representation and homology, and test procedures on accuracy,
PR(39), No. 12, December 2006, pp. 2323-2343.
WWW Version. 0609
Protein structural class; SCOP; Machine learning; Homology; Prediction; Secondary protein structure BibRef

Chen, C.Y.[Chien-Yu], Chung, W.C.[Wen-Chin], Su, C.T.[Chung-Tsai],
Exploiting homogeneity in protein sequence clusters for construction of protein family hierarchies,
PR(39), No. 12, December 2006, pp. 2356-2369.
WWW Version. 0609
Protein sequence clustering; Family analysis; Hierarchical algorithm BibRef

Baldacci, L., Golfarelli, M., Lumini, A., Rizzi, S.,
Clustering techniques for protein surfaces,
PR(39), No. 12, December 2006, pp. 2370-2382.
WWW Version. 0609
BibRef
Earlier:
A Template-Matching Approach for Protein Surface Clustering,
ICPR06(III: 340-343).
IEEE DOI Link 0609
Clustering; Region growing; Template matching; Protein surface BibRef

Mundra, P.[Piyushkumar], Kumar, M.[Madhan], Kumar, K.K.[K. Krishna], Jayaraman, V.K.[Valadi K.], Kulkarni, B.D.[Bhaskar D.],
Using pseudo amino acid composition to predict protein subnuclear localization: Approached with PSSM,
PRL(28), No. 13, 1 October 2007, pp. 1610-1615.
WWW Version. 0709
Nuclear protein; Subnuclear localization; Multiclass SVM; Factor solution score; PSSM BibRef

Karnik, S.[Shreyas], Mitra, J.[Joydeep], Singh, A.[Arunima], Kulkarni, B.D., Sundarajan, V., Jayaraman, V.K.,
Identification of N-Glycosylation Sites with Sequence and Structural Features Employing Random Forests,
PReMI09(146-151).
Springer DOI Link 0912
BibRef

Karnik, S.[Shreyas], Prasad, A.[Ajay], Diwevedi, A.[Alok], Sundararajan, V., Jayaraman, V.K.,
Identification of Defensins Employing Recurrence Quantification Analysis and Random Forest Classifiers,
PReMI09(152-157).
Springer DOI Link 0912
BibRef

McLaren, G.[Gina], Ellis, R.[Robert], Douglass, J.W.[James W.], Riding, T.J.[Thomas J.], Ring, J.E.[James E.],
Automated detection of objects in a biological sample,
US_Patent7,177,454, Feb 13, 2007
WWW Version. Proteins. BibRef 0702

Li, Y.L.[Yun-Lei], de Ridder, D.[Dick], Duin, R.P.W.[Robert P.W.], Reinders, M.J.T.[Marcel J.T.],
Integration of prior knowledge of measurement noise in kernel density classification,
PR(41), No. 1, January 2008, pp. 320-330.
WWW Version. 0710
Prior knowledge; Measurement noise; Kernel method; Parzen; Protein complex; mRNA co-expression coefficient BibRef

Tsai, C.Y.[Chieh-Yuan], Chiu, C.C.[Chuang-Cheng],
An efficient conserved region detection method for multiple protein sequences using principal component analysis and wavelet transform,
PRL(29), No. 5, 1 April 2008, pp. 616-628.
WWW Version. 0802
Protein sequence analysis; Conserved region detection; Principal component analysis; Wavelet transform BibRef

Savvides, A.[Alexios], Promponas, V.J.[Vasilis J.], Fokianos, K.[Konstantinos],
Clustering of biological time series by cepstral coefficients based distances,
PR(41), No. 7, July 2008, pp. 2398-2412.
WWW Version. 0804
Exponential model; Likelihood; Distance measures; Spectral analysis; Periodogram; Data mining; Protein sequence analysis BibRef

Ding, Y.S.[Yong-Sheng], Zhang, T.L.[Tong-Liang],
Using Chou's pseudo amino acid composition to predict subcellular localization of apoptosis proteins: An approach with immune genetic algorithm-based ensemble classifier,
PRL(29), No. 13, 1 October 2008, pp. 1887-1892.
WWW Version. 0804
Apoptosis protein subcellular location; Pseudo amino acid composition; Approximate entropy; Ensemble classifier; Fuzzy K-nearest neighbor classifier BibRef

Buske, F.A.[Fabian A.], Maetschke, S.[Stefan], Boden, M.[Mikael],
It's about time: Signal recognition in staged models of protein translocation,
PR(42), No. 4, April 2009, pp. 567-574.
Elsevier DOI Link
WWW Version. 0812
Bioinformatics; Machine learning; Protein secretory pathway; Signal peptide; Conditional random field; Amino acid sequence BibRef

von Wegner, F., Schurmann, S., Fink, R.H.A., Vogel, M., Friedrich, O.,
Motor Protein Function in Skeletal Muscle: A Multiple Scale Approach to Contractility,
MedImg(28), No. 10, October 2009, pp. 1632-1642.
IEEE DOI Link 0910
BibRef

Barash, E., Dinn, S., Sevinsky, C., Ginty, F.,
Multiplexed Analysis of Proteins in Tissue Using Multispectral Fluorescence Imaging,
MedImg(29), No. 8, August 2010, pp. 1457-1462.
IEEE DOI Link 1008
BibRef

Sabarinathan, R., Banerjee, N.[Nirjhar], Balakrishnan, N., Sekar, K.,
An algorithm to find distant repeats in a pair of protein sequences,
PRL(31), No. 14, 15 October 2010, pp. 2161-2169.
Elsevier DOI Link
WWW Version. 1003
Distant repeats; Protein sequences; PAM matrix BibRef

Diniz, M.C.[Michely C.], Pacheco, A.C.L.[Ana Carolina L.], Girao, K.T.[Karen T.], Araujo, F.F.[Fabiana F.], Walter, C.A.[Cezar A.], Oliveira, D.M.[Diana M.],
The tetratricopeptide repeats (TPR)-like superfamily of proteins in Leishmania spp., as revealed by multi-relational data mining,
PRL(31), No. 14, 15 October 2010, pp. 2178-2189.
Elsevier DOI Link
WWW Version. 1003
Multi-relational data mining; Hidden Markov models; Viterbi algorithm; Tetratricopeptide repeat motif; Leishmania proteins BibRef

Wang, H.Y.[Hai-Ying], Zheng, H.[Huiru], Browne, F.[Fiona], Glass, D.H.[David H.], Azuaje, F.[Francisco],
Integration of Gene Ontology-based similarities for supporting analysis of protein-protein interaction networks,
PRL(31), No. 14, 15 October 2010, pp. 2073-2082.
Elsevier DOI Link
WWW Version. 1003
Gene ontology; Protein interaction networks; Bayesian networks; Classification BibRef

Jancura, P.[Pavol], Marchiori, E.[Elena],
Dividing protein interaction networks for modular network comparative analysis,
PRL(31), No. 14, 15 October 2010, pp. 2083-2096.
Elsevier DOI Link
WWW Version. 1003
Protein interaction network division; Modular network alignment; Conserved protein complexes BibRef

Anand, A.[Ashish], Pugalenthi, G.[Ganesan], Fogel, G.B.[Gary B.], Suganthan, P.N.,
Identification and analysis of transcription factor family-specific features derived from DNA and protein information,
PRL(31), No. 14, 15 October 2010, pp. 2097-2102.
Elsevier DOI Link
WWW Version. 1003
Transcription factor; TF family-specific features; TF-TFBS interaction; Multi-class classification; TFBS; Feature selection BibRef

Horst, J.A.[Jeremy A.], Samudrala, R.[Ram],
A protein sequence meta-functional signature for calcium binding residue prediction,
PRL(31), No. 14, 15 October 2010, pp. 2103-2112.
Elsevier DOI Link
WWW Version. 1003
Protein sequence analysis; Protein function prediction; Calcium; Protein binding site; Functional signature BibRef

Mirceva, G.[Georgina], Davcev, D.[Danco],
Incorporating several features in the protein ray descriptor for more accurate protein 3D structure retrieval,
3DOR10(51-56).
WWW Version. 1111
BibRef

Vegas, E.[Esteban], Reverter, F.[Ferran], Oller, J.M.[Josep M.], Elías, J.M.[José M.],
A Comparison of Spectrum Kernel Machines for Protein Subnuclear Localization,
IbPRIA11(734-741).
Springer DOI Link 1106
BibRef

Guerra, C.[Concettina], Mina, M.[Marco],
Computational Methods for the Prediction of Protein-Protein Interactions,
IWCIA11(13-16).
Springer DOI Link 1105
BibRef

Sakar, O.[Okan], Kursun, O.[Olcay], Seker, H.[Huseyin], Gurgen, F.[Fikret],
Prediction of Protein Sub-nuclear Location by Clustering mRMR Ensemble Feature Selection,
ICPR10(2572-2575).
IEEE DOI Link 1008
BibRef

Mamidipally, C.[Chandrasekhar], Noronha, S.B.[Santosh B.], Roy, S.D.[Sumantra Dutta],
Automated Identification of Protein Structural Features,
PReMI09(171-176).
Springer DOI Link 0912
BibRef

Stamatopoulos, V.G., Karras, D.A., Moschopoulos, C., Kossida, S.,
Interpretation of Coherence Phase and Rhythmic Cumulant Results: A Simulation Study,
WSSIP09(1-6).
IEEE DOI Link 0906
BibRef

Moschopoulos, C., Likothanassis, S., Stamatopoulos, V.G., Kossida, S.,
Applying Graph Theory on Protein-Protein Interaction Data,
WSSIP09(1-4).
IEEE DOI Link 0906
BibRef

Cai, J.[Jinhai],
Enhanced HMM for the Recognition of Sigma70 Promoters in Escherichia coli,
DICTA08(46-51).
IEEE DOI Link 0812
BibRef

Cantoni, V.[Virginio], Gatti, R.[Riccardo], Lombardi, L.[Luca],
Towards Protein Interaction Analysis through Surface Labeling,
CIAP09(604-612).
Springer DOI Link 0909
BibRef

Kuksa, P.P.[Pavel P.], Pavlovic, V.[Vladimir],
Spatial Representation for Efficient Sequence Classification,
ICPR10(3320-3323).
IEEE DOI Link 1008
BibRef

Kuksa, P.P.[Pavel P.], Huang, P.H.[Pai-Hsi], Pavlovic, V.[Vladimir],
Fast protein homology and fold detection with sparse spatial sample kernels,
ICPR08(1-4).
IEEE DOI Link 0812
BibRef

Jung, J.[Jaehee], Thon, M.R.[Michael R.],
Gene function prediction using protein domain probability and hierarchical Gene Ontology information,
ICPR08(1-4).
IEEE DOI Link 0812
BibRef

Kim, D.[Donguk], Lee, C.H.[Chang-Hee], Cho, Y.S.[Young-Song], Kim, D.S.[Deok-Soo],
Manifoldization of beta-Shapes by Topology Operators,
GMP08(xx-yy).
Springer DOI Link 0804
BibRef

Xiang, J.P.[Jun-Ping], Hu, M.L.[Mao-Lin],
Protein Surface Modeling Using Active Contour Model,
GMP08(xx-yy).
Springer DOI Link 0804
BibRef

Xu, D.[Dong], Li, H.[Hua], Gu, T.J.[Tong-Jun],
Shape Representation and Invariant Description of Protein Tertiary Structure in Applications to Shape Retrieval and Classification,
GMP08(xx-yy).
Springer DOI Link 0804
BibRef

Kumar, P.[Pankaj], Jayaraman, V.K., Kulkarni, B.D.,
Granular Support Vector Machine Based Method for Prediction of Solubility of Proteins on Overexpression in Escherichia Coli,
PReMI07(406-415).
Springer DOI Link 0712
BibRef

Tsatsaias, V., Daras, P., Strintzis, M.G.,
3D Protein Classification using Topological, Geometrical and Biological Information,
ICIP07(VI: 537-540).
IEEE DOI Link 0709
See also Ellipsoidal Harmonics for 3-D Shape Description and Retrieval. BibRef

Gedda, M.[Magnus], Svensson, S.[Stina],
Flexibility Description of the MET Protein Stalk Based on the Use of Non-uniform B-Splines,
CAIP07(173-180).
Springer DOI Link 0708
BibRef

Bonet, I.[Isis], Saeys, Y.[Yvan], Ábalo, R.G.[Ricardo Grau], García, M.M.[María M.], Sanchez, R.[Robersy], van de Peer, Y.[Yves],
Feature Extraction Using Clustering of Protein,
CIARP06(614-623).
Springer DOI Link 0611
BibRef

Yu, Z.Y.[Ze-Yun], Bajaj, C.,
A Structure Tensor Approach for 3D Image Skeletonization: Applications in Protein Secondary Structure Analysis,
ICIP06(2513-2516).
IEEE DOI Link 0610
BibRef

Mallick, S.P.[Satya P.], Agarwal, S.[Sameer], Kriegman, D.J.[David J.], Belongie, S.J.[Serge J.],
Vision in the Small: Reconstructing the Structure of Protein Macromolecules from Cryo-Electron Micrographs,
BMVC06(I:1).
PDF Version. 0609
BibRef

Wen, Q.[Quan], Gao, J.[Jean], Luby-Phelps, K.[Kate],
Markov Chain Monte Carlo Data Association for Merge and Split Detection in Tracking Protein Clusters,
ICPR06(I: 1030-1033).
IEEE DOI Link 0609
BibRef

Sintorn, I.M.[Ida-Maria], Borgefors, G.[Gunilla],
Shape Based Identification of Proteins in Volume Images,
SCIA05(253-262).
Springer DOI Link 0506
BibRef

Bouchaffra, D., Tan, J.,
Protein Fold Recognition using a Structural Hidden Markov Model,
ICPR06(III: 186-189).
IEEE DOI Link 0609
BibRef

Zhang, Y.[Ya], Zha, H.Y.[Hong-Yuan], Chu, C.H.[Chao-Hisen], Ji, X.[Xiang],
Protein Interaction Inference as a MAX-SAT Problem,
BioInfo05(III: 146-146).
IEEE DOI Link 0507
BibRef

Daras, P., Zarpalas, D., Tzovaras, D., Strintzis, M.G.,
3D Shape-Based Techniques for Protein Classification,
ICIP05(II: 1130-1133).
IEEE DOI Link 0512
BibRef

Wen, Q., Gao, J., Kosaka, A., Iwaki, H., Luby-Phelps, K., Mundy, D.,
A Particle Filter Framework Using Optimal Importance Function for Protein Molecules Tracking,
ICIP05(I: 1161-1164).
IEEE DOI Link 0512
BibRef

Sintorn, I.M.[Ida-Maria], Gedda, M.[Magnus], Mata, S.[Susana], Svensson, S.[Stina],
Medial Grey-Level Based Representation for Proteins in Volume Images,
IbPRIA05(II:421).
Springer DOI Link 0509
BibRef

Hao, Y.[Yu], Zhu, X.Y.[Xiao-Yan], Li, M.[Ming],
A New Algorithm for Pattern Optimization in Protein-Protein Interaction Extraction System,
IbPRIA05(II:397).
Springer DOI Link 0509
BibRef

Burkhardt, S., Fredriksson, K., Ojamies, T., Ravantti, J., Ukkonen, E.,
Local approximate 3D matching of proteins in viral cryo-EM density maps,
3DPVT04(979-986).
IEEE Abstract. 0412
BibRef

Colle, G., Pelillo, M.,
Relaxation labeling processes for protein secondary structure prediction,
ICPR04(II: 355-358).
IEEE DOI Link 0409
BibRef

Rogers, M., Graham, J., Tonge, R.P.,
Automatic Construction of Statistical Shape Models for Protein Spot Analysis in Electrophoresis Gels,
BMVC03(xx-yy).
HTML Version. 0409
BibRef

Persson, M.[Martin], Bigun, J.[Josef],
Protein Spot Detection by Symmetry Derivatives of Gaussians,
SCIA03(520-525).
WWW Version. 0310
BibRef

Vendruscolo, M.,
Protein folding using inter-residue contact,
3DPVT02(724-728). 0206
BibRef

Zhang, B.H.[Bio-Hong], Godzik, A.,
The neaning and limitations of protein structure alignments,
3DPVT02(729-736). 0206
BibRef

Guerra, C., Lonardi, S., Zanotti, G.,
Analysis of secondary structure elements of proteins using indexing techniques,
3DPVT02(812-821).
IEEE DOI Link 0206
BibRef

Pedersen, L., Ersbøll, B.K.,
Protein Spot Correspondence in Two-dimensional Electrophoresis Gels,
SCIA01(P-W3A). 0206
BibRef

Fischer, D., Lin, S.L., Nusainov, R., Wolfson, H.,
Docking of protein molecules,
ICPR94(B:145-149).
IEEE DOI Link 9410
BibRef

Vargas, J.R.[J. Reynaldo], Appel, R.D.[Ron D.], Hochstrasser, D.F.[Denis F.], Pellegrini, C.[Christian],
Modeling and quantification of protein maps by Gaussian fitting,
CAIP93(627-633).
Springer DOI Link 9309
BibRef

Chapter on Medical Applications, CAT, MRI, Ultrasound, Heart Models, Brain Models continues in
Blood Cells, Counting, Extraction, Analysis .