Finding optimal interaction interface alignments between biological complexes (English)
- New search for: Cui, Xuefeng
- New search for: Naveed, Hammad
- New search for: Gao, Xin
- New search for: Cui, Xuefeng
- New search for: Naveed, Hammad
- New search for: Gao, Xin
In:
Bioinformatics
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31
, 12
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i133-
;
2015
- Article (Journal) / Electronic Resource
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Title:Finding optimal interaction interface alignments between biological complexes
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Contributors:
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Published in:Bioinformatics ; 31, 12 ; i133-
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Publisher:
- New search for: Oxford University Press
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Publication date:2015-06-15
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ISSN:
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DOI:
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Type of media:Article (Journal)
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Type of material:Electronic Resource
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Language:English
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Source:
Table of contents – Volume 31, Issue 12
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
- 1881
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GenoMetric Query Language: a novel approach to large-scale genomic data managementMasseroli, Marco / Pinoli, Pietro / Venco, Francesco / Kaitoua, Abdulrahman / Jalili, Vahid / Palluzzi, Fernando / Muller, Heiko / Ceri, Stefano et al. | 2015
- 1889
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A novel statistical method for quantitative comparison of multiple ChIP-seq datasetsChen, Li / Wang, Chi / Qin, Zhaohui S. / Wu, Hao et al. | 2015
- 1897
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Analysis of nanopore data using hidden Markov modelsSchreiber, Jacob / Karplus, Kevin et al. | 2015
- 1904
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Methods for the detection and assembly of novel sequence in high-throughput sequencing dataHoltgrewe, Manuel / Kuchenbecker, Leon / Reinert, Knut et al. | 2015
- 1913
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Starcode: sequence clustering based on all-pairs searchZorita, Eduard / Cuscó, Pol / Filion, Guillaume J. et al. | 2015
- 1920
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Reference-based compression of short-read sequences using path encodingKingsford, Carl / Patro, Rob et al. | 2015
- 1929
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Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolutionMao, Wenzhi / Kaya, Cihan / Dutta, Anindita / Horovitz, Amnon / Bahar, Ivet et al. | 2015
- 1938
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mFASD: a structure-based algorithm for discriminating different types of metal-binding sitesHe, Wei / Liang, Zhi / Teng, Maikun / Niu, Liwen et al. | 2015
- 1945
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Evolutionary profiles improve protein-protein interaction prediction from sequenceHamp, Tobias / Rost, Burkhard et al. | 2015
- 1951
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MESMER: minimal ensemble solutions to multiple experimental restraintsIhms, Elihu C. / Foster, Mark P. et al. | 2015
- 1959
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Mobility-based prediction of hydration structures of protein surfacesJeszenői, Norbert / Horváth, István / Bálint, Mónika / van der Spoel, David / Hetényi, Csaba et al. | 2015
- 1966
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Extending P450 site-of-metabolism models with region-resolution dataZaretzki, Jed M. / Browning, Michael R. / Hughes, Tyler B. / Swamidass, S. Joshua et al. | 2015
- 1974
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Identification of cell types from single-cell transcriptomes using a novel clustering methodXu, Chen / Su, Zhengchang et al. | 2015
- 1981
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Application of clinical text data for phenome-wide association studies (PheWASs)Hebbring, Scott J. / Rastegar-Mojarad, Majid / Ye, Zhan / Mayer, John / Jacobson, Crystal / Lin, Simon et al. | 2015
- 1988
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A multiobjective memetic algorithm for PPI network alignmentClark, Connor / Kalita, Jugal et al. | 2015
- 1999
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Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasetsWandy, Joe / Daly, Rónán / Breitling, Rainer / Rogers, Simon et al. | 2015
- 2007
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Large-scale exploration and analysis of drug combinationsLi, Peng / Huang, Chao / Fu, Yingxue / Wang, Jinan / Wu, Ziyin / Ru, Jinlong / Zheng, Chunli / Guo, Zihu / Chen, Xuetong / Zhou, Wei et al. | 2015
- 2017
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Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometryNikolskiy, Igor / Siuzdak, Gary / Patti, Gary J. et al. | 2015
- 2024
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Characterizing spatial distributions of astrocytes in the mammalian retinaJammalamadaka, Aruna / Suwannatat, Panuakdet / Fisher, Steven K. / Manjunath, B. S. / Höllerer, Tobias / Luna, Gabriel et al. | 2015
- 2032
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Sambamba: fast processing of NGS alignment formatsTarasov, Artem / Vilella, Albert J. / Cuppen, Edwin / Nijman, Isaac J. / Prins, Pjotr et al. | 2015
- 2035
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NxTrim: optimized trimming of Illumina mate pair readsOConnell, Jared / Schulz-Trieglaff, Ole / Carlson, Emma / Hims, Matthew M. / Gormley, Niall A. / Cox, Anthony J. et al. | 2015
- 2038
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PolyMarker: A fast polyploid primer design pipelineRamirez-Gonzalez, Ricardo H. / Uauy, Cristobal / Caccamo, Mario et al. | 2015
- 2040
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A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencingWang, Xuefeng / Yu, Xiaoqing / Zhu, Wei / McCombie, W. Richard / Antoniou, Eric / Powers, R. Scott / Davidson, Nicholas O. / Li, Ellen / Williams, Jennie et al. | 2015
- 2043
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Crossfinder-assisted mapping of protein crosslinks formed by site-specifically incorporated crosslinkersMueller-Planitz, Felix et al. | 2015
- 2046
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SOMP: web server for in silico prediction of sites of metabolism for drug-like compoundsRudik, Anastasia / Dmitriev, Alexander / Lagunin, Alexey / Filimonov, Dmitry / Poroikov, Vladimir et al. | 2015
- 2049
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TarPred: a web application for predicting therapeutic and side effect targets of chemical compoundsLiu, Xian / Gao, Yuan / Peng, Jianlong / Xu, Yuan / Wang, Yulan / Zhou, Nannan / Xing, Jing / Luo, Xiaomin / Jiang, Hualiang / Zheng, Mingyue et al. | 2015
- 2052
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FUN-L: gene prioritization for RNAi screensLees, Jonathan G. / Hériché, Jean-Karim / Morilla, Ian / Fernández, José M. / Adler, Priit / Krallinger, Martin / Vilo, Jaak / Valencia, Alfonso / Ellenberg, Jan / Ranea, Juan A. et al. | 2015
- 2054
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Whiteboard: a framework for the programmatic visualization of complex biological analysesSundström, Görel / Zamani, Neda / Grabherr, Manfred G. / Mauceli, Evan et al. | 2015
- 2056
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The GPMDB REST interfaceFenyö, David / Beavis, Ronald C. et al. | 2015
- 2059
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Message from ISCB: Outstanding contributions to ISCB awardFogg, Christiana N. / Kovats, Diane E. et al. | 2015
- i1
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ISMB/ECCB 2015Moreau, Yves / Beerenwinkel, Niko et al. | 2015
- i3
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ISMB/ECCB 2015 Proceedings Papers Committee| 2015
- i9
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De novo meta-assembly of ultra-deep sequencing dataMirebrahim, Hamid / Close, Timothy J. / Lonardi, Stefano et al. | 2015
- i17
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A hierarchical Bayesian model for flexible module discovery in three-way time-series dataAmar, David / Yekutieli, Daniel / Maron-Katz, Adi / Hendler, Talma / Shamir, Ron et al. | 2015
- i27
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Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing dataNumanagić, Ibrahim / Malikić, Salem / Pratt, Victoria M. / Skaar, Todd C. / Flockhart, David A. / Sahinalp, S. Cenk et al. | 2015
- i35
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Reconstructing 16S rRNA genes in metagenomic dataYuan, Cheng / Lei, Jikai / Cole, James / Sun, Yanni et al. | 2015
- i44
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ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genesMirarab, Siavash / Warnow, Tandy et al. | 2015
- i53
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IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysisSafonova, Yana / Bonissone, Stefano / Kurpilyansky, Eugene / Starostina, Ekaterina / Lapidus, Alla / Stinson, Jeremy / DePalatis, Laura / Sandoval, Wendy / Lill, Jennie / Pevzner, Pavel A. et al. | 2015
- i62
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Reconstruction of clonal trees and tumor composition from multi-sample sequencing dataEl-Kebir, Mohammed / Oesper, Layla / Acheson-Field, Hannah / Raphael, Benjamin J. et al. | 2015
- i71
-
Robust reconstruction of gene expression profiles from reporter gene data using linear inversionZulkower, Valentin / Page, Michel / Ropers, Delphine / Geiselmann, Johannes / de Jong, Hidde et al. | 2015
- i80
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Misassembly detection using paired-end sequence reads and optical mapping dataMuggli, Martin D. / Puglisi, Simon J. / Ronen, Roy / Boucher, Christina et al. | 2015
- i89
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Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot dataOcone, Andrea / Haghverdi, Laleh / Mueller, Nikola S. / Theis, Fabian J. et al. | 2015
- i97
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Inferring orthologous gene regulatory networks using interspecies data fusionPenfold, Christopher A. / Millar, Jonathan B. A. / Wild, David L. et al. | 2015
- i106
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MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphismsZickmann, Franziska / Renard, Bernhard Y. et al. | 2015
- i116
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Large-scale model quality assessment for improving protein tertiary structure predictionCao, Renzhi / Bhattacharya, Debswapna / Adhikari, Badri / Li, Jilong / Cheng, Jianlin et al. | 2015
- i124
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Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteinsSoltan Ghoraie, Laleh / Burkowski, Forbes / Zhu, Mu et al. | 2015
- i133
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Finding optimal interaction interface alignments between biological complexesCui, Xuefeng / Naveed, Hammad / Gao, Xin et al. | 2015
- i142
-
Deconvolving molecular signatures of interactions between microbial coloniesHarn, Y.-C. / Powers, M. J. / Shank, E. A. / Jojic, V. et al. | 2015
- i151
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cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactionsOliwa, Tomasz / Shen, Yang et al. | 2015
- i161
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Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignmentsYamanishi, Yoshihiro / Tabei, Yasuo / Kotera, Masaaki et al. | 2015
- i171
-
Exploring the structure and function of temporal networks with dynamic graphletsHulovatyy, Y. / Chen, H. / Milenković, T. et al. | 2015
- i181
-
Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analysesPark, Danny S. / Brown, Brielin / Eng, Celeste / Huntsman, Scott / Hu, Donglei / Torgerson, Dara G. / Burchard, Esteban G. / Zaitlen, Noah et al. | 2015
- i190
-
Inferring parental genomic ancestries using pooled semi-Markov processesZou, James Y. / Halperin, Eran / Burchard, Esteban / Sankararaman, Sriram et al. | 2015
- i197
-
Integrative random forest for gene regulatory network inferencePetralia, Francesca / Wang, Pei / Yang, Jialiang / Tu, Zhidong et al. | 2015
- i206
-
Identification of causal genes for complex traitsHormozdiari, Farhad / Kichaev, Gleb / Yang, Wen-Yun / Pasaniuc, Bogdan / Eskin, Eleazar et al. | 2015
- i214
-
Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patternsChilds, Dorothee / Grimbs, Sergio / Selbig, Joachim et al. | 2015
- i221
-
Improving compound-protein interaction prediction by building up highly credible negative samplesLiu, Hui / Sun, Jianjiang / Guan, Jihong / Zheng, Jie / Zhou, Shuigeng et al. | 2015
- i230
-
Gene network inference by fusing data from diverse distributionsŽitnik, Marinka / Zupan, Blaž et al. | 2015
- i240
-
Genome-wide detection of intervals of genetic heterogeneity associated with complex traitsLlinares-López, Felipe / Grimm, Dominik G. / Bodenham, Dean A. / Gieraths, Udo / Sugiyama, Mahito / Rowan, Beth / Borgwardt, Karsten et al. | 2015
- i250
-
PAGER: constructing PAGs and new PAG-PAG relationships for network biologyYue, Zongliang / Kshirsagar, Madhura M. / Nguyen, Thanh / Suphavilai, Chayaporn / Neylon, Michael T. / Zhu, Liugen / Ratliff, Timothy / Chen, Jake Y. et al. | 2015
- i258
-
Inferring models of multiscale copy number evolution for single-tumor phylogeneticsChowdhury, Salim Akhter / Gertz, E. Michael / Wangsa, Darawalee / Heselmeyer-Haddad, Kerstin / Ried, Thomas / Schäffer, Alejandro A. / Schwartz, Russell et al. | 2015
- i268
-
Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discoverySpeicher, Nora K. / Pfeifer, Nico et al. | 2015
- i276
-
Phenome-driven disease genetics prediction toward drug discoveryChen, Yang / Li, Li / Zhang, Guo-Qiang / Xu, Rong et al. | 2015
- i284
-
MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer typesKim, Yoo-Ah / Cho, Dong-Yeon / Dao, Phuong / Przytycka, Teresa M. et al. | 2015
- i293
-
Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survivalSchissler, A. Grant / Gardeux, Vincent / Li, Qike / Achour, Ikbel / Li, Haiquan / Piegorsch, Walter W. / Lussier, Yves A. et al. | 2015
- i303
-
In silico phenotyping via co-training for improved phenotype prediction from genotypeRoqueiro, Damian / Witteveen, Menno J. / Anttila, Verneri / Terwindt, Gisela M. / van den Maagdenberg, Arn M.J.M. / Borgwardt, Karsten et al. | 2015
- i311
-
FERAL: network-based classifier with application to breast cancer outcome predictionAllahyar, Amin / de Ridder, Jeroen et al. | 2015
- i320
-
A generic methodological framework for studying single cell motility in high-throughput time-lapse dataSchoenauer Sebag, Alice / Plancade, Sandra / Raulet-Tomkiewicz, Céline / Barouki, Robert / Vert, Jean-Philippe / Walter, Thomas et al. | 2015
- i329
-
Comparing genomes with rearrangements and segmental duplicationsShao, Mingfu / Moret, Bernard M.E. et al. | 2015
- i339
-
MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidenceLiu, Ke / Peng, Shengwen / Wu, Junqiu / Zhai, Chengxiang / Mamitsuka, Hiroshi / Zhu, Shanfeng et al. | 2015
- i348
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Knowledge-driven geospatial location resolution for phylogeographic models of virus migrationWeissenbacher, Davy / Tahsin, Tasnia / Beard, Rachel / Figaro, Mari / Rivera, Robert / Scotch, Matthew / Gonzalez, Graciela et al. | 2015
- i357
-
Exploiting ontology graph for predicting sparsely annotated gene functionWang, Sheng / Cho, Hyunghoon / Zhai, ChengXiang / Berger, Bonnie / Peng, Jian et al. | 2015
- i365
-
Protein (multi-)location prediction: utilizing interdependencies via a generative modelSimha, Ramanuja / Briesemeister, Sebastian / Kohlbacher, Oliver / Shatkay, Hagit et al. | 2015
- i375
-
Using collective expert judgements to evaluate quality measures of mass spectrometry imagesPalmer, Andrew / Ovchinnikova, Ekaterina / Thuné, Mikael / Lavigne, Régis / Guével, Blandine / Dyatlov, Andrey / Vitek, Olga / Pineau, Charles / Borén, Mats / Alexandrov, Theodore et al. | 2015
- i385
-
Author Index| 2015