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—the_list_of_computational_biology_papers_in_nature_methods [2018/06/25 12:26] (current) – created - external edit 127.0.0.1
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 + The following articles were published in Nature Methods in 2015 in anti-chronological order. Application notes, brief communications, and alike are mostly excluded.\\ \\ 
  
 +  - Walzthoeni, Thomas, et al. "xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry." //Nature [[http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3631.html|methods]]// 12.12 (2015): 1185-1190.
 +  - Rubin-Delanchy, Patrick, et al. "Bayesian cluster identification in single-molecule localization microscopy data." //Nature [[http://www.nature.com/nmeth/journal/v12/n11/full/nmeth.3612.html|methods]]// (2015).
 +  - Levet, Florian, et al. "SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data." //Nature [[http://www.nature.com/nmeth/journal/v12/n11/full/nmeth.3579.html|methods]]// 12.11 (2015): 1065-1071.
 +  - Schmid-Burgk, Jonathan L., and Veit Hornung. "BrowserGenome. org: web-based RNA-seq data analysis and visualization." //Nature [[http://www.nature.com/nmeth/journal/v12/n11/full/nmeth.3615.html|methods]]// 12.11 (2015): 1001-1001.
 +  - Zhou, Wanding, et al. "TransVar: a multilevel variant annotator for precision **genomics**." //Nature [[http://www.nature.com/nmeth/journal/v12/n11/full/nmeth.3622.html|methods]]// 12.11 (2015): 1002-1003.
 +  - Wiwie, Christian, Jan Baumbach, and Richard Röttger. "Comparing the performance of biomedical clustering methods." //Nature [[http://www.nature.com/nmeth/journal/v12/n11/full/nmeth.3583.html|methods]] //12.11 (2015): 1033-1038.
 +  - Noble, William Stafford. "Mass spectrometrists should search only for peptides they care about."//Nature [[http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3450.html|Methods]]// 12.7 (2015): 605-608.
 +  - Ewing, Adam D., et al. "Combining tumor **genome simulation** with crowdsourcing to benchmark somatic single-nucleotide-variant detection."//Nature [[http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3407.html|methods]]// (2015).
 +  - Potrzebowski, Wojciech, and Ingemar André. "Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement." //Nature [[http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3399.html|methods]]// (2015).
 +  - Zhang, Qing, and Xinshu Xiao. "**Genome** sequence-independent identification of RNA editing sites." //Nature [[http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3314.html|methods]]// 12.4 (2015): 347-350.
 +  - Jain, Miten, et al. "Improved data analysis for the MinION nanopore sequencer." //Nature [[http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3290.html|methods]]//(2015).
 +  - Kim, Daehwan, Ben Langmead, and Steven L. Salzberg. "HISAT: a fast spliced **aligner** with low memory requirements." //Nature [[http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3317.html|methods]]// 12.4 (2015): 357-360.
 +  - Viner, Coby, and Michael M. Hoffman. "Determining the epigenome using DNA alone."//Nature [[http://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3291.html|methods]]// 12.3 (2015): 191-192.\\  A computational method predicts epigenomic marks and DNA methylation patterns from DNA sequence.
 +  - Zhu, Qian, et al. "Targeted exploration and analysis of large cross-platform human **transcriptomic** compendia." //Nature [[http://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3249.html|methods]]// 12.3 (2015): 211-214. Describes [[http://seek.princeton.edu/|SEEK]]'s, which identifies the datasets in which a list of query genes are coexpressed.
 +  - Hart, Yuval, et al. "Inferring biological tasks using Pareto analysis of high-dimensional data." //Nature [[http://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3254.html|methods]]// 12.3 (2015): 233-235.
 +  - Tsou, Chih-Chiang, et al. "DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics." //Nature [[http://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3255.html|methods]]// 12.3 (2015): 258-264.
 +  - Whitaker, John W., Zhao Chen, and Wei Wang. "**Predicting** the human epigenome from DNA motifs." //Nature [[http://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3065.html|methods]]// 12.3 (2015): 265-272.
 +  - Huber, Wolfgang, et al. "Orchestrating high-throughput genomic analysis with Bioconductor."//Nature [[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html|methods]]// 12.2 (2015): 115-121.
 +  - Taşan, Murat, et al. "Selecting causal genes from genome-wide association studies via functionally coherent **subnetworks**." //Nature [[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html|methods]]// 12.2 (2015): 154-159.
 +  - Johnson, Graham T., et al. "cellPACK: a virtual mesoscope to model and visualize structural systems biology." //Nature [[http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3204.html|methods]]// 12.1 (2015): 85-91.