Differences

This shows you the differences between two versions of the page.

Link to this comparison view

the_list_of_computational_biology_papers_in_nature_methods [2018/06/25 15:26] (current)
Line 1: Line 1:
 + 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.