Literature DB >> 24916345

A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals.

Giovanni Strona1, Domenico Nappo1, Francesco Boccacci1, Simone Fattorini2, Jesus San-Miguel-Ayanz1.   

Abstract

A well-known problem in numerical ecology is how to recombine presence-absence matrices without altering row and column totals. A few solutions have been proposed, but all of them present some issues in terms of statistical robustness (that is, their capability to generate different matrix configurations with the same probability) and their performance (that is, the computational effort that they require to generate a null matrix). Here we introduce the 'Curveball algorithm', a new procedure that differs from existing methods in that it focuses rather on matrix information content than on matrix structure. We demonstrate that the algorithm can sample uniformly the set of all possible matrix configurations requiring a computational effort orders of magnitude lower than that required by available methods, making it possible to easily randomize matrices larger than 10(8) cells.

Year:  2014        PMID: 24916345     DOI: 10.1038/ncomms5114

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  32 in total

1.  Comprehensive single-cell transcriptional profiling of a multicellular organism.

Authors:  Junyue Cao; Jonathan S Packer; Vijay Ramani; Darren A Cusanovich; Chau Huynh; Riza Daza; Xiaojie Qiu; Choli Lee; Scott N Furlan; Frank J Steemers; Andrew Adey; Robert H Waterston; Cole Trapnell; Jay Shendure
Journal:  Science       Date:  2017-08-18       Impact factor: 47.728

2.  RNA-protein coevolution study of Gemin5 uncovers the role of the PXSS motif of RBS1 domain for RNA binding.

Authors:  Rosario Francisco-Velilla; Azman Embarc-Buh; Sergio Rangel-Guerrero; Sudipto Basu; Sudip Kundu; Encarnacion Martinez-Salas
Journal:  RNA Biol       Date:  2020-05-31       Impact factor: 4.652

3.  What makes a reaction network "chemical"?

Authors:  Stefan Müller; Christoph Flamm; Peter F Stadler
Journal:  J Cheminform       Date:  2022-09-19       Impact factor: 8.489

4.  Randomizing bipartite networks: the case of the World Trade Web.

Authors:  Fabio Saracco; Riccardo Di Clemente; Andrea Gabrielli; Tiziano Squartini
Journal:  Sci Rep       Date:  2015-06-01       Impact factor: 4.379

5.  Topological constraints on network control profiles.

Authors:  Colin Campbell; Justin Ruths; Derek Ruths; Katriona Shea; Réka Albert
Journal:  Sci Rep       Date:  2015-12-22       Impact factor: 4.379

6.  Efficient randomization of biological networks while preserving functional characterization of individual nodes.

Authors:  Francesco Iorio; Marti Bernardo-Faura; Andrea Gobbi; Thomas Cokelaer; Giuseppe Jurman; Julio Saez-Rodriguez
Journal:  BMC Bioinformatics       Date:  2016-12-20       Impact factor: 3.169

7.  Does a Species' Extinction-Proneness Predict Its Contribution to Nestedness? A Test Using a Sunbird-Tree Visitation Network.

Authors:  Charles A Nsor; Hazel M Chapman; William Godsoe
Journal:  PLoS One       Date:  2017-01-19       Impact factor: 3.240

8.  Niche overlap and species co-occurrence patterns in carabid communities of the northern Chinese steppes.

Authors:  Noelline Tsafack; Xinpu Wang; Yingzhong Xie; Simone Fattorini
Journal:  Zookeys       Date:  2021-06-16       Impact factor: 1.546

9.  FALCON: a software package for analysis of nestedness in bipartite networks.

Authors:  Stephen J Beckett; Chris A Boulton; Hywel T P Williams
Journal:  F1000Res       Date:  2014-08-06

10.  Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors.

Authors:  Jaegil Kim; Kent W Mouw; Paz Polak; Lior Z Braunstein; Atanas Kamburov; David J Kwiatkowski; Jonathan E Rosenberg; Eliezer M Van Allen; Alan D'Andrea; Gad Getz
Journal:  Nat Genet       Date:  2016-04-25       Impact factor: 38.330

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