Paulo Nuin › Comments

Definitely! - Mr. Gunn

Muchas excellentos - Graham Steel

How many of you have a professional programming qualification? Either from an educational institution (e.g. a CS degree) or something like Sun Java certification? Is it even possible, useful or desirable to get "recognised" qualifications in other programming languages? Or are most of us self-taught? - Neil Saunders

I have no certification, just a master's in Bioinformatics where I was taught Java, Linux and R. I taught myself Ruby. I've got no interest in certification and I think Chris Wansworth's short essay is a good guide to follow - https://gist.github.com/0a2655a... . I think this echoes the same sentiments expressed above. - Michael Barton

Journal of molecular evolution, Vol. 39, No. 3. (September 1994), pp. 306-314. Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the "discrete gamma model," uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous distribution. The second method, called "fixed-rates model", classifies sites into several classes according to their rates predicted assuming the star tree.... - Paulo Nuin

Science, Vol. 294, No. 5550. (14 December 2001), pp. 2310-2314. 10.1126/science.1065889 John Huelsenbeck, Fredrik Ronquist, Rasmus Nielsen, Jonathan Bollback - Paulo Nuin

Molecular Phylogenetics and Evolution, Vol. 17, No. 2. (November 2000), pp. 231-243. The rate of evolutionary change associated with a character determines its utility for the reconstruction of phylogenetic history. For a given age of lineage splits, we examine the information content of a character to assess the magnitude and range of an optimal rate of substitution. On the one hand an optimal transition rate must provide sufficiently many character changes to distinguish subclades, whereas on the other hand changes must be sufficiently rare that reversals on a single branch (and hence homoplasy) are uncommon. In this study, we evolve binary characters over three tree topologies with fixed branch lengths, while varying transition rate as a parameter. We use the character state distribution obtained to measure the “information content” of a character given a transition rate. This is done with respect to several criteria—the probability of obtaining the correct tree using parsimony,... - Paulo Nuin

Journal of Molecular Evolution, Vol. 44, No. 1. (24 January 1997), pp. 112-119. Abstract. A method is presented for estimating the transition/transversion ratio (TI/TV), based on phylogenetically independent comparisons. TI/TV is a parameter of some models used in phylogeny estimation intended to reflect the fact that nucleotide substitutions are not all equally likely. Previous attempts to estimate TI/TV have commonly faced three problems: (1) few taxa; (2) nonindependence among pairwise comparisons; and (3) multiple hits make the apparent TI/TV between two sequences decrease over time since their divergence, giving a misleading impression of relative substitution probabilities. We have made use of the time dependency, modeling how the observed TI/TV changes over time and extrapolating to estimate the “instantaneous” TI/TV—the relevant parameter for phylogenetic inference. To illustrate our method, TI/TV was estimated for two mammalian mitochondrial genes. For 26 pairs of cytochrome... - Paulo Nuin

Molecular Phylogenetics and Evolution, Vol. 16, No. 3. (September 2000), pp. 317-330. Multiple sequence alignment is discussed in light of homology assessments in phylogenetic research. Pairwise and multiple alignment methods are reviewed as exact and heuristic procedures. Since the object of alignment is to create the most efficient statement of initial homology, methods that minimize nonhomology are to be favored. Therefore, among all possible alignments, the one that satisfies the phylogenetic optimality criterion the best should be considered the best alignment. Since all homology statements are subject to testing and explanation this way, consistency of optimality criteria is desirable. This consistency is based on the treatment of alignment gaps as character information and the consistent use of a cost function (e.g., insertion–deletion, transversion, and transition) through analysis from alignment to phylogeny reconstruction. Cost functions are not subject to testing via... - Paulo Nuin

Cladistics, Vol. 14, No. 2. (1998), pp. 193-200. Using outgroup(s) is the most frequent method to root trees. Rooting through unconstrained simultaneous analysis of several outgroups is a favoured option because it serves as a test of the supposed monophyly of the ingroup. When contradiction occurs among the characters of the outgroups, the branching pattern of basal nodes of the rooted tree is dependent on the order of the outgroups listed in the data matrix, that is, on the prime outgroup (even in the case of exhaustive search). Different equally parsimonious rooted trees (=cladograms) can be obtained by permutation of prime outgroups. An alternative to a common implicit practice (select one outgroup to orientate the tree) is that the accepted cladogram is the strict consensus of the different equally parsimonious rooted trees. The consensus tree is less parsimonious but is not hampered with extra assumption such as the choice of one outgroup (or more) among the initial number of... - Paulo Nuin

Wot no http://www.citeulike.org ? Which one is betamax, which one VHS? http://en.wikipedia.org/wiki... - Duncan Hull

because they do not have a Pr machine ... - Paulo Nuin

Cool article - looks really similar to the Channel 4 one though! - Euan

Confirmed! :) - Ricardo Vidal

I´m around ... - Paulo Nuin

the links are still bad ... - Paulo Nuin

Why install/configure it then? - Benjamin Tseng

Skype is the only app that can correctly do video calls in my laptop (maybe kopete/amsn have some issues with V4L). I also have found that TeamSpeak is very useful for small groups as you can install a private server for use of your lab, research group, etc. - Marcos de Carvalho

Bioinformatics (Oxford, England) (7 November 2008) SUMMARY: The amount of genomic sequence data being generated and made available through public databases continues to increase at an ever-expanding rate. Downloading, copying, sharing and manipulating these large data sets is becoming difficult and time-consuming for researchers. We need to consider using advanced compression techniques as part of a standard data format for genomic data. The inherent structure of genome data allows for more efficient lossless compression than can be obtained through the use of generic compression programs. We present a series of techniques that in combination reduces a single genome to a size small enough to be sent as an email attachment. AVAILABILITY: Our algorithms are implemented in C++ and are freely available from http://www.ics.uci.edu/~xhx.... CONTACT: xhx@ics.uci.edu or chenli@ics.uci.edu. Scott Christley, Yiming Lu, Chen Li, Xiaohui Xie - Paulo Nuin

What happened? (Or didn't happen?) - Chris Lasher

win7! Been running it since beta came out and now have the final version (out ahead of time by our uni) on all my work machines. Best OS for me so far (and I've tried most of them). - Björn Brembs

Sent! - Walter Jessen

Thanks a lot! - Paulo Nuin

Evolution, Vol. 9999, No. 9999. (2009) How often do the early stages of speciation occur in the presence of gene flow? To address this enduring question, a number of recent papers have used computational approaches, estimating parameters of simple divergence models from multilocus polymorphism data collected in closely related species. Applications to a variety of species have yielded extensive evidence for migration, with the results interpreted as supporting the widespread occurrence of parapatric speciation. Here, we conduct a simulation study to assess the reliability of such inferences, using a program that we recently developed MCMC estimation of the isolation-migration model allowing for recombination (MIMAR) as well as the program isolation-migration (IM) of Hey and Nielsen (2004). We find that when one of many assumptions of the isolation2013migration model is violated, the methods tend to yield biased estimates of the parameters, potentially lending spurious support for... - Paulo Nuin

Bioinformatics (Oxford, England) (25 August 2009), btp515. MOTIVATION: With the availability of many 'omics' data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology platforms is becoming crucial to unravel the relationships between different biological functional levels. However, the development of such an analysis is a major computational and technical challenge as most approaches suffer from high data dimensionality. New methodologies need to be developed and validated. RESULTS: integrOmics efficiently performs integrative analyses of two types of 'omics' variables that are measured on the same samples. It includes a regularized version of Canonical Correlation Analysis to enlighten correlations between two data sets, and a sparse version of Partial Least Square regression that includes simultaneous variable selection in both data sets. The usefulness of both approaches has been demonstrated... - Paulo Nuin

Nature genetics, Vol. advance online publication (30 August 2009) Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable owing to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. We estimate that, on average, 73-87 genes vary in copy number between any two individuals and find that these genic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based... - Paulo Nuin

BMC Bioinformatics, Vol. 10, No. 1. (2009), 280. BACKGROUND:The ability to generate transcriptional data on the scale of entire genomes has been a boon both in the improvement of biological understanding and in the amount of data generated. The latter, the amount of data generated, has implications when it comes to effective storage, analysis and sharing of these data. A number of software tools have been developed to store, analyze, and share microarray data. However, a majority of these tools do not offer all of these features nor do they specifically target the commonly used two color Agilent DNA microarray platform. Thus, the motivating factor for the development of EDGE3 was to incorporate the storage, analysis and sharing of microarray data in a manner that would provide a means for research groups to collaborate on Agilent-based microarray experiments without a large investment in software-related expenditures or extensive training of end-users.RESULTS:EDGE3 has been developed... - Paulo Nuin

"Ideally publishers should help on the extraction, maybe adding better metadata to the pdfs, even creating better filenames. But we know they won't do that if there's no clear commercial benefit, so we have to rely on Google's mammoth structure to actually spend some time working on it, or expect that that Mendeley's PR gets halted and allow them to spend some time actually coding. About my harsh critics of Mendeley, they are not without merit. First, it's a PR-only-software with horrible usability and even worse performance. Second, the hype. And third, the attempted censorship of my critics. But that's just me." - Paulo Nuin

PLoS computational biology, Vol. 5, No. 9. (25 September 2009), e1000520. As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. The introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. Here we introduce a Bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. By implementing character mapping in a Bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. Standard Markov model inference is extended with a stochastic search variable... - Paulo Nuin

BMC Bioinformatics, Vol. 10, No. 1. (22 September 2009), 303. BACKGROUND:One of the most neglected areas of biomedical Text Mining (TM) is the development of systems based on carefully assessed user needs. We have recently investigated the user needs of an important task yet to be tackled by TM --- Cancer Risk Assessment (CRA). Here we take the first step towards the development of TM technology for the task: identifying and organizing the scientific evidence required for CRA in a taxonomy which is capable of supporting extensive data gathering from biomedical literature.RESULTS:The taxonomy is based on expert annotation of 1297 abstracts downloaded from relevant PubMed journals. It classifies 1742 unique keywords found in the corpus to 48 classes which specify core evidence required for CRA. We report promising results with inter-annotator agreement tests and automatic classification of PubMed abstracts to taxonomy classes. A simple user test is also reported in a near real-world CRA... - Paulo Nuin

Bioinformatics (Oxford, England) (7 September 2009), btp527. MOTIVATION: Next-generation parallel sequencing technologies produce large quantities of short sequence reads. Due to experimental procedures various types of artifacts are commonly sequenced alongside the targeted RNA or DNA sequences. Identification of such artifacts is important during the development of novel sequencing assays and for the downstream analysis of the sequenced libraries. RESULTS: Here we present TagDust, a program identifying artifactual sequences in large sequencing runs. Given a user-defined cutoff for the false discovery rate (FDR), TagDust identifies all reads explainable by combinations and partial matches to known sequences used during library preparation. We demonstrate the quality of our method on sequencing runs performed on Illumina's Genome Analyzer platform. AVAILABILITY: Executables and documentation are available from http://genome.gsc.riken.jp/osc.... CONTACT:... - Paulo Nuin

BMC Bioinformatics, Vol. 10, No. 1. (19 September 2009), 298. BACKGROUND:To effectively apply evolutionary concepts in genomic-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted. RESULTS:Here, we present a new software library, PhyloPattern, for automating tree manipulations and analysis. PhyloPattern includes three main modules, that address essential tasks in high-throughput phylogenetic tree analysis: node annotation, pattern matching, and tree comparison. PhyloPattern thus allows the programmer to focus on: i) the use of predefined or user defined annotation functions to perform immediate or deferred evaluation of node properties, ii) the search for user-defined patterns in large phylogenetic trees, iii) the pairwise comparison of trees by dynamically generating patterns from one tree and applying them... - Paulo Nuin

PLoS computational biology, Vol. 5, No. 9. (11 September 2009), e1000502. With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only mismatches, but also insertions and deletions. Current evaluations indicate, however, that very different error models apply to the novel high-throughput sequencing methods. While the most frequent error-type in Illumina reads are mismatches, reads produced by 454's GS FLX predominantly contain insertions and deletions (indels). Even though 454 sequencers are able to produce longer reads, the method is frequently applied to small RNA (miRNA and siRNA) sequencing. Fast and accurate matching in particular of short reads with diverse errors is therefore a pressing practical problem. We introduce a matching model for short reads that can, besides mismatches, also cope with indels. It addresses different error models. For... - Paulo Nuin

PLoS biology, Vol. 7, No. 9. (15 September 2009), e1000197. Peter Lawrence - Paulo Nuin

Nature reviews. Genetics, Vol. 10, No. 10. (01 October 2009), pp. 681-690. Bayesian statistical methods have recently made great inroads into many areas of science, and this advance is now extending to the assessment of association between genetic variants and disease or other phenotypes. We review these methods, focusing on single-SNP tests in genome-wide association studies. We discuss the advantages of the Bayesian approach over classical (frequentist) approaches in this setting and provide a tutorial on basic analysis steps, including practical guidelines for appropriate prior specification. We demonstrate the use of Bayesian methods for fine mapping in candidate regions, discuss meta-analyses and provide guidance for refereeing manuscripts that contain Bayesian analyses. Matthew Stephens, David Balding - Paulo Nuin

BMC Bioinformatics, Vol. 10, No. 1. (2009), 313. BACKGROUND:Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource. Here we characterize the current and prospective contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate... - Paulo Nuin

"That Mendeley page is nauseating. And why would they keep Ricardo's My Biotech Life "review" there when he's a paid employee of the company? The problem of extracting metadata from publications is a problem too hard for Mendeley's staff to understand. They are too busy praising themselves and seeing ways to improve their failed PR machine. It's sad that Google is not investing hard on this type of problem, it would be a godsend." - Paulo Nuin

Algorithms for Molecular Biology, Vol. 1, No. 1. (24 October 2006), 19. BACKGROUND:The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for the RNA alignment problem, as was demonstrated in the first RNA alignment benchmark published so far. For example, the twilight zone - the similarity range where alignment quality drops drastically - starts at 60 % for RNAs in comparison to 20 % for proteins. In this study we enhance the previous benchmark.RESULTS:The RNA sequence sets in the benchmark database are taken from an increased number of RNA families to avoid unintended impact by using only a few families. The size of sets varies from 2 to 15 sequences to assess the influence of the number of sequences on program performance. Alignment quality is scored by two measures: one takes into account only nucleotide matches, the other measures... - Paulo Nuin