- MrBayes 3: Bayesian phylogenetic inference under mixed models
Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 752 36 Uppsala, Sweden
Bioinformatics 19:1572-4. 2003
..g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters...
- Inference of population structure using multilocus genotype data
J K Pritchard
Department of Statistics, University of Oxford, United Kingdom
Genetics 155:945-59. 2000
..g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html...
- A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
LIRMM, CNRS, 161 rue Ada, 34392, Montpellier Cedex 5, France
Syst Biol 52:696-704. 2003
..This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/...
- PAML 4: phylogenetic analysis by maximum likelihood
Department of Biology, Galton Laboratory, University College London, London, UK
Mol Biol Evol 24:1586-91. 2007
..The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html)...
- A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
B M Bolstad
Group in Biostatistics, University of California, Berkeley, CA 94720, USA
Bioinformatics 19:185-93. 2003
..Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations...
- Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
Genetics 164:1567-87. 2003
..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu...
- Prediction of total genetic value using genome-wide dense marker maps
T H Meuwissen
Research Institute of Animal Science and Health, 8200 AB Lelystad, The Netherlands
Genetics 157:1819-29. 2001
..It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval...
- ProtTest: selection of best-fit models of protein evolution
Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
Bioinformatics 21:2104-5. 2005
..We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment...
- Application of phylogenetic networks in evolutionary studies
Daniel H Huson
Center for Bioinformatics ZBIT, Tubingen University, Tubingen, Germany
Mol Biol Evol 23:254-67. 2006
..Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees...
- R/qtl: QTL mapping in experimental crosses
Karl W Broman
Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
Bioinformatics 19:889-90. 2003
- A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
Nat Genet 38:203-8. 2006
..As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping...
- Bayesian coalescent inference of past population dynamics from molecular sequences
A J Drummond
Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 22:1185-92. 2005
- CAP3: A DNA sequence assembly program
Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA
Genome Res 9:868-77. 1999
..PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints...
- The structure of haplotype blocks in the human genome
Stacey B Gabriel
Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
Science 296:2225-9. 2002
..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
Nathaniel D Heintzman
Ludwig Institute for Cancer Research, University of California San Diego UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653 USA
Nat Genet 39:311-8. 2007
..Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide a new tool for the functional annotation of the human genome...
- RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
Department of Computer Science, Technical University of Munich Boltzmannstrasse 3, D 85748 München, Germany
Bioinformatics 21:456-63. 2005
..Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa...
- A new multipoint method for genome-wide association studies by imputation of genotypes
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Nat Genet 39:906-13. 2007
..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
- Not so different after all: a comparison of methods for detecting amino acid sites under selection
Sergei L Kosakovsky Pond
Antiviral Research Center, University of California San Diego, USA
Mol Biol Evol 22:1208-22. 2005
..We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments...
- HyPhy: hypothesis testing using phylogenies
Sergei L Kosakovsky Pond
Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
Bioinformatics 21:676-9. 2005
..AVAILABILITY: http://www.hyphy.org CONTACT: firstname.lastname@example.org SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
- Human MicroRNA targets
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
PLoS Biol 2:e363. 2004
..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
- Microsatellites: simple sequences with complex evolution
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE 752 36 Uppsala, Sweden
Nat Rev Genet 5:435-45. 2004
- JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Jan Christian Bryne
Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N 5008 Bergen, Norway
Nucleic Acids Res 36:D102-6. 2008
..JASPAR is available at http://jaspar.genereg.net...
- Approximate Bayesian computation in population genetics
Mark A Beaumont
School of Animal and Microbial Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, United Kingdom
Genetics 162:2025-35. 2002
..We also compare the relative efficiency of inferences obtained using methods based on summary statistics with those obtained directly from the data using MCMC...
- A comparison of bayesian methods for haplotype reconstruction from population genotype data
Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
Am J Hum Genet 73:1162-9. 2003
..The new algorithm is included in the software package PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/software.html)...
- A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec Canada
Mol Biol Evol 21:1095-109. 2004
- Efficient methods to compute genomic predictions
P M Vanraden
Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 2350, USA
J Dairy Sci 91:4414-23. 2008
..Actual gains may differ because the simulation did not account for linkage disequilibrium in the base population or selection in subsequent generations...
- The evolutionary fate and consequences of duplicate genes
Department of Biology, University of Oregon, Eugene, OR 97403, USA
Science 290:1151-5. 2000
..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
- Improved microbial gene identification with GLIMMER
A L Delcher
Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA
Nucleic Acids Res 27:4636-41. 1999
..When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses <1% of known genes...
- Generating samples under a Wright-Fisher neutral model of genetic variation
Richard R Hudson
Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA
Bioinformatics 18:337-8. 2002
..The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models...
- Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
Mol Biol Evol 22:2472-9. 2005
..Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power...
- Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
Sharon R Browning
Department of Statistics, The University of Auckland, Auckland, New Zealand
Am J Hum Genet 81:1084-97. 2007
..1 days of computing time, with 99% of masked alleles imputed correctly. Our method is implemented in the Beagle software package, which is freely available...
- Statistical properties of new neutrality tests against population growth
Sebastian E Ramos-Onsins
Departament de Genetica, Universitat de Barcelona, E 08071 Barcelona, Spain
Mol Biol Evol 19:2092-100. 2002
..The behavior of the R(2) test is superior for small sample sizes, whereas F(S) is better for large sample sizes. We also show that some popular statistics based on the mismatch distribution are very conservative...
- Genomic selection: prediction of accuracy and maximisation of long term response
Department of Primary Industries, University of Melbourne, Victoria, Australia
Genetica 136:245-57. 2009
..This index varies the weight given to a marker according to its frequency such that markers where the favourable allele has low frequency receive more weight in the index...
- Hsp90 as a capacitor for morphological evolution
S L Rutherford
Howard Hughes Medical Institute, University of Chicago, Illinois 60637, USA
Nature 396:336-42. 1998
..This provides a plausible mechanism for promoting evolutionary change in otherwise entrenched developmental processes...
- Darwinian evolution can follow only very few mutational paths to fitter proteins
Daniel M Weinreich
Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Science 312:111-4. 2006
..This implies that the protein tape of life may be largely reproducible and even predictable...
- Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection
Y X Fu
Human Genetics Center, University of Texas, Houston 77225, USA
Genetics 147:915-25. 1997
..We show that Fu and Li's tests are among the most powerful tests against background selection. Implications of these results are discussed...
- Preservation of duplicate genes by complementary, degenerative mutations
Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
Genetics 151:1531-45. 1999
..Cooke et al. 1997 (p. 362)..
- MicroRNA targeting specificity in mammals: determinants beyond seed pairing
Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Mol Cell 27:91-105. 2007
..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
- MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals
Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Mol Cell 26:753-67. 2007
..Our results strongly suggest that coordinated transcriptional and miRNA-mediated regulation is a recurrent motif to enhance the robustness of gene regulation in mammalian genomes...
- Bayesian phylogenetic analysis of combined data
Johan A A Nylander
Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, SE 752 36 Uppsala, Sweden
Syst Biol 53:47-67. 2004
..Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates...
- Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits
Social, Genetics and Developmental Psychiatry Research Centre, Institute of Psychiatry, King s College London, De Crespigny Park, UK
Bioinformatics 19:149-50. 2003
..A website for performing power calculations for the design of linkage and association genetic mapping studies of complex traits...
- Variance stabilization applied to microarray data calibration and to the quantification of differential expression
Department of Molecular Genome Analysis, German Cancer Research Center, INF 280, Heidelberg, 69120, Germany
Bioinformatics 18:S96-104. 2002
..We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays...
- Efficiency and power in genetic association studies
Paul I W de Bakker
Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6818, Boston, Massachusetts 02114 2790, USA
Nat Genet 37:1217-23. 2005
..Power is robust to the completeness of the reference panel from which tags are selected. These findings have implications for prioritizing tag SNPs and interpreting association studies...
- An algorithm for progressive multiple alignment of sequences with insertions
European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom
Proc Natl Acad Sci U S A 102:10557-62. 2005
..Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms...
- GARD: a genetic algorithm for recombination detection
Sergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
Bioinformatics 22:3096-8. 2006
..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments...
- RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
Program of Computational Genomics, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, A P 565 A, Cuernavaca, Morelos 62100, Mexico
Nucleic Acids Res 36:D120-4. 2008
..The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine...
- Is a new and general theory of molecular systematics emerging?
Scott V Edwards
Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Evolution 63:1-19. 2009
- Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
Mol Biol Evol 23:7-9. 2006
- Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions
Department Biologie II, Ludwig Maximilians Universitat, Grosshadernerstr 2, Planegg Martinsried, Germany
Nat Rev Genet 8:104-15. 2007
..Understanding how the dynamic nature of the positioning of genetic material in the nuclear space and the higher-order architecture of the nucleus are integrated is therefore essential to our overall understanding of gene regulation...
- MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?
Department de Biologie, Universite Laval, Ste Foy, Quebec, Canada
J Evol Biol 16:363-77. 2003
..We conclude this review by proposing several directions where future research is needed...
- Use of within-array replicate spots for assessing differential expression in microarray experiments
Gordon K Smyth
Walter and Eliza Hall Institute of Medical Research, Melbourne, Vic, Australia
Bioinformatics 21:2067-75. 2005
..The usual practice is to average the duplicate or triplicate results for each probe before assessing differential expression. This results in the loss of valuable information about genewise variability...
- Bayesian inference of recent migration rates using multilocus genotypes
Gregory A Wilson
Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
Genetics 163:1177-91. 2003
- A model-based method for identifying species hybrids using multilocus genetic data
E C Anderson
Department of Statistics, University of Washington, Seattle, Washington 98195, USA
Genetics 160:1217-29. 2002
..We demonstrate the method on allozyme data from two species of hybridizing trout, as well as on two simulated data sets...
- Solving the riddle of codon usage preferences: a test for translational selection
Mario dos Reis
School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
Nucleic Acids Res 32:5036-44. 2004
..Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model...
- Engineering stability in gene networks by autoregulation
EMBL, Structures and Biocomputing, Heidelberg, Germany
Nature 405:590-3. 2000
..Here we have designed and constructed simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli and we show the gain of stability produced by negative feedback...
- Gene prediction with a hidden Markov model and a new intron submodel
Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
Bioinformatics 19:ii215-25. 2003
..Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons...
- A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility
Jason H Moore
Computational Genetics Laboratory, Department of Genetics, Dartmouth Hitchcock Medical Center, One Medical Center Dr, 706 Rubin Bldg, HB7937, Lebanon, NH 03756, USA
J Theor Biol 241:252-61. 2006
..We then apply this strategy to detecting, characterizing, and interpreting epistatic models in a genetic study (n = 500) of atrial fibrillation and show that both classification and model interpretation are significantly improved...
- A fine-scale map of recombination rates and hotspots across the human genome
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Science 310:321-4. 2005
- Chromosome inversions, local adaptation and speciation
Section of Integrative Biology, University of Texas, Austin 78712, USA
Genetics 173:419-34. 2006
..We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests...
- An integrative genomics approach to infer causal associations between gene expression and disease
Eric E Schadt
Rosetta Inpharmatics, Seattle, Washington 98109, USA
Nat Genet 37:710-7. 2005
..We also demonstrate the utility of this approach by identifying and experimentally validating the involvement of three new genes in susceptibility to obesity...
- Network motifs: theory and experimental approaches
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
Nat Rev Genet 8:450-61. 2007
..Here I review network motifs and their functions, with an emphasis on experimental studies. Network motifs in other biological networks are also mentioned, including signalling and neuronal networks...
- Neighbor-net: an agglomerative method for the construction of phylogenetic networks
McGill Centre for Bioinformatics, Montreal, Quebec, Canada
Mol Biol Evol 21:255-65. 2004
..and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package...
- TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
Department of Statistics, University of Munich, Ludwigstr, 33, D 80539 Munich, Germany
BMC Evol Biol 4:18. 2004
..Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience...
- Bayesian selection of continuous-time Markov chain evolutionary models
M A Suchard
Department of Biomathematics, UCLA School of Medicine, Los Angeles, CA 90095-7088, USA
Mol Biol Evol 18:1001-13. 2001
- Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
School of Computational Science and Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 4120, USA
Bioinformatics 22:341-5. 2006
..Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance...
- Using genomic data to unravel the root of the placental mammal phylogeny
William J Murphy
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A and M University, College Station, TX 77843, USA
Genome Res 17:413-21. 2007
..We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny...
- The impact of recombination on nucleotide substitutions in the human genome
Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Universite Lyon 1, CNRS, UMR 5558, Villeurbanne, France
PLoS Genet 4:e1000071. 2008
..Our results also shed light on variations in the rate of crossover relative to non-crossover events, along chromosomes and according to sex, and also on the conservation of hotspot density between human and chimp...
- Identifying differentially expressed genes using false discovery rate controlling procedures
Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
Bioinformatics 19:368-75. 2003
..The procedures are studied using simulated microarray data, and their performance is examined relative to their ease of implementation...
- Bayesian inference of epistatic interactions in case-control studies
Department of Statistics, The Pennsylvania State University, Thomas Building 422A, University Park, Pennsylvania 16802, USA
Nat Genet 39:1167-73. 2007
- BioGRID: a general repository for interaction datasets
Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
Nucleic Acids Res 34:D535-9. 2006
..User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID...
- Trends between gene content and genome size in prokaryotic species with larger genomes
Konstantinos T Konstantinidis
Center for Microbial Ecology and Departments of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824 1325, USA
Proc Natl Acad Sci U S A 101:3160-5. 2004
..These trends suggest that larger genome-sized species may dominate in environments where resources are scarce but diverse and where there is little penalty for slow growth, such as soil...
- Recombination and linkage disequilibrium in Arabidopsis thaliana
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
Nat Genet 39:1151-5. 2007
..LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms...
- An evolutionary view of human recombination
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Rev Genet 8:23-34. 2007
- Mechanisms of, and barriers to, horizontal gene transfer between bacteria
Christopher M Thomas
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
Nat Rev Microbiol 3:711-21. 2005
..However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition...
- Using Bayesian networks to analyze expression data
School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
J Comput Biol 7:601-20. 2000
..We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998)...
- OGG1 initiates age-dependent CAG trinucleotide expansion in somatic cells
Irina V Kovtun
Department of Pharmacology and Experimental Therapeutics, Mayo Clinic and Foundation, 200 First Street SW, Rochester, Minnesota 55905, USA
Nature 447:447-52. 2007
..Age-dependent CAG expansion provides a direct molecular link between oxidative damage and toxicity in post-mitotic neurons through a DNA damage response, and error-prone repair of single-strand breaks...
- Stochastic mRNA synthesis in mammalian cells
Courant Institute of Mathematical Sciences, New York University, New York, New York, USA
PLoS Biol 4:e309. 2006
..These results demonstrate that gene expression in mammalian cells is subject to large, intrinsically random fluctuations and raise questions about how cells are able to function in the face of such noise...
- Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests
Departamento de Bioquimica, Genética e Inmunología, Facultad de Biologia, Universidad de Vigo, Vigo 36200, Spain
Syst Biol 53:793-808. 2004
..To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus(genus Carabus) ground beetles described by Sota and Vogler (2001)...
- Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level
A L Hughes
Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
Heredity (Edinb) 99:364-73. 2007
..Rather adaptive phenotypes are much more likely to result from other causes, including single amino-acid changes; deletion or silencing of genes or changes in the pattern of gene expression...
- A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
Travis N Mavrich
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 18:1073-83. 2008
..3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping...
- Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix
The Ministry of Education MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing, People s Republic of China
Heredity (Edinb) 95:221-7. 2005
..With its efficiency and accuracy, the M(eff) method provides an alternative to computationally intensive methods such as the permutation test...
- A synthetic oscillatory network of transcriptional regulators
M B Elowitz
Department of Molecular Biology and Physics, Princeton University, New Jersey 08544, USA
Nature 403:335-8. 2000
..Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks...
- Genomic scans for selective sweeps using SNP data
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genome Res 15:1566-75. 2005
..Evidence for selective sweeps is also found in many other regions, including genes known to be associated with disease risk such as DPP10 and COL4A3...
- A slow RNA polymerase II affects alternative splicing in vivo
Manuel De la Mata
Laboratorio de Fisiologia y Biologia Molecular, Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, Buenos Aires, Argentina
Mol Cell 12:525-32. 2003
..These results provide a direct proof for the elongation control of alternative splicing in vivo...
- A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders
Jennifer A Lee
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, 77030, USA
Cell 131:1235-47. 2007
..We propose that complex duplication and deletion rearrangements associated with PMD, and potentially other nonrecurrent rearrangements, may be explained by this replication-based mechanism...
- The distribution of fitness effects of new mutations
Centre for the Study of Evolution, University of Sussex, Brighton, BN1 9QG, UK
Nat Rev Genet 8:610-8. 2007
- Hybrid speciation
Galton Laboratory, Department of Biology, University College London, 4 Stephenson Way, London NW1 2HE, UK
Nature 446:279-83. 2007
..Now, new genetic evidence suggests that hybrid speciation, even without polyploidy, is more common in plants and also animals than we thought...
- A relationship matrix including full pedigree and genomic information
INRA, UR631 SAGA, BP 52627, 32326 Castanet Tolosan, France
J Dairy Sci 92:4656-63. 2009
..Numerical examples and alternative expressions are discussed. Matrix H is suitable for iteration on data algorithms that multiply a vector times a matrix, such as preconditioned conjugated gradients...
- A microRNA in a multiple-turnover RNAi enzyme complex
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 825, 364 Plantation Street, Worcester, MA 01605, USA
Science 297:2056-60. 2002
..Each let-7-containing complex directs multiple rounds of RNA cleavage, which explains the remarkable efficiency of the RNAi pathway in human cells...
- Active genes dynamically colocalize to shared sites of ongoing transcription
Cameron S Osborne
Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, CB2 4AT, UK
Nat Genet 36:1065-71. 2004
..Thus, rather than recruiting and assembling transcription complexes, active genes migrate to preassembled transcription sites...
- Comparisons of dN/dS are time dependent for closely related bacterial genomes
Eduardo P C Rocha
Atelier de BioInformatique, Universite Paris VI, 75005 Paris, France
J Theor Biol 239:226-35. 2006
..We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points...
- Defining genetic interaction
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 105:3461-6. 2008
..Additionally, we show that the Additive and Log definitions, each commonly used in population genetics, lead to differing conclusions related to the selective advantages of sexual reproduction...
- Bayesian estimation of concordance among gene trees
Department of Statistics, University of Wisconsin, USA
Mol Biol Evol 24:412-26. 2007
..We demonstrate the method on a set of 106 genes from 8 yeast species...
- Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation
Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
Curr Biol 13:784-9. 2003
..These results indicate that DCL1 mRNA is subject to negative feedback regulation through the activity of a miRNA...
- Transcriptional regulation in constraints-based metabolic models of Escherichia coli
Markus W Covert
Department of Bioengineering, University of California, San Diego, La Jolla, California 92093 0412, USA
J Biol Chem 277:28058-64. 2002
..This combined metabolic/regulatory model is thus an important step toward the goal of synthesizing genome-scale models that accurately represent E. coli behavior...
- Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
Nat Genet 33:245-54. 2003
..The extent to which environmental effects can provoke epigenetic responses represents an exciting area of future research...
- Selection on codon bias
Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
Annu Rev Genet 42:287-99. 2008
- Testing for phylogenetic signal in comparative data: behavioral traits are more labile
Simon P Blomberg
Department of Biology, University of California, Riverside, California 92521, USA
Evolution 57:717-45. 2003
- Heritability in the genomics era--concepts and misconceptions
Peter M Visscher
Queensland Institute of Medical Research, Royal Brisbane Hospital Post Office, Brisbane 4029, Queensland, Australia
Nat Rev Genet 9:255-66. 2008
..Recent reports of substantial heritability for gene expression and new estimation methods using marker data highlight the relevance of heritability in the genomics era...
- Testing congruence in phylogenomic analysis
Jessica W Leigh
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
Syst Biol 57:104-15. 2008
..Investigating phylogenomic data sets for conflicting signals has the potential to both improve phylogenetic accuracy and inform our understanding of genome evolution...
- Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon
S L Martin
Department of Cellular and Structural Biology, University of Colorado School of Medicine, Denver, Colorado 80262, USA
Mol Cell Biol 21:467-75. 2001
..These findings suggest a role for L1 ORF1p in mediating nucleic acid strand transfer steps during L1 reverse transcription...