BOL: Related items

GPS DNA tracking - University of Sheffield

Sat, 10 May 2014 04:33:28 -0500

University of Sheffield geneticist and bioinformatics expert Dr Eran Elhaik demonstrates the power of his new DNA research, which allows people to discover their genetic homeland from 1000 years ago. Find out more about our biological research here http://www.sheffield.ac.uk/aps

Center for Molecular Dynamics Nepal (CMDN), Nepal

Wed, 23 Jul 2014 13:54:51 -0500

Center for Molecular Dynamics Nepal (CMDN), established 2007 prides itself as a research driven nongovernmental organization. Unlike other civil society organizations, CMDN is dedicated entirely to promoting research in the country. With its team of energetic and highly motivated experts, CMDN is now recognized as the leading public health and wildlife research organization of the country.

More at http://www.cmdn.org.np/main/index.php

Post-Doc Positions at the Institute of Evolution, University of Haifa, Haifa, Israel

Thu, 04 Sep 2014 03:59:38 -0500

We are looking for independent, motivated, diligent, laborious, dedicated Bioinformaticians as post-doctorate fellows for a project aimed at revealing the mechanisms of cancer-resistance and anti-cancer activity of the hypoxia-tolerant subterranean, blind mole-rat, Spalax along its underground evolutionary adaptations. Our project has captured the interest of the scientific community and we have ample financial support for the studies. Generous fellowships ($30K to $40K according to qualifications and performance) are available, immediately, for Post-Docs experts in bioinformatics with a background of good understanding biological questions. That is that can independently handle raw output data of RNA-seq / miR seq/ Genomic, analyze it and can interpret intelligently the relevant biological background. Outstanding candidates for PhD experienced in Bioinformatics will also be considered. Familiarity with cancer research is an advantage. Experience of writing manuscripts for publication and a publication record in relevant journals are expected. English skills both oral and written are required. American, Western-European or Israeli education is a significant benefit.

Our present objectives is to identify and isolate the substances secreted by Spalax cells, resolve with which components they interact that are active only on cancer cells, in order to unravel the biological mechanisms and pathways that evolved in Spalax cell machinery and ultimately lead to the death of cancer-cells. The study could attest to be a breakthrough in cancer research, using the long lived, hypoxia- and cancer-tolerant Spalax as a significant biological resource for biomedical research that hopefully could open new horizons in treatment and prevention of cancer in humans.

Contact: The applications should be submitted, together with extended CV and bibliography, summary of past accomplishments, and contact information of 3 referees, to Prof of Research Aaron Avivi (aaron@research.haifa.ac.il) AND Dr. Imad Shams (imadshams@gmail.com). (http://bit.ly/1lywShk) aaron@research.haifa.ac.il

More at http://evolution.haifa.ac.il/index.php/29-people/personal-websites/77-personal-site-avivi

Computer simulation of genetic mechanism !!

Jit — Sun, 13 Mar 2016 09:29:56 -0500

Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output. Simulation embodies the principle of ``learning by doing'' --- to learn about the system we must first build a model of some sort and then operate the model. The use of simulation is an activity that is as natural as a child who role plays. Children understand the world around them by simulating (with toys and figurines) most of their interactions with other people, animals and objects. As adults, we lose some of this childlike behavior but recapture it later on through computer simulation. To understand reality and all of its complexity, we must build artificial objects and dynamically act out roles with them. Computer simulation is the electronic equivalent of this type of role playing and it serves to drive synthetic environments and virtual worlds. Within the overall task of simulation, there are three primary sub-fields: model design, model execution and model analysis

Simulation models have become important tools in Bioinformatics studies. There are many reasons for this, but we emphasize three of the more important:

(1) they enable exploration of hypotheses, and as such, have become invaluable means to guide research;

(2) they are unique approaches to integrate (in the literal term of the word) biological knowledge, in the form of experimental results; and

(3) they enable connecting biology with other fields of study ranging from physiology to genomics;

This blog, and this software list, is intended to guide the potential user of simulation models.
It is not, in any way, meant to be comprehensive on the very diverse simulation tools that already exist, but focuses on mechanistic, dynamic models. Similarly, it is not meant to provide any coverage of the breadth of applications; however, for interested readers, we provide references to use as a possible starting point.

Simulation models are meant to answer questions which scientists have in a dynamic, quantitative, and often, a pictorial way. Much of the bioinformatics research and its applications, in particular, involve a large number of components, actors, and factors. Assembling these in a coherent framework may seem a daunting task, especially for beginners, and can lead to confusion, even for experienced scientists, especially if the objectives of such an exercise are not well defined. Followings are the list of tools bioinformatician may use to analyze and provide answers to complex biological mechanisms and related problems.

Software Resource	Brief Description and Homepage
Aladyn	Tools to investigate how demographic parameters, populations genetics and abiotic conditions affect the rate of adaptation http://www.katja-schiffers.eu/research.html
ALF	A Simulation Framework for Genome Evolution http://www.cbrg.ethz.ch/alf
ART	ART is a set of simulation tools to generate synthetic next-generation sequencing data by mimicking real sequencing process with empirical error models or quality profiles. http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
BAMSurgeon	Methods for realistic simulation of mutations in real data. https://github.com/adamewing/bamsurgeon
Bayesian Serial SimCoal	Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. http://www.stanford.edu/group/hadlylab/ssc/index.html
BaySICS	An integral platform with a graphical interface for statistical inference based on approximate Bayesian computation. https://sites.google.com/site/baysicsabc/
BEERS	BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data http://cbil.upenn.edu/beers/
BOTTLENECK	Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html
BottleSim	BottleSim is a computer simulation program for simulating the process of population bottlenecks http://chkuo.name/software/bottlesim.html
CASS	Protein Sequence Simulation https://liberles.cst.temple.edu/software/cass/index.html
CDPOP	CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior. http://cel.dbs.umt.edu/cdpop
Classical Genetics Simulator	Web-based simulation software http://www.cgslab.com/
CoaSim	CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. http://users-birc.au.dk/mailund/coasim/index.html
cosi	The cosi package is written in C and is available as a tar file. http://www.broadinstitute.org/~sfs/cosi/
CS-PSeq-Gen	A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen/
DAWG	An application designed to simulate the evolution of recombinant DNA sequences in continuous time http://scit.us/projects/dawg
Easypop	EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions http://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html
EggLib	EggLib is a C++/Python library and program package for evolutionary genetics and genomics. http://egglib.sourceforge.net/
EpiSIM	EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis https://sourceforge.net/projects/episimsimulator/files/
EvolSimulator	A simulation test bed for hypotheses of genome evolution http://acb.qfab.org/acb/evolsim/
EvolveAGene	A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions http://bellinghamresearchinstitute.com/software/index.html
fastsimcoal	A continuous-‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios http://cmpg.unibe.ch/software/fastsimcoal/
FastSLINK	Simulation of Marker and Phenotype Data in Pedigrees https://watson.hgen.pitt.edu/
FFPopSim	C++/Python library for population genetics. http://webdav.tuebingen.mpg.de/ffpopsim/
FLUX SIMULATOR	The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. http://sammeth.net/confluence/display/sim/home
forqs	Forward-in-time simulation of Recombination, Quantitative Traits, and Selection https://bitbucket.org/dkessner/forqs
ForSim	ForSim: A Forward Evolutionary Computer Simulation http://anth.la.psu.edu/research/weiss-lab/research/research
ForwSim	The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. http://badri-populationgeneticsimulators.blogspot.com/
FPG	Forward Population Genetic simulation https://bio.cst.temple.edu/~hey/software/software.htm#fpg
FREGENE	FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. http://www.ebi.ac.uk/projects/bargen
FIGG	FIGG is a genome simulation tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied mutations for use in analysis http://insilicogenome.sourceforge.net/
fwdpp	A C++ template library for implementing efficient forward simulations. http://molpopgen.github.io/fwdpp/
GAMETES	Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. http://sourceforge.net/projects/gametes/?source=navbar
GASP	Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. http://research.nhgri.nih.gov/gasp/
GCTA	Genome-wide Complex Trait Analysis http://www.complextraitgenomics.com/software/gcta/download.html
GemSIM	Next generation sequencing read simulator http://sourceforge.net/projects/gemsim/
GeneArtisan	Simulation of Markers in Case-Control Study Designs http://www.rannala.org/?page_id=241
GENOME	A rapid coalescent-based whole genome simulator http://www.sph.umich.edu/csg/liang/genome/
GenomePop2	GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. https://ritchielab.psu.edu/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla
GenomeSimla	GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested http://chgr.mc.vanderbilt.edu/genomesimla/
GENS2	Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. https://sourceforge.net/projects/gensim/
GWAsimulator	A rapid whole genome simulation program http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator
HAP-SAMPLE	An association simulator for candidate regions or genome scans http://www.hapsample.org/
HAPGEN	A simulator for the simulation of case control datasets at SNP markers https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
HapSim	A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients http://cran.r-project.org/web/packages/hapsim/index.html
HAPSIMU	A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model http://l.web.umkc.edu/liujian/
IBDsim	IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. http://raphael.leblois.free.fr/
indel-Seq-Gen	A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies http://bioinfolab.unl.edu/~cstrope/isg/
Indelible	A powerful and flexible simulator of biological evolution http://abacus.gene.ucl.ac.uk/software/indelible/
invertFREGENE	InvertFREGENE is a forward-in-time simulator of inversions in population genetic data http://www.ebi.ac.uk/projects/bargen/
kernalPop	A spatially explicit population genetic simulation engine http://cran.r-project.org/src/contrib/archive/kernelpop/
MaCS	Markovian Coalescent Simulator http://www-hsc.usc.edu/~garykche/
Marlin	Marlin provides a user-friendly interface for performing forward-in-time population genetic simulations. http://www.patrickmeirmans.com/software/marlin.html
Mason	A package for the simulation of nucleotide data. http://www.seqan.de/projects/mason/
mbs	modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html
Mendel's Accountant	Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine http://mendelsaccount.sourceforge.net/
MetaPopGen	Simulates genetics in large size metapopulations https://sites.google.com/site/marcoandrello/metapopgen
MetaSim	A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets http://ab.inf.uni-tuebingen.de/software/metasim/
mlcoalsim	Multilocus Coalescent Simulations http://code.google.com/p/mlcoalsim-v1/
ms	The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/source/mksamples.html
msHOT	The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/
msms	A coalescent Simlation tool with selection. http://www.mabs.at/ewing/msms/index.shtml
MySSP	A program for the simulation of DNA sequence evolution across a phylogenetic tree http://www.rosenberglab.net/software.html
Nemo	A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework. http://nemo2.sourceforge.net/
NetRecodon	Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography http://code.google.com/p/netrecodon/
OncoSimulR	BioConductor package for Forward Genetic Simulation of Cancer Progresion with Epistasis https://github.com/rdiaz02/oncosimul
PEDAGOG	Software for simulating eco-evolutionary population dynamics https://bcrc.bio.umass.edu/pedigreesoftware/node/5
phenosim	A tool to add phenotypes to simulated genotypes http://evoplant.uni-hohenheim.de/doku.php?id=software:software
PhyloSim	An R package for the Monte Carlo simulation of sequence evolution http://www.ebi.ac.uk/goldman-srv/phylosim/
pIRS	Profile-based Illumina pair-end reads simulator https://code.google.com/p/pirs/
ProteinEvolver	Simulation of protein evolution along phylogenies under structure-based substitution models http://code.google.com/p/proteinevolver/
QMSim	QTL and Marker Simulator http://www.aps.uoguelph.ca/~msargol/qmsim/
quantiNEMO	An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population http://www2.unil.ch/popgen/softwares/quantinemo/
RECOAL	Simulates new haplotype data from a reference population of haplotypes. ftp://popgen.usc.edu/
Recodon	Coalescent simulation of coding DNA sequences with recombination, migration and demography http://code.google.com/p/recodon/
rlsim	A package for simulating RNA-seq library preparation with parameter estimation http://bit.ly/rlsim-git
Rmetasim	Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R http://cran.r-project.org/web/packages/rmetasim/index.html
RNA Seq Simulator	RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator
Rose	Random model of sequence evolution http://bibiserv.techfak.uni-bielefeld.de/rose/
scrm	A coalescent simulator optimized for long sequences and large samples. https://scrm.github.io/
SelSim	SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection http://www.well.ox.ac.uk/~spencer/selsim/
Seq-Gen	An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. http://tree.bio.ed.ac.uk/software/seqgen/
SEQPower	Statistical power analysis for sequence-based association studies http://bioinformatics.org/spower/
SeqSIMLA	SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. http://seqsimla.sourceforge.net/
Serial NetEvolve	A flexible utility for generating serially-sampled sequences along a tree or recombinant network http://biorg.cis.fiu.edu/sne/
SFS_CODE	SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. http://sfscode.sourceforge.net/sfs_code/index/index.html
SIBSIM	Quantitative phenotype simulation in extended pedigrees http://sourceforge.net/projects/sibsim/
SimAdapt	A spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton. https://www.openabm.org/model/3137
SIMCOAL2	A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models http://cmpg.unibe.ch/software/simcoal2/
SimCopy	An R package simulating the evolution of copy number profiles along a tree. http://bit.ly/simcopy
SIMLA	SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. http://dmpi.duke.edu/simla-simulation-software-version-32
SimPed	A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures http://bioinformatics.org/simped/
Simprot	A program to simulate protein evolution by substitution, insertion and deletion http://www.uhnresearch.ca/labs/tillier/software.htm#3
SimRare	Rare variant simulation and analysis tool http://code.google.com/p/simrare/
simuGWAS	A forward-time simulator that simulates realistic samples for genome-wide association studies. http://simupop.sourceforge.net/cookbook/simugwas
simuPOP	simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. http://simupop.sourceforge.net/
SISSI	A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. http://www.cibiv.at/software/sissi/
SMARTPOP	Simulating Mating Alliance as a Reproductive Tactic for Populations http://smartpop.sourceforge.net/
SNPsim	Coalescent simulation of hotspot recombination http://code.google.com/p/phylosoftware/
SPIP	SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user http://swfsc.noaa.gov/textblock.aspx?division=fed&id=3434
Splatche	Spatial and Temporal Coalescences in Heterogeneous Environment http://www.splatche.com/
srv	Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. http://simupop.sourceforge.net/cookbook/simurarevariants
SUP	SLINK/FastSLINK utility program http://mlemire.freeshell.org/software.html
TreesimJ	A flexible, forward-time population genetic simulator http://code.google.com/p/treesimj/
Variant Simulation Tools	A simulation tool for post-GWAS genetic epidemiological studies using whole-genome or whole-exome next-gen sequencing data, with an emphasis on user-friendliness and reproducibility. http://varianttools.sourceforge.net/simulation/homepage
Vortex	VORTEX is an individual-based simulation model for population viability analysis (PVA). http://www.vortex9.org/vortex.html
Wessim	Whole Exome Sequencing SIMulator http://sak042.github.io/wessim/

The Kingsley Lab

Fri, 03 Jun 2016 09:55:10 -0500

The Molecular Basis of Vertebrate Evolution. Naturally occurring species show spectacular differences in morphology, physiology, behavior, disease susceptibility, and life span. Although the genomes of many organisms have now been completely sequenced, Kingsley lab still know relatively little about the specific DNA sequence changes that underlie interesting species-specific traits. Kingsley lab laboratory is using a combination of genetic and genomic approaches to identify the detailed molecular mechanisms that control evolutionary change in vertebrates.

Postdoctoral Research Assistant at RVC

Mon, 09 Jul 2018 00:47:38 -0500

This is a fixed term post for 24 months.

We wish to recruit a highly motivated, postdoctoral scientist to carry out a BBSRC funded project in the laboratory of Dr. Denis Larkin. The project is focused on developing and applying new methods and algorithms to study genome and chromosome evolution in mammals and other animals using whole-genome sequences and existing algorithms (e.g., Damas et al. Genome Res. 2017. 27(5):875-884; Kim et al., Proc Natl Acad Sci USA. 2013. 110 (5)). The post holder will use cutting edge computational and laboratory approaches to generate chromosomal assemblies for sequenced genomes, study chromosomal structures and differences between mammalian and other vertebrate genomes in attempt to identify species- and clade-specific genome signatures.

Applicants must have a Ph.D. and a track record of success, as indicated by first-author publications in international journals. They must possess excellent organisation skills and be capable of individual initiative and of interacting as part of a team. Applicants with extensive practical experience in bioinformatics or computer science, programming, visualization, handling of large data sets, high-performance computing are encouraged to apply. The post will involve collaboration with a wide range of academic partners both within the EU and worldwide.

Experience in programming, bioinformatics and comparative genome analysis is essential. Applicants should have a minimum of a degree and preferably a higher degree in a relevant subject.

The Royal Veterinary College has the largest range of veterinary, para-veterinary and animal science undergraduate and postgraduate courses of any veterinary school in the world and is one of the largest veterinary schools in Europe.

Prospective applicants are encouraged to contact Dr. Denis Larkin, Comparative Biomedical Sciences Department on +442071211906 or email: dlarkin@rvc.ac.uk

We offer a generous reward package.

For further information and to apply on-line please visit our website: www.rvc.ac.uk
Job reference CBS-0084-18

https://jobs.rvc.ac.uk/Vacancy.aspx?ref=CBS-0084-18

Blaxter Lab

Thu, 19 Nov 2020 08:05:28 -0600

Using these high quality genomes we explore

the evolutionary history of genes and species, building phylogenetic trees of life
the contrasting roles of horizontal gene transfer and introgression in shaping evolution
the biology of symbioses, especially symbioses between eukaryotes and bacteria, and between parasites and their hosts
the processes that drive the evolution of pattern in the structure of chromosomes
the diversity of meiofauna, particularly tardigrades, nematodes and other Ecdysozoa
the genomics of extremophilia

More at https://www.sanger.ac.uk/group/blaxter-group/

Online resources on must-read papers in evolutionary biology

BioStar — Fri, 26 Jul 2024 01:39:14 -0500

Online resources on must-read papers in evolutionary biology, for a literature club.

Below is a summary of all answers that we received.

All the best,

Jana and Xiaoyan

1.       *Nick Barton:*

- The textbook "Evolution" by Nick Barton, with resources for
  exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J.
  A., Goldstein, D. B., & Patel, N. H. (2007). Evolution. Cold Spring
  Harbor Laboratory Press.

- Papers from a course named "Classics in Evolutionary Biology":

Evolutionary Synthesis
1. Haldane, J. B. S. 1932. The causes of evolution. Longmans. New York.
   (esp. Ch. IV).
2. Fisher, R. A. 1930. The genetical theory of natural selection. Oxford
   University Press, Oxford. Selected Sections - Fundamental Theorem.

Genetic Variation
1a. Lewontin, R. C., and J. L. Hubby. 1966. A molecular approach to
the study of genic heterozygosity in natural populations. II. Amount
of variation and degree of heterozygosity in natural populations of
Drosophila pseudoobscura. Genetics. 54:595-609.

1b. Sachidandam et al. 2001. A map of human genome sequence variation
containing 1.42 million single nucleotide polymorphisms. 409: 928-33.

2. Wright S., Dobzhansky T., Hovanitz W. 1942 Genetics of natural
populations VII The allelism of lethals in the third chromosome of
Drosophila pseudoobscura. Genetics 27: 363-394.

Recombination and evolution
1. Hill, W. G., and A. Robertson. 1966. The effect of linkage on limits
to artificial selection. Genet. Res. 8:269-294.

2. Maynard Smith and Haigh. 1974. The hitch-hiking effect of a favourable
gene. Genet. Res. 23: 23-35.

Understanding sequence variation
1. Begun D. J., Aquadro C. F., 1992 Levels of naturally occurring DNA
polymorphism correlate with recombination rate in Drosophila melanogaster.
Nature 356: 519-520.

2. Green R. E., Reich D., Pääbo S., 2010 A draft sequence of the
Neandertal genome. Science 328: 710-722.

Quantitative Genetics:  variation in complex traits
1. Galton F., 1877 Typical laws of heredity. Nature 15: 492-495-
512-514- 532-533.

2. Turelli M., 1984 Heritable genetic variation via
mutation-selection balance: Lerch's Zeta meets the abdominal
bristle. Theor. Popul. Biol. 25: 138-193.

Quantitative Genetics:  finding the genes
1. Shrimpton A. E., Robertson A., 1988 The Isolation of polygenic factors
controlling bristle score in Drosophila melanogaster II Distribution of
third chromosome bristle effects within chromosome sections. Genetics
118: 445-459.

2. Boyle E. A., Li Y. I., Pritchard J. K., 2017 An expanded view of
complex traits: from polygenic to omnigenic. Cell 169: 1177-1186.

Neutral Evolution
1. Kimura, M. 1968. Evolutionary rate at the molecular level. Science.
217:624-626.

2a. Kern A. D., Hahn M. W., 2018 The Neutral Theory in Light of Natural
Selection. Molecular Biology and Evolution 110: 21077-6.

2b. Jensen J. D., Payseur B. A., Stephan W., Aquadro C. F., Lynch M.,
Charlesworth D., Charlesworth B., 2018 The importance of the Neutral Theory
in 1968 and 50 years on: a response to Kern and Hahn 2018. Evolution 112:
2109-4.

2c. Ellegren & Galtier. 2016. Determinants of genetic diversity. Nature
Reviews Genetics.

Mutation and Genetic Variability
1. Luria, S. E., and M. Delbrück. 1943. Mutations of Bacteria from Virus
Sensitivity to Virus Resistance. Genetics. 28(6):491-511.

2. Hill, W G. 1982. "Rates of Change in Quantitative Traits From Fixation
of New Mutations." Proceedings of the National Academy of Sciences (U.S.A.)
79: 142-45.

Testing for selection
1. McDonald & Kreitman. 1991. Adaptive protein evolution at the Adh locus
in Drosophila. Nature.

2. Begun, et al. Mol. Biol. Evol. 16, 1816-1819 (1999).

3. Siddiq et al. 2016. Experimental test and refutation of a classic case
of molecular adaptation in Drosophila melanogaster.  Nature Ecology &
Evolution.

The shifting balance
1. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and
selection in evolution. Proceedings of the VI International Congress of
Genetics: 1. pp 356-366.

2. Coyne, J.A., N.H. Barton, and M. Turelli. 1997. A critique of Wright's
shifting balance theory of evolution.  Evolution 51: 643-671.

3. Barton. 2016. Sewall Wright on Evolution in Mendelian Populations and
the "Shifting Balance". Genetics.

Evolution of Sex
1.  Muller, H.J. 1964. The relation of recombination to mutational advance.
Mutation Res. 1(1):2-9

2. McDonald et al. 2016. Sex speeds adaptation by altering the dynamics of
molecular evolution. Nature.

Kin Selection, Cooperation, and Conflict
1. Hamilton, W. D. 1964. The genetical evolution of social behaviour I.
Journal of Theoretical Biology. 7:1-52.

2. Trivers, R. L. 1974 Parent-offspring conflict. American Zoologist.
14(1):249-264.

Sexual Selection
1. Zahavi, A. 1975. Mate selection - a selection of a handicap. J. Theor.
Biol. 53:205-214.

2. Kirkpatrick, M., and Ryan, M.J. 1991. The evolution of mating
preferences and the paradox of the lek. Nature. 350:33-38.

Fitness Landscapes
1. Dean, A. 1995. A Molecular Investigation of Genotype by Environment
Interactions. Genetics. 139:19-33.

2. Costanzo et al. 2010. The Genetic Landscape of a Cell. Science.

Speciation
1. Coyne, J. A., and H. A. Orr. 1989. Patterns of speciation in Drosophila.
Evolution. 43:362-381.

2. Corbett-Detig et al. 2013. Genetic incompatibilities are widespread
within species. Nature.

2.       *Marcos Antezana:*

Valen, L. v. 1975. Energy and Evolution. University of Chicago, Department
of Biology.

3.       *Remco Folkertsma:*

1. The work by Hopi Hoekstra on local adaptation and oldfield mice

2. Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller,
I., ... & Wolf, J. B. (2014). The genomic landscape underlying phenotypic
integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414.

4.       *Joshka Kaufmann and Leslie Turner*

They offer us a link to 'papers every evolutionary biologist should read',
the papers are collected by Leslie Turner.
https://static1.squarespace.com/static/53e8cb7ce4b02c4bc3aeeee4/t/5ab8fcb670a6ad55c67fcdf4/1522072758665/EvoBioClassicsRefList.pdf

5.       *Sarah Stockwell*

Matt Ridley collected classic papers in evolutionary biology and printed
part of these papers in his book Evolution (see Matt Ridley. Evolution
(Univ. of Oxford Press, 2nd edition, 2004))

Postdoctoral Fellow in Genomics and Comparative Genomics

Thu, 09 Apr 2026 02:12:32 -0500

Environnement de travail (Work environment):
The successful candidate will join a dynamic research group working
on the ecology and evolution of host'parasite'environment
interactions in non-model organisms, particularly snail vectors and
its trematode parasites. She/He will conduct genomic analyses aimed at
understanding host'parasite coevolution and the genetic architecture
of resistance in the invasive snail Pseudosuccinea columella to the
zoonotic parasite Fasciola hepatica. This thematic line is embedded
within the regional scientific project InvaSnail financed by the
ExposUM initiative from the Montpellier. The position is based in
Montpellier, a vibrant scientific hub in Southern France internationally
recognized for excellence in ecology and evolutionary biology. The IHPE
laboratory provides a collaborative research environment with access
to high-performance computing facilities, sequencing platforms, and
strong interdisciplinary interactions across research institutions in
the Montpellier area. University

Main mission:

Develop and implement strategies for whole-genome sequencing of non-model
species
Generate high-quality de novo genome assemblies using short- and long-read
sequencing technologies
Perform genome annotation and structural/functional characterization
Conduct comparative genomic analyses across related species or populations
Design and implement genome-wide association studies (GWAS) to identify
loci associated with phenotypic or adaptive traits
Integrate genomic, phenotypic, and environmental datasets
Contribute to the development of reproducible bioinformatics pipelines

Lead the genomic component of the research project
High-molecular-weight DNA extraction optimization
Long-read genome assembly (PacBio HiFi / ONT)
Genome polishing and quality assessment (BUSCO, QUAST)
Structural and functional annotation
Variant discovery (SNPs, indels, SVs)
Population genomic analyses (FST, demographic inference)
Mixed-model GWAS accounting for structure
Workflow development (Snakemake/Nextflow)
HPC-based pipeline implementation
Publish results in peer-reviewed journals
Present findings at international conferences
Collaborate with experimental and computational team members
Contribute to project development
Mentor graduate students when appropriate

More at https://evol.mcmaster.ca/brian/evoldir/PostDocs//MontpellierU.ComparativeGenomics

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Jit — Fri, 24 Aug 2018 09:50:01 -0500

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/