BOL: Related items

Mike Ritchie Lab

Wed, 02 Oct 2013 15:25:45 -0500

Mike Ritchie Lab primary research focus is the detection of susceptibility genes for common diseases such as cancer, diabetes, hypertension, and cardiovascular disease, among others. The approaches will involve the development and application of new statistical methods with a focus on the detection of gene-gene interactions associated with human disease.

Gene expression and protein expression patterns between normal and non-normal tissues is a growing area of research that may lead to the identification of candidate genes for understanding the etiology of common, complex diseases.

Lab homepage @ http://ritchielab.psu.edu/ritchielab/

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

Manolis Kellis Lab

Sun, 31 Jan 2016 20:51:06 -0600

A major focus of our lab is understanding the effects of genetic variation on molecular phenotypes and human disease. We develop methods for integrating diverse functional genomic datasets of transcription, chromatin modifications, regulator binding, and their changes across multiple conditions to interpret genetic associations, identify causal variants, and predict the effects of genetic perturbations.

More at http://compbio.mit.edu

Andi

Jit — Fri, 13 May 2016 05:16:35 -0500

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full

16th Congress of the European Society for Evolutionary Biology (ESEB)

Thu, 22 Dec 2016 08:08:37 -0600

Abstract submissions for our upcoming symposium on the Genomics of Adaptation that will take place as part of the 16th Congress of the European Society for Evolutionary Biology (ESEB). The conference will take place from August 20th - August 25th, 2017 in Groningen, the Netherlands.

SYMPOSIUM DESCRIPTION: Genomics of Adaptation [S16] Model organisms for life-history research are mainly studied in the lab where functional genetics is assessable. In general, however, knowledge about their eco-evolutionary dynamics, such as biotic interactions, is rare. By contrast, in organisms for which the ecology and adaptation strategies in the field are well known, we typically lack the appropriate genetic tools to investigate functionality. Advances in genomics and statistics as well as investments in evolutionary model organisms are now providing access to putatively adaptive genome-wide variation within species from across the tree of life. In this symposium, we focus on integrating life-history biology, genetics and evolutionary ecology in the genomics era.

We wish to (1) highlight the role of genetic architecture of complex traits, such as adaptations to biotic interactions or life-history traits; (2) contrast this to morphological traits which are generally thought to have a less complex genetic architecture; and (3) discuss the opportunities and drawbacks of specific model systems.

INVITED SPEAKERS: Josephine Pemberton, University of Cambridge (http://bit.ly/2hJWytJ ) Peter Tiffin, University of Minnesota (http://bit.ly/2hK7HuS )

ABSTRACT SUBMISSION The deadline for abstract submission is January 10, 2017. For more information and to submit abstracts online, please visit: http://bit.ly/2fBXlvN We look forward to an exciting symposium and seeing you all in Groningen! Sincerely, Ben Blackman, UC Berkeley Maaike de Jong, University of Bristol Bart Pannebakker, Wageningen University Noah Whiteman, UC Berkeley Jelle Zandveld, Wageningen University

Vicoso group

Wed, 02 Feb 2022 02:51:27 -0600

The Vicoso group investigates how sex chromosomes evolve over time, and what biological forces are driving their patterns of differentiation.

The Vicoso group is interested in understanding several aspects of the biology of sex chromosomes, and the evolutionary processes that shape their peculiar features. By combining the use of next-generation sequencing technologies with studies in several model and non-model organisms, they can address a variety of standing questions, such as: Why do some Y chromosomes degenerate while others remain homomorphic, and how does this relate to the extent of sexual dimorphism of the species? What forces drive some species to acquire global dosage compensation of the X, while others only compensate specific genes? What are the frequency and molecular dynamics of sex-chromosome turnover?

More at https://ist.ac.at/en/research/vicoso-group/
http://pub.ist.ac.at/~bvicoso/

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))

Genomic Basis of Evolutionary Innovations (GEvol)

BioStar — Sat, 06 Dec 2025 06:11:00 -0600

The Priority Programme (SPP 2349) funded by German Science Foundation (DFG) started 2022: „Genomic Basis of Evolutionary Innovations (GEvol)“

GEvol is unique as it will use, for the first time, a large taxonomic group to focus on one goal: to characterise the dynamics and mechanisms of genomic innovations underlying novel traits using comparative evolutionary genomics (and related data).
Thus, projects participating in GEvol we will ask fundamental evolutionary questions such as:
1. At what level is evolution repeatable?
2. How does genomic plasticity interfere with phenotypic plasticity during evolution?
3. How do inter- and intra-specific interactions influence genomic architectures?
4. How predictable is phenotypic variation given some knowledge about the dynamics and mechanisms of underlying genome evolution?

Address of the bookmark: https://g-evol.uni-muenster.de/open-positions/