BOL: Related items

Troyanskaya Lab

Tue, 04 Feb 2020 06:40:36 -0600

The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods for systems-level pathway modeling through integrative analysis of genome-scale datasets. We apply these approaches in studying challenging biological problems, such as how pathways function in diverse cell types and how they change dynamically.

https://function.princeton.edu/

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

Shruti Paniwala — Tue, 28 Jun 2022 07:29:08 -0500

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))

The Story of You: ENCODE and the human genome

Sat, 24 Aug 2013 18:49:03 -0500

Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE

Immune response to cancer cells! AWESOME

Fri, 20 Sep 2013 06:20:47 -0500

Awesome viddeo explaining the way in which the antibody, HuLuc 63, appears to induce anti-tumor effects by binding to a protein that is only expressed on the surface of myeloma cells. This initiates antibody-dependent cellular cytotoxicity activity that kills myeloma cells and leaves healthy cells intact.

Microbiome - Making better use of bacteria

Mon, 14 Oct 2013 16:22:42 -0500

Bacterial cells outnumber human cells 10-to-1 in the average person. Bacterial genes outnumber human genes 100-to-1. Mayo Clinic and the Center for Individualized Medicine are working to understand these diverse populations and design better diagnoses and therapies that can be individualized to the patient. Diseases, such as clostridium difficile, celiac disease, and gluten sensitivities, are being studied. We're also gaining more insight in the many connections between digestive bacteria and autoimmune disorders, like diabetes, rheumatoid arthritis and multiple sclerosis.

Immunology in the Gut Mucosa

Mon, 17 Mar 2014 11:10:29 -0500

The gut mucosa hosts the body's largest population of immune cells. Nature Immunology in collaboration with Arkitek Studios have produced an animation unravelling the complexities of mucosal immunology in health and disease. Nature Immunology homepage: http://www.nature.com/ni/index.html Nature has full responsibility for all editorial content, including NatureVideo content. This content is editorially independent of sponsors.

Introduction to programming. Write short programs that generate graphics and animation.

Ram Yash Pal — Thu, 14 Aug 2014 23:29:04 -0500

Introduction to programming. Write short programs that generate graphics and animation.

http://funprogramming.org/

An entire genome written in lab

Rahul Nayak — Fri, 25 Oct 2013 09:43:03 -0500

This is the first time ever the genetic code has been fundamentally changed. The breakthrough is a huge step forward in synthetic biology and opens up the possibility of turning re-coded bacteria into biofactories, capable of producing potent new forms of protein that could fight disease or generate sustainable materials.

More @ http://news.yale.edu/2013/10/17/researchers-rewrite-entire-genome-and-add-healthy-twist

News Reference: Yale news

Image Source: Sciencedaily.

Postodoc in Computational/Systems Biology and Machine Learning

Wed, 09 Apr 2014 20:47:57 -0500

One profile of Computational/Systems Biology and Machine Learning at Postdoc level is needed at the Laboratory of Immunobiology of Neurological Disorders led by Cinthia Farina, Institute of Experimental Neurology, Ospedale San Raffaele, Milano. The projects of interest for this application involve research on translational bioinformatics in complex human disorders.

You have a PhD in Computational Science, Bioinformatics, or equivalent.

Especially relevant skills for the profile are:
1. In-depth understanding and implementation of methods and development of
algorithms for statistical and machine learning classification, clustering, predictive
modelling.
2. Experience on transcriptomics and clinical data analysis, in particular gene regulatory networks, protein interactomes, development of diagnostic tools.

3. Solid experience with data mining, bioinformatics programming and statistics for bioinformatics.
4. Flexibility and willing to work across multiple projects and technology in a rapidly evolving scientific context.

Candidates with programming/scripting experience are also welcome. In particular, proficiency in one or more mainstream programming languages (C, C++, Java, Python, Perl, etc.), together with the understanding of relational database design and SQL/DBMS systems (e.g. MySQL, PHP, Oracle).
Experience with the analysis of next-generation sequencing data is a plus.
Clear demonstration of experience in analysis and modelling of omics and clinical data must be provided.

Interested candidates should send to farina.cinthia@hsr.it:

1. CV (please show evidences of relevant titles, projects, courses, references, etc.)
2. One page with a list of research topics (i.e. ongoing projects)
3. earliest availability
4. 2-3 contact names

Assistant Professor at SARDAR PATEL UNIVERSITY

Mon, 21 Apr 2014 21:03:55 -0500

SARDAR PATEL UNIVERSITY
Centre for Interdisciplinary Studies in Science and Technology

No.: SPU/CISST/Advt./2014-15/519

ADVERTISEMENT for Teaching Positions (Contractual)

Applications for the following Contractual Teaching Position are invited for Centre for Interdisciplinary Studies in Science and Technology (CISST), Sardar Patel University:

2. Assistant Professor (ONE) (Contractual)

For the subject of Bioinformatics

Qualifications:

(I) Good academic record as defined by the concerned university with at least 55 % marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master’s level

(II) Ph.D. degree in the concerned subject or in a relevant interdisciplinary subject
from an Indian University or NET/SLET clearance Contractual appointment carries a total Fixed Emoluments of Rs. 30,000/- p.m without any assurance of permanent Positions and related benefits.

An Application Form in prescribed Performa, available on University Website: www.spuvvn.edu should be filled in completely in Twelve Copies with self attested copies of certificates of qualifications and experience. Only one copy of each mark sheet be attached with the first copy of the application form. All 12 (Twelve) Application forms should be sent to Registrar’s office along with Demand Draft of Application form fee of Rs. 250/- (Non-refundable) in favour of “REGISTRAR, SARDAR PATEL UNIVERSITY, VALLABH VIDYANAGAR”. The S.C. and S.T. category candidates need not to pay Application fee.

Applicants who are in service should apply through their present employers. Candidates called for interview shall be required to attend at their own cost.

In absence of suitable candidate, the University may relax the eligibility criteria, for conditional appointment.

The last date of receipt of application by the University is 30th April, 2014

Advertisement: www.spuvvn.edu/careers/CISST%20Advt.%20April%202014.pdf