1. sequenced and analyzed the genome of the invasive red fire ant Solenopsis invicta (PNAS 2011)

2. discovered that a fundamental social trait in this species (how many queens are accepted in the colony) is determined by variants of a social chromosome (Nature 2013).

3. described the gene expression changes that occur in a virgin queen when she is given the opportunity of replacing her mother (Mol Ecol 2010).

Homepage: http://yannick.poulet.org/

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

• Importantly, this study found many large population groups from India in which individuals were more related to each other by descent. These groups are similar to the Finnish population group where many disease gene discoveries were made. The Finnish-equivalent Indian groups are going to be a great resource for disease gene discovery and they will aid in target identification, drug development and disease management. 

• This study has identified many genetic variants that are specific to Indian population groups that were previously not known. Some of these are common variants in the Indian groups, but when first identified by previous studies from India involving smaller sample size, they were thought to be disease causing (for example in diabetes) as they were not represented in the Eurocentric variant database. 

• Several variants that pre-dispose individuals to higher cancer risk were identified in this study. Once this part of the work is expanded, the data from this can be used to screen individuals to understand the disease risk and provide appropriate monitoring and proactive treatment. Similarly, variants linked to increase in adverse effect in individuals for certain drugs were found. Understanding this will allow doctors to provide alternate safer drugs to such patients.

More at https://www.nature.com/articles/s41586-019-1793-z

https://www.nature.com/nature/volumes/576/issues/7785

Deciphering Life at the Molecular Level DNA sequencing is the key that opens the door to invaluable knowledge. By understanding the genes that make up Chilean species, we unravel the secrets of their evolution, their resistance and their adaptation to the environment. In a world where biodiversity faces constant threats, sequencing becomes crucial for the conservation and understanding of our natural heritage.

Involving Everyone: A Nationwide Effort The 1000 Genomes Chile Project is not just a task for scientists. It is a country-wide effort that seeks the participation of everyone: from citizens to the government to the private sector. We believe in the importance of sharing knowledge, involving society in the selection of species to sequence, in monitoring progress and in applying the results to preserve our environment.

Address of the bookmark: https://1000genomas.cl/

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Address of the bookmark: http://genomicus.biologie.ens.fr/genomicus-90.01/cgi-bin/search.pl

(i) can be used for HGT detection in both prokaryotes and eukaryotes,

(ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and

(iii) is fully automated (requires minimal human intervention), as well as very easy to install and run. 

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626719/

Address of the bookmark: http://ecogenomics.github.io/CheckM/

CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - groups of genes that are consistently located close to each other, in the same order, across a wide range of taxa. CSBFinder incorporates an efficient algorithm that identifies CSBs in large genomic datasets. The discovered CSBs are ranked according to a probabilistic score and clustered to families according to their gene content similarity.

Address of the bookmark: https://github.com/dinasv/CSBFinder

Initial versions of PhiSpy were written by

Sajia Akhter (sajia@stanford.edu) Edwards Bioinformatics Lab

Improvements, bug fixes, and other changes were made by

Katelyn McNair Edwards Bioinformatics Lab and Przemyslaw Decewicz DEMB at the University of Warsaw

Address of the bookmark: https://github.com/linsalrob/PhiSpy

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl