Publications

@article{Nag2023,

title = {Whole genomes from bacteria collected at diagnostic units around the world 2020},

author = {Sidsel Nag and Gunhild Larsen and Judit Szarvas and Laura Elmlund Kohl Birkedahl and G\'{a}bor M\'{a}t\'{e} Guly\'{a}s and Wojchiech Jakub Ciok and Timmie Mikkel Lagermann and Silva Tafaj and Susan Bradbury and Peter Collignon and Denise Daley and Victorien Dougnon and Kafayath Fabiyi and Boubacar Coulibaly and Ren\'{e} Demb\'{e}l\'{e} and Georgette Nikiema and Natama Magloire and Isidore Juste Ouindgueta and Zenat Zebin Hossain and Anowara Begum and Deyan Donchev and Mathew Diggle and Lee Ann Turnbull and Simon L\'{e}vesque and Livia Berlinger and Kirstine Kobberoe Sogaard and Paula Diaz Guevara and Carolina Duarte Valderrama and Panagiota Maikanti and Jana Amlerova and Pavel Drevinek and Jan Tkadlec and Milica Dilas and Achim Kaasch and Henrik Torkil Westh and Mohamed Azzedine Bachtarzi and Wahiba Amhis and Carolina Elisabeth Sat\'{a}n Salazar and Jos\'{e}Eduardo E. Villacis and M\'{a}ria Angeles Dominguez L\'{u}zon and D\'{a}maris Berbel Palau and Claire Duployez and Maxime Paluche and Solomon Asante-Sefa and Mie Moller and Margaret Ip and Ivana Marekovi\'{c} and Agnes P\'{a}l-Sonnevend and Clementiza Elvezia Cocuzza and Asta Dambrauskiene and Alexandre Macanze and Anelsio Cossa and In\'{a}cio Mandomando and Philip Nwajiobi-Princewill and Iruka N. Okeke and Aderemi O. Kehinde and Ini Adebiyi and Ifeoluwa Akintayo and Oluwafemi Popoola and Anthony Onipede and Anita Blomfeldt and Nora Elisabeth Nyquist and Kiri Bocker and James Ussher and Amjad Ali and Nimat Ullah and Habibullah Khan and Natalie Weiler Gustafson and Ikhlas Jarrar and Arif Al-Hamad and Viravarn Luvira and Wantana Paveenkittiporn and Irmak Baran and James C. L. Mwansa and Linda Sikakwa and Kaunda Yamba and Rene Sjogren Hendriksen and Frank Moller Aarestrup},

url = {https://pubmed.ncbi.nlm.nih.gov/37717051/},

doi = {10.1038/S41597-023-02502-7},

issn = {2052-4463},

year  = {2023},

date = {2023-01-01},

journal = {Scientific data},

volume = {10},

issue = {1},

publisher = {Sci Data},

abstract = {The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.},

keywords = {Bacteria* / genetics, Bacterial*, Computational Biology, Databases, Dataset, doi:10.1038/s41597-023-02502-7, Factual, Frank Moller Aarestrup, Genome, Gunhild Larsen, MEDLINE, Metadata, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, NCBI, NIH, NLM, PMC10505216, pmid:37717051, PubMed Abstract, Sidsel Nag},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation.},

author = {Julius Mulindwa and Harry Noyes and Hamidou Ilboudo and Luca Pagani and Oscar Nyangiri and Magambo Phillip Kimuda and Bernardin Ahouty and Olivier Fataki Asina and Elvis Ofon and Kelita Kamoto and Justin Windingoudi Kabore and Mathurin Koffi and Dieudonne Mumba Ngoyi and Gustave Simo and John Chisi and Issa Sidibe and John Enyaru and Martin Simuunza and Pius Alibu and Vincent Jamonneau and Mamadou Camara and Andy Tait and Neil Hall and Bruno Bucheton and Annette MacLeod and Christiane Hertz-Fowler and Enock Matovu},

doi = {10.1016/j.ajhg.2020.07.007},

issn = {1537-6605 0002-9297},

year  = {2020},

date = {2020-09-01},

urldate = {2020-09-01},

journal = {American journal of human genetics},

volume = {107},

issue = {3},

pages = {473-486},

abstract = {Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.},

keywords = {*Nilo-Saharan, *population genetic variation, *signatures of selection, Adaptation, Antiporters/genetics, Blacks/genetics, Data Management, Ethiopia/epidemiology, Female, Genetic Variation/*genetics, Genetic/*genetics, Genetics, Genome, Haplotypes/genetics, Human/genetics, Humans, Male, Membrane Glycoproteins/genetics, Oxidoreductases/genetics, Physiological/*genetics, Polymorphism, Population, Selection, Single Nucleotide/genetics, Skin Pigmentation/*genetics, Sorting Nexins/genetics, Tumor Suppressor Proteins/genetics, Uganda/epidemiology},

pubstate = {published},

tppubtype = {article}

}