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1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans

Marc Pybus, Giovanni M. Dall'Olio, Pierre Luisi, Manu Uzkudun, Angel Carreño-Torres, Pavlos Pavlidis, Hafid Laayouni, Jaume Bertranpetit, Johannes Engelken
2013 Nucleic Acids Research  
Here we present the 1000 Genomes Selection Browser 1.0 ( as a resource for signatures of recent natural selection in modern humans.  ...  Searching for Darwinian selection in natural populations has been the focus of a multitude of studies over the last decades.  ...  Genomes Project (  ... 
doi:10.1093/nar/gkt1188 pmid:24275494 pmcid:PMC3965045 fatcat:vvjqea2qxbgqhinrpmdjlupxjq

Crossbrowse: A versatile genome browser for visualizing comparative experimental data [article]

Sol Shenker, Eric Lai
2018 bioRxiv   pre-print
Our platform permits users with minimal informatics capacity to select arbitrary sets of genomes for display, upload and configure multiple datasets, and interact with vertebrate-sized genomic datasets  ...  We utilize data standards and graphic representation of popular browsers, and incorporate an intuitive graphical visualization of genome synteny that facilitates and drives human interrogation of comparative  ...  S.S. was supported by the Tri-Institutional Training Program in Computational Biology and Medicine. Work in E.C.L.'s group was supported by the National Institutes of Health (R01-  ... 
doi:10.1101/272880 fatcat:e6nocrxwg5bihnlg636mwz6haa

Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver

Johannes Engelken, Guadalupe Espadas, Francesco M. Mancuso, Nuria Bonet, Anna-Lena Scherr, Victoria Jímenez-Álvarez, Marta Codina-Solà, Daniel Medina-Stacey, Nino Spataro, Mark Stoneking, Francesc Calafell, Eduard Sabidó (+1 others)
2015 Molecular biology and evolution  
Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive  ...  In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances  ...  Acknowledgments This article is dedicated to the memory of our friend and colleague Johannes Engelken, who passed away unexpectedly on October 23, 2015.  ... 
doi:10.1093/molbev/msv267 pmid:26582562 pmcid:PMC4760079 fatcat:m3ljxta3xfhohpqx5sv44ji6fm

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, David Molik, Daniela C. Soto, Fawaz Dabbaghie, Ahmad Al Khleifat, Medhat Mahmoud, Luis F Paulin, Muhammad Sohail Raza, Susanne P. Pfeifer (+47 others)
2022 F1000Research  
The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software.  ...  In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon.  ...  We'd like to thank Richard Gibbs and the Baylor College of Medicine Human Genome Sequencing Center for hosting the hackathon.  ... 
doi:10.12688/f1000research.110194.1 fatcat:2yqiygmc7fdhzk3dhwcvvyuwmi

Systematic integration of biomedical knowledge prioritizes drugs for repurposing [article]

Daniel S. Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L. Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E. Baranzini
2016 bioRxiv   pre-print
The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval.  ...  Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types.  ...  Acknowledgements We are immensely grateful to our Thinklab contributors who joined us in our experiment of radically open science.  ... 
doi:10.1101/087619 fatcat:drln54if6baajkxj3knmc2b5cq

Systematic integration of biomedical knowledge prioritizes drugs for repurposing

Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
2017 eLife  
The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval.  ...  Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types.  ...  Acknowledgements We are immensely grateful to our Thinklab contributors who joined us in our experiment of radically open science.  ... 
doi:10.7554/elife.26726 pmid:28936969 pmcid:PMC5640425 fatcat:4brx7dtpo5eznlgygn4a4aqz4m

Definition of the Cattle Killer Cell Ig–like Receptor Gene Family: Comparison with Aurochs and Human Counterparts

Nicholas D. Sanderson, Paul J. Norman, Lisbeth A. Guethlein, Shirley A. Ellis, Christina Williams, Matthew Breen, Steven D. E. Park, David A. Magee, Farbod Babrzadeh, Andrew Warry, Mick Watson, Daniel G. Bradley (+3 others)
2014 Journal of Immunology  
Acknowledgments We thank Ivan Morrison for kindly providing a cell line derived from the same Holstein-Friesian used to construct our BAC library, and we acknowledge James Birch and Steve Banner for help  ...  in preparing the BAC library for screening.  ...  It is therefore reasonable to assume that despite altering selection processes, the KIR gene diversity that we observe in modern cattle evolved under natural selection.  ... 
doi:10.4049/jimmunol.1401980 pmid:25398326 pmcid:PMC4258407 fatcat:5nrj5iyexjf2porkjafpp34754

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

A. Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, Joaquim Bellmunt, Guangwu Guo, Andrew D. Cherniack, Toshinori Hinoue, Peter W. Laird, Katherine A. Hoadley, Rehan Akbani, Mauro A.A. Castro, Ewan A. Gibb (+201 others)
2017 Cell  
G.B.M. is a member of the scientific advisory board and receives research support from AstraZeneca. D.J.M. has stock options in ApoCell, Inc.  ...  C.J.W. is a cofounder and advisory board member of Neon Therapeutics. No other conflicts of interest declared.  ...  We appreciate the dedication of Ina Felau for her administrative support throughout this project, and of Lee Ann Chastain for her invaluable organizational skills in final manuscript preparation.  ... 
doi:10.1016/j.cell.2017.09.007 pmid:28988769 pmcid:PMC5687509 fatcat:fwsc7zoecvbetcpnmumlpyfdw4

Untitled Item

Daniele Traversa
This is the final document of my thesis based on the analysis performed during my internship experience  ...  Additionally, most modern sequencing technologies were not able to provide a complete representation of the human genome until recently when the last gaps of the human genome were filled [43] .  ...  in 1000 Genome Project.  ... 
doi:10.6084/m9.figshare.21184690.v1 fatcat:6ix7izpidzftngpwtp7rzqn64i

Early farmers from across Europe directly descended from Neolithic Aegeans

Zuzana Hofmanová, Susanne Kreutzer, Garrett Hellenthal, Christian Sell, Yoan Diekmann, David Díez-del-Molino, Lucy van Dorp, Saioa López, Athanasios Kousathanas, Vivian Link, Karola Kirsanow, Lara M. Cassidy (+27 others)
2016 Proceedings of the National Academy of Sciences of the United States of America  
Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe.  ...  Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes.  ...  modern Europeans (1000 Genomes EUR frequency > 0.99 [155] ), including modern Greek (> 0.99) and Turkish (> 0.98) populations [156] , and known to be under strong natural selection [130, 157] .  ... 
doi:10.1073/pnas.1523951113 pmid:27274049 pmcid:PMC4922144 fatcat:xpumcqf3bnhtxfbbqim777ljfy

Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia

Suzanne Freilich, Harald Ringbauer, Dženi Los, Mario Novak, Dinko Tresić Pavičić, Stephan Schiffels, Ron Pinhasi
2021 Scientific Reports  
AbstractAncient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies.  ...  To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia.  ...  Open access funding provided by University of Vienna.  ... 
doi:10.1038/s41598-021-94932-9 pmid:34408163 pmcid:PMC8373892 fatcat:ivcepxj635ck7jddxfjpbvkxgu

Characterization and evolutionary dynamics of complex regions in eukaryotic genomes

José Ranz, Bryan Clifton
2019 Science China Life Sciences  
This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across  ...  Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity  ...  Acknowledgements This work was supported by a National Science Foundation Grant (MCB-1157876) to J.M.R.  ... 
doi:10.1007/s11427-018-9458-0 pmid:30810961 fatcat:mu6tt5liffgtjne6myg45nksce

Ensemble outlier detection and gene selection in triple-negative breast cancer data

Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
2018 BMC Bioinformatics  
Moreover, the model consensus approach leads to the selection of a set of genes that may be linked to the disease.  ...  These results are robust to a resampling approach, either by selecting a subset of patients or a subset of genes, with a significant overlap of the outlier patients identified.  ...  Availability of data and materials All the implementations described can be found in a R Markdown document available at, which allows full reproducibility  ... 
doi:10.1186/s12859-018-2149-7 pmid:29728051 pmcid:PMC5936001 fatcat:kzzfuprrwvfnrf4gnphrauzkne

EMBnet.journal 18 Suppl. A

EMBnet Journal
2012 EMBnet journal  
Protein Structure and Function Acknowledgments This work was supported by NFSR of Bulgaria project DVU 01/197.  ...  and embeds a graphical browser to provide an overview of results at genome level.  ...  browsers to obtain hints about the possible functional impact of candidate genomic variations.  ... 
doi:10.14806/ej.18.a.497 fatcat:2aexioifkfgfnipbo3btxqwvia

Indigenous peoples in eastern Brazil: insights from 19th century genomes and metagenomes [article]

Diana Ivette Cruz Dávalos, Yami Ommar Arizmendi Cárdenas, Miriam Jetzabel Bravo-Lopez, Samuel Neuenschwander, Silvia Reis, Murilo Q. R. Bastos, Jesper Stenderup, Fulya Eylem Yediay, Viridiana Villa-Islas, Carlos S. Reyna-Blanco, Claudia Rodrigues-Carvalho, Tábita Hünemeier (+5 others)
2022 bioRxiv   pre-print
Unlike Mesoamericans, the "Botocudos" and Amazonians do not seem to have experienced a population expansion once in the Americas.  ...  Finally, whole genomes of likely ancient pathogens were recovered, including lineages of human parvovirus B19 that were possibly introduced after the European contact.  ...  JS and FEY were funded by a Swedish Foundation for Humanities and Social Sciences grant (M16-0455:1, The Rise III) to Kristian Kristiansen. MJBL was funded by project IA201219 PAPIIT-DGAPA-UNAM.  ... 
doi:10.1101/2022.01.27.477466 fatcat:7x4fc4u3f5awnbjiqnqyk3yjnq
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