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Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project

Dmitry Prokopenko, Julian Hecker, Edwin K. Silverman, Marcello Pagano, Markus M. Nöthen, Christian Dina, Christoph Lange, Heide Loehlein Fier
2015 Bioinformatics  
Using sequencing data from the 1000 Genomes Project, the features of the approach are illustrated and compared to existing methodology (i.e. EIGENSTRAT).  ...  Here, we present a novel approach for the identification of population substructure in high-density genotyping data/next generation sequencing data.  ...  number of markers, which Utilizing the Jaccard index to reveal population stratification in sequencing data satisfy g ik ¼ 0^g jk ¼ 1.  ... 
doi:10.1093/bioinformatics/btv752 pmid:26722118 pmcid:PMC5860507 fatcat:rk3d5v7ovzdkhit2txmbsgnktq

Unsupervised genome-wide cluster analysis: nucleotide sequences of the omicron variant of SARS-CoV-2 are similar to sequences from early 2020 [article]

Georg Hahn, Sanghun Lee, Dmitry Prokopenko, Tanya Novak, Julian Hecker, Surender Khurana, Lindsey R. Baden, Adrienne G. Randolph, Scott T. Weiss, Christoph Lange
2021 bioRxiv   pre-print
We applied unsupervised cluster analysis to the SARS-CoV-2 genomes, assessing their similarity at a genome-wide level based on the Jaccard index and principal component analysis.  ...  Our analysis results show that the omicron variant sequences are most similar to sequences that have been submitted early in the pandemic around January 2020.  ...  A detailed list of contributors is available in the  ... 
doi:10.1101/2021.12.29.474469 fatcat:7qwrlauew5f37bf62gtomix4vm

Ancestral Spectrum Analysis With Population-Specific Variants

Gang Shi, Qingmin Kuang
2021 Frontiers in Genetics  
The methods are implemented in a program, Ancestral Spectrum Analyzer (ASA), and are applied in analyzing high-coverage sequencing data from the 1000 Genomes Project and the Human Genome Diversity Project  ...  With the advance of sequencing technology, an increasing number of populations have been sequenced to study the histories of worldwide populations, including their divergence, admixtures, migration, and  ...  Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 genomes project.  ... 
doi:10.3389/fgene.2021.724638 pmid:34646302 pmcid:PMC8503515 fatcat:u6dcls6d5zfcnnonsi3zf2lp5e

scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data

Wenbin Ye, Guoli Ji, Pengchao Ye, Yuqi Long, Xuesong Xiao, Shuchao Li, Yaru Su, Xiaohui Wu
2019 BMC Genomics  
Single-cell RNA-sequencing (scRNA-seq) is fast becoming a powerful tool for profiling genome-scale transcriptomes of individual cells and capturing transcriptome-wide cell-to-cell variability.  ...  to augment gene-gene relationships in a data driven manner.  ...  Acknowledgements Not applicable. Availability of data and materials Datasets used for the analyses in this study are summarized in Additional file 2: Table S1 .  ... 
doi:10.1186/s12864-019-5747-5 pmid:31068142 pmcid:PMC6505295 fatcat:zwt6xpuuwjgl7mrwp5fbwz4iy4

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer

Leticia De Mattos-Arruda, Stephen-John Sammut, Edith M. Ross, Rachael Bashford-Rogers, Erez Greenstein, Havell Markus, Sandro Morganella, Yvonne Teng, Yosef Maruvka, Bernard Pereira, Oscar M. Rueda, Suet-Feung Chin (+22 others)
2019 Cell Reports  
The data further identify variable tumor microenvironments and reveal, through analyses of T cell receptor repertoires, that adaptive immune responses appear to co-evolve with the metastatic genomes.  ...  The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting.  ...  The data were reshuffled to assign the TCR sequences to ''randomized'' metastases, and then on the reshuffled repertoire clustering by the Jaccard index was performed.  ... 
doi:10.1016/j.celrep.2019.04.098 pmid:31141692 pmcid:PMC6546974 fatcat:zdisif3f4jdyzjpn4644sirpby

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease

Steven N. Baldassano, Danielle S. Bassett
2016 Scientific Reports  
The gut microbiome plays a key role in human health, and alterations of the normal gut flora are associated with a variety of distinct disease states.  ...  Here we use a network-based approach to characterize microbial co-occurrence in individuals with inflammatory bowel disease (IBD) and healthy (non-IBD control) individuals.  ...  Acknowledgements This data was previously published as a supplementary dataset in Levy and Borenstein, "Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly  ... 
doi:10.1038/srep26087 pmid:27188829 pmcid:PMC4870640 fatcat:iea52e3unramxls4cufzz5o7la

Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease

Travis S. Johnson, Christina Y. Yu, Zhi Huang, Siwen Xu, Tongxin Wang, Chuanpeng Dong, Wei Shao, Mohammad Abu Zaid, Xiaoqing Huang, Yijie Wang, Christopher Bartlett, Yan Zhang (+4 others)
2022 Genome Medicine  
the feasibility, flexibility, and broad applications of the DEGAS framework.  ...  Using simulated data and ten diverse single-cell and patient bulk tissue transcriptomic datasets from glioblastoma multiforme (GBM), Alzheimer's disease (AD), and multiple myeloma (MM), we demonstrate  ...  for Brain Science for the data generated as part of their cell types database, and Mount Sinai/JJ Peters VA Medical Center for the data generated as a part of their brain bank.  ... 
doi:10.1186/s13073-022-01012-2 pmid:35105355 pmcid:PMC8808996 fatcat:aq2ate52ancfdacut2jc37wyum

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
Acknowledgements The Onco-i2b2 project is funded by the "Regione Lombardia" in Italy. We gratefully acknowledge Prof. Carlo Bernasconi and the Collegio Ghislieri in Pavia for their active support.  ...  Acknowledgements The authors are partially supported by the FLAGSHIP "InterOmics" project (PB.P05) funded by the Italian MIUR and CNR institutions, and by the cooperative programme 2010-2012 between the  ...  This application has been used in several population genetics studies recently published by our group to analyze the 1000 genomes project data.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways

Vikram Khurana, Jian Peng, Chee Yeun Chung, Pavan K. Auluck, Saranna Fanning, Daniel F. Tardiff, Theresa Bartels, Martina Koeva, Stephen W. Eichhorn, Hadar Benyamini, Yali Lou, Andy Nutter-Upham (+18 others)
2017 Cell Systems  
" toxicity map links parkinsonism genes and druggable targets to a-syn d Common pathologies identified in patient neurons harboring distinct disease genes In Brief Khurana et al. develop a computational  ...  Modifiers from genome-wide screens against alphasynuclein toxicity in yeast yield a "humanized" network that interconnects genetic forms of parkinsonism and predicts pathologies in patient-derived neurons  ...  We dedicate this manuscript to Dr Susan Lindquist, our incomparable mentor and colleague, who passed away while this manuscript was in its final stages of revision.  ... 
doi:10.1016/j.cels.2016.12.011 pmid:28131822 pmcid:PMC5388136 fatcat:temccumfpnfs5heg5ndjd7zoae

Xxxii Scar Open Science Conference 'Antarctic Science And Policy Advice In A Changing World - Conference Abstracts [article]

Eoghan Griffin, Renuka Badhe
2016 Zenodo  
Abstracts from the 2012 Open Science Conference of the Scientific Committee on Antarctic Research (SCAR), Antarctic Science and Policy Advice in a Changing World, held in Portland, Oregon, USA  ...  These new magnetic data together with survey data that were not previously in the public domain can significantly upgrade the ADMAP compilation for crustal studies of the Antarctic.  ...  The synthesis of these magnetic data into the next generation ADMAP compilation will enable a better understanding of the geological structure and tectonic history of the Antarctic region.  ... 
doi:10.5281/zenodo.53122 fatcat:o56w4vr3n5bsvkyj6vnetfem3e

International Conference on Emerging Infectious Diseases 2018 Poster and Oral Presentation Abstracts

2018 Emerging Infectious Diseases  
A live simulation exercise is conducted to test the direct applicability of the plan in real-time.  ...  In this continuing study, SDPHL will pilot the use of the GHOST protocol for HAV to demonstrate and compare the NGS data to the Sanger sequence data for a HAV outbreak.  ...  A meta-population model of MERS-CoV transmission reproduces the long-term persistence of MERS-CoV in camel populations in Africa and the Arabian Peninsula and may be useful for simulating camel vaccination  ... 
doi:10.3201/eid2409.nn2409 fatcat:ba2ez7c45zg2plezo64wusdcqu

On Fitting Finite Dirichlet Mixture Using ECM and MML [chapter]

Nizar Bouguila, Djemel Ziou
2005 Lecture Notes in Computer Science  
We study a fluid system with single on/off source in which the active (on) and silent periods (off) follow General and Exponential distributions respectively.  ...  The system is analysed for different active periods corresponding to the service time of an M/G/1 queue and the busy period of an M/G/1 queue.  ...  The above method is verified in a simulation study especially with the bootstrap approach and in application to some of the rainfall data sets of South Korea.  ... 
doi:10.1007/11551188_19 fatcat:gtzi5u6emvfyxea3zbklobnvom

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

Kelvin Li, Monika Bihan, Barbara A. Methé, Bryan A. White
2013 PLoS ONE  
A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to  ...  The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across  ...  Additional information is also available at: http://www.jcvi.org/cms/research/projects/corbata. 16S rRNA Sequence Data Processing and Data Set Sequence reads were processed using a pipeline constructed  ... 
doi:10.1371/journal.pone.0063139 pmid:23671663 pmcid:PMC3646044 fatcat:r54xxshkzna2zcyitmhpzulf2i

Conference program and abstracts. International Biogeography Society 6th Biennial Meeting – 9-13 January 2013, Miami, Florida, USA

Joaquín Hortal, Karen Faller, Kenneth Feeley, Richard Field, Catherine Graham, François Guilhaumon, Daniel Gavin
2012 Frontiers of Biogeography  
The geography of divergence and disparity: how landscapes help understand the decoupling of genetic structure and phenotypic diversity. 43A Assembly of plant communities in climate space Benjamin Blonder  ...  Sloat 1,3 , Bill Piel 3,15 , Nathan Kraft 3,16 , Jens-Christian Svenning 3,17 , Naia Morueta-Holme 3,17 , Nick Spensor 3,18 , Susan Wiser 3,18 , Jeff Ott 3,7 , Barbara Dobrin 1,3 , Sandy Andelman 3,19 and  ...  Between 3.3% and 7.6% of the study area is projected to change, mostly towards an increase in vertical structure.  ... 
doi:10.21425/f5fbg15702 fatcat:lwyauz5kbvcwbmimvei4iota3a

SEQUENCE ANALYSIS SUGGESTS POSITIVE SELECTION ON THE BOVINE PRODYNORPHIN GENE
ANÁLISIS DE SECUENCIAS GENÓMICAS SUGIEREN QUE EL GEN DE LA PRODINORFINA ESTÁ BAJO SELECCIÓN POSITIVA EN BOVINOS

M.F. Suqueli García, M.A. Castellote, P.M. Corva
2020 BAG. Journal of basic and applied genetics  
The putative promoter of PDYN showed a population structure that is in agreement with the criteria considered to make the groups.  ...  Despite its physiological relevance, PDYN has not emerged as a candidate gene associated with puberty in genomic association studies conducted in cattle.  ...  ., Stephens M. (2006) A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase. Am. J. Hum. Genet. 78: 629-644.  ... 
doi:10.35407/bag.2020.31.02.02 fatcat:etxjwju7vrfonmg6w3uj6tflki
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