A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project
2015
Bioinformatics
Preserved Fulltext
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]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2021
Frontiers in Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is text/html.
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
2019
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2019
Cell Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2016
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2022
Genome Medicine
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2012
EMBnet journal
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2017
Cell Systems
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
" 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]
2016
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2005
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2013
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2012
Frontiers of Biogeography
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2020
BAG. Journal of basic and applied genetics
ANÁLISIS DE SECUENCIAS GENÓMICAS SUGIEREN QUE EL GEN DE LA PRODINORFINA ESTÁ BAJO SELECCIÓN POSITIVA EN BOVINOS
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 50 results