المؤلفون: Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, Mehmet Somel

المصدر: PLoS Computational Biology, Vol 18, Iss 12, p e1010788 (2022)

مصطلحات موضوعية: Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

URL الوصول: https://doaj.org/article/8baa21f9e2a4439c83ca775f05660d95

المؤلفون: Sevim Seda Çokoğlu, Dilek Koptekin, Fatma Rabia Fidan, Mehmet Somel

المصدر: Evolutionary Applications, Vol 17, Iss 7, Pp n/a-n/a (2024)

مصطلحات موضوعية: ancient DNA, DNA methylation, epigenetics, genomics/proteomics, human evolution, Neolithic transition, Evolution, QH359-425

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1752-4571

URL الوصول: https://doaj.org/article/becb1f6a9a5f4b87a3a66474fe4854dc

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/journal_contribution/Command_lines_and_supplementary_notes_1-4_/21727774

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s001

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Heatmaps_of_CONGA-genotyped_n_10_002_human-derived_deletions_across_ancient_genomes_/21727783

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s004

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Precision_Recall_plots_for_simulations_/21727780

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s003

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Length_distribution_of_CNVs_inserted_into_the_simulated_genomes_/21727777

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s002

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Technical_comparisons_of_divergent_n_21_and_coherent_n_50_genome_sets_/21727789

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s006

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Correlations_between_SNP-_and_deletion-based_deleterious_load_estimates_in_50_ancient_genomes_/21727798

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s009

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Multivariate_analysis_of_deletion_frequencies_reveal_outlier_genomes_/21727786

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s005

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Deleterious_load_estimates_among_50_ancient_genomes_/21727795

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s008

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/IGV_visualization_of_two_high_scoring_i_e_high_likelihood_deletions_and_duplications_predicted_by_CONGA_/21727807

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s012

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Effect_of_minimum_read-pair_support_on_the_F-Score_for_duplications_using_various_depths_of_coverage_values_in_simulated_genomes_/21727804

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s011

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Site-frequency_spectra_of_deletions_genotyped_in_low_and_high_coverage_genomes_/21727792

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s007

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/dataset/Performance_comparison_of_multiple_tools_and_CONGA_performance_analysis_/21727822

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s017

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/A_sample_deletion_missed_due_to_poor_signal_/21727810

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s013

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/General_characteristics_of_deletions_in_the_refined_dataset_n_50_genomes_and_n_8_780_deletions_obtained_after_applying_ancestry_state_filters_and_removing_outlier_genomes_/21727816

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s015

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/dataset/Information_on_the_ancient_genomes_used_in_this_study_/21727825

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s018

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Overall_workflow_of_CONGA_/21727828

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.g001

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/Split-read_approach_to_emulate_paired-end_using_single-end_reads_/21727819

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.s016

المؤلفون: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)

مصطلحات موضوعية: Genetics, Evolutionary Biology, Ecology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, systematic cnv analyses, single nucleotide polymorphisms, sampling experiments suggest, nine different laboratories, copy number variants, technical challenges posed, ancient genome analyses, conga thus paves, ascertained deletions across, technical factors, genotyped deletions, genotype deletions, ancient shotgun, ancient genomes, %22">xlink ">, used conga, snps ), sequenced genomes, read length, present conga, population origin, major contributor, largely confined

Relation: https://figshare.com/articles/figure/CNV_prediction_performances_of_CONGA_GenomeSTRiP_FREEC_and_CNVnator_on_simulated_genomes_/21727831

الاتاحة: https://doi.org/10.1371/journal.pcbi.1010788.g002