article-journal | The Makova Lab at Penn State http://www.bx.psu.edu/makova_lab/publication_types/article-journal/ article-journal HugoBlox Kit (https://hugoblox.com)en-usThu, 06 Aug 2026 00:01:00 +0000 http://www.bx.psu.edu/makova_lab/media/icon_hu_eee4a95885829ab2.png article-journal http://www.bx.psu.edu/makova_lab/publication_types/article-journal/ The complete genome of a songbird http://www.bx.psu.edu/makova_lab/publication/2026-08-cell_formenti/ Thu, 06 Aug 2026 00:01:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-08-cell_formenti/ A Complete Genome for the Common Marmoset http://www.bx.psu.edu/makova_lab/publication/2026-08-cell/ Thu, 06 Aug 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-08-cell/ Protocol for Duplex Sequencing of Mitochondrial DNA in Single Human Oocytes http://www.bx.psu.edu/makova_lab/publication/2026-08-jove/ Thu, 06 Aug 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-08-jove/ HPRC2: A human pangenome reference with near-complete coverage of common genetic variation http://www.bx.psu.edu/makova_lab/publication/2026-07-biorxiv/ Wed, 22 Jul 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-07-biorxiv/ Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes http://www.bx.psu.edu/makova_lab/publication/2026-07-genome_res/ Tue, 07 Jul 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-07-genome_res/ The Vertebrate Genomes Project Phase I: A global reference genome resource http://www.bx.psu.edu/makova_lab/publication/2026-06-biorxiv-formenti/ Fri, 26 Jun 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-06-biorxiv-formenti/ Variation and selection at predicted G-quadruplexes across the human pangenome http://www.bx.psu.edu/makova_lab/publication/2026-06-biorxiv_mohanty/ Tue, 23 Jun 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-06-biorxiv_mohanty/ Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures http://www.bx.psu.edu/makova_lab/publication/2026-06-biorxiv/ Sat, 06 Jun 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-06-biorxiv/ Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes http://www.bx.psu.edu/makova_lab/publication/2026-05-annu_rev/ Wed, 06 May 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-05-annu_rev/ How and why ampliconic genes survive on the human Y chromosome http://www.bx.psu.edu/makova_lab/publication/2026-04-biorxiv/ Mon, 20 Apr 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-04-biorxiv/ Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA-lncRNA classification http://www.bx.psu.edu/makova_lab/publication/2026-04-17-biorxiv/ Fri, 17 Apr 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-04-17-biorxiv/ Non-canonical DNA and sequencing challenges in bird genomes http://www.bx.psu.edu/makova_lab/publication/2026-03-biorxiv/ Sat, 28 Mar 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-03-biorxiv/ Substitution spectrum and selection at G-quadruplexes in great ape telomere-to-telomere genomes http://www.bx.psu.edu/makova_lab/publication/2026-02-genome_biol_evol/ Tue, 17 Feb 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-02-genome_biol_evol/ Mammalian Mitochondrial DNA Accumulates Insertions and Deletions with Age in Energetically Demanding Tissues http://www.bx.psu.edu/makova_lab/publication/2026-01-mol_biol_evol/ Thu, 29 Jan 2026 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2026-01-mol_biol_evol/ Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes http://www.bx.psu.edu/makova_lab/publication/2025-11-biorxiv/ Tue, 04 Nov 2025 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2025-11-biorxiv/ Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations http://www.bx.psu.edu/makova_lab/publication/2025-07-sci_adv/ Wed, 06 Aug 2025 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2025-07-sci_adv/ Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes http://www.bx.psu.edu/makova_lab/publication/2025-06-genome_biol/ Wed, 11 Jun 2025 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2025-06-genome_biol/ Replicative DNA polymerase Epsilon and Delta holoenzymes show wide ranging inhibition at G-Quadruplexes in the human genome http://www.bx.psu.edu/makova_lab/publication/2025-05-nucleic_acids_hile_res/ Thu, 08 May 2025 00:00:01 +0000 http://www.bx.psu.edu/makova_lab/publication/2025-05-nucleic_acids_hile_res/ Complete sequencing of ape genomes http://www.bx.psu.edu/makova_lab/publication/2025-05-nature/ Thu, 08 May 2025 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2025-05-nature/ Non-canonical DNA in human and other ape telomere-to-telomere genomes http://www.bx.psu.edu/makova_lab/publication/2025-04-nucleic_acids_res_smeds/ Mon, 14 Apr 2025 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2025-04-nucleic_acids_res_smeds/ The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes http://www.bx.psu.edu/makova_lab/publication/2024-05-nature/ Wed, 29 May 2024 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2024-05-nature/ Methylation profiles at birth linked to early childhood obesity http://www.bx.psu.edu/makova_lab/publication/2024-04-j_dev_orig_health_dis/ Thu, 25 Apr 2024 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2024-04-j_dev_orig_health_dis/ Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes http://www.bx.psu.edu/makova_lab/publication/2023-11-biol_evol/ Wed, 15 Nov 2023 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2023-11-biol_evol/ The complete sequence of a human Y chromosome http://www.bx.psu.edu/makova_lab/publication/2023-08-nature/ Wed, 23 Aug 2023 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2023-08-nature/ Accurate sequencing of DNA motifs able to form alternative (non-B) structures http://www.bx.psu.edu/makova_lab/publication/2023-07-genome_res/ Tue, 11 Jul 2023 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2023-07-genome_res/ Transcription factor binding sites are frequently under accelerated evolution in primates http://www.bx.psu.edu/makova_lab/publication/2023-02-nat_commun/ Sat, 11 Feb 2023 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2023-02-nat_commun/ Constructing a polygenic risk score for childhood obesity using functional data analysis http://www.bx.psu.edu/makova_lab/publication/2023-01-econom-stat/ Wed, 25 Jan 2023 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2023-01-econom-stat/ Noncanonical DNA structures are drivers of genome evolution http://www.bx.psu.edu/makova_lab/publication/2023-01-trends_genet/ Tue, 03 Jan 2023 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2023-01-trends_genet/ Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch) http://www.bx.psu.edu/makova_lab/publication/2022-09-j_hered/ Fri, 23 Sep 2022 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2022-09-j_hered/ Variation in G-quadruplex Sequence and Topology Differentially Impacts Human DNA Polymerase Fidelity http://www.bx.psu.edu/makova_lab/publication/2022-09-dna_repair/ Fri, 09 Sep 2022 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2022-09-dna_repair/ Exploring the effects of mitonuclear interactions on mitochondrial DNA gene expression in humans http://www.bx.psu.edu/makova_lab/publication/2022-06-front_genet/ Wed, 29 Jun 2022 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2022-06-front_genet/ Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues http://www.bx.psu.edu/makova_lab/publication/2022-04-p_natl_acad_sci_usa/ Fri, 08 Apr 2022 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2022-04-p_natl_acad_sci_usa/ INSIGHT responsive parenting educational intervention for firstborns is associated with growth of secondborn siblings http://www.bx.psu.edu/makova_lab/publication/2022-01-obesity/ Sat, 01 Jan 2022 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2022-01-obesity/ Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes http://www.bx.psu.edu/makova_lab/publication/2022-01-ped_obesity/ Sat, 01 Jan 2022 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2022-01-ped_obesity/ Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome http://www.bx.psu.edu/makova_lab/publication/2021-05-genome_res/ Mon, 24 May 2021 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2021-05-genome_res/ Towards complete and error-free genome assemblies of all vertebrate species http://www.bx.psu.edu/makova_lab/publication/2021-01-nature/ Wed, 28 Apr 2021 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2021-01-nature/ Non-B DNA: A major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome http://www.bx.psu.edu/makova_lab/publication/2020-12-nucleic_acids_res/ Mon, 22 Feb 2021 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2020-12-nucleic_acids_res/ Associations between stool micro-transcriptome, gut microbiota, and infant growth http://www.bx.psu.edu/makova_lab/publication/2020-11-j_dev_orig_hlth_dis/ Thu, 07 Jan 2021 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2020-11-j_dev_orig_hlth_dis/ Dynamic evolution of great ape Y chromosomes http://www.bx.psu.edu/makova_lab/publication/2020-10-p_natl_acad_sci_usa/ Mon, 05 Oct 2020 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2020-10-p_natl_acad_sci_usa/ Human L1 Transposition Dynamics Unraveled with Functional Data Analysis http://www.bx.psu.edu/makova_lab/publication/2020-07-mol_biol_evol/ Tue, 28 Jul 2020 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2020-07-mol_biol_evol/ Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues http://www.bx.psu.edu/makova_lab/publication/2020-07-plos_biol/ Wed, 15 Jul 2020 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2020-07-plos_biol/ Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels http://www.bx.psu.edu/makova_lab/publication/2020-05-genome_biol_evol/ Wed, 06 May 2020 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2020-05-genome_biol_evol/ Family reunion via error correction: an efficient analysis of duplex sequencing data http://www.bx.psu.edu/makova_lab/publication/2020-03-bmc_bioinformatics/ Wed, 04 Mar 2020 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2020-03-bmc_bioinformatics/ Pronounced somatic bottleneck in mitochondrial DNA of human hair http://www.bx.psu.edu/makova_lab/publication/2019-12-philos_t_r_soc_b/ Mon, 02 Dec 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-12-philos_t_r_soc_b/ Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees http://www.bx.psu.edu/makova_lab/publication/2019-11-p_natl_acad_sci_usa/ Fri, 22 Nov 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-11-p_natl_acad_sci_usa/ Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes http://www.bx.psu.edu/makova_lab/publication/2019-09-plos_genet/ Mon, 16 Sep 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-09-plos_genet/ DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies http://www.bx.psu.edu/makova_lab/publication/2019-08-bmc_genomics/ Fri, 09 Aug 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-08-bmc_genomics/ Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data http://www.bx.psu.edu/makova_lab/publication/2019-07-bioinformatics/ Wed, 10 Jul 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-07-bioinformatics/ High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-read Technologies http://www.bx.psu.edu/makova_lab/publication/2019-07-mol_biol_evol/ Tue, 02 Jul 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-07-mol_biol_evol/ Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity http://www.bx.psu.edu/makova_lab/publication/2019-04-biorxiv/ Thu, 11 Apr 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-04-biorxiv/ Functional data analysis for computational biology http://www.bx.psu.edu/makova_lab/publication/2019-01-bioinformatics/ Tue, 22 Jan 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-01-bioinformatics/ Investigating mitonuclear interactions in human admixed populations http://www.bx.psu.edu/makova_lab/publication/2019-01-nat_ecol_evol/ Mon, 14 Jan 2019 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2019-01-nat_ecol_evol/ Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate http://www.bx.psu.edu/makova_lab/publication/2018-11-genome_res/ Tue, 06 Nov 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-11-genome_res/ Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon http://www.bx.psu.edu/makova_lab/publication/2018-11-nat_commun/ Fri, 02 Nov 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-11-nat_commun/ Correcting palindromes in long reads after whole-genome amplification http://www.bx.psu.edu/makova_lab/publication/2018-11-bmc_genomics/ Thu, 01 Nov 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-11-bmc_genomics/ Child Weight Gain Trajectories Linked To Oral Microbiota Composition http://www.bx.psu.edu/makova_lab/publication/2018-09-sci_rep_uk/ Wed, 19 Sep 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-09-sci_rep_uk/ IWTomics: testing high-resolution sequence-based `Omics' data at multiple locations and scales http://www.bx.psu.edu/makova_lab/publication/2018-07-bioinformatics/ Sun, 01 Jul 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-07-bioinformatics/ High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups http://www.bx.psu.edu/makova_lab/publication/2018-05-genome_biol_evol/ Tue, 01 May 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-05-genome_biol_evol/ RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly http://www.bx.psu.edu/makova_lab/publication/2018-04-bioinformatics/ Sun, 01 Apr 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-04-bioinformatics/ A Population Phylogenetic View of Mitochondrial Heteroplasmy http://www.bx.psu.edu/makova_lab/publication/2018-03-genetics/ Thu, 01 Mar 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-03-genetics/ Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives http://www.bx.psu.edu/makova_lab/publication/2018-02-genes_basel/ Mon, 26 Feb 2018 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2018-02-genes_basel/ Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent http://www.bx.psu.edu/makova_lab/publication/2017-09-evol_appl/ Fri, 01 Sep 2017 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2017-09-evol_appl/ Y and W Chromosome Assemblies: Approaches and Discoveries http://www.bx.psu.edu/makova_lab/publication/2017-04-trends_genet/ Sat, 01 Apr 2017 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2017-04-trends_genet/ Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications http://www.bx.psu.edu/makova_lab/publication/2016-12-dna_res/ Thu, 01 Dec 2016 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2016-12-dna_res/ Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats http://www.bx.psu.edu/makova_lab/publication/2016-10-mol_biol_evol/ Sat, 01 Oct 2016 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2016-10-mol_biol_evol/ Streamlined analysis of duplex sequencing data with Du Novo http://www.bx.psu.edu/makova_lab/publication/2016-08-genome_biol/ Mon, 01 Aug 2016 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2016-08-genome_biol/ Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis http://www.bx.psu.edu/makova_lab/publication/2016-06-plos_comput_biol/ Wed, 01 Jun 2016 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2016-06-plos_comput_biol/ A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y http://www.bx.psu.edu/makova_lab/publication/2016-01-genome_res/ Fri, 01 Jan 2016 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2016-01-genome_res/ The effects of chromatin organization on variation in mutation rates in the genome http://www.bx.psu.edu/makova_lab/publication/2015-03-nat_rev_genet/ Tue, 03 Mar 2015 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2015-03-nat_rev_genet/ Accurate typing of short tandem repeats from genome-wide sequencing data and its applications http://www.bx.psu.edu/makova_lab/publication/2015-01-genome_res/ Thu, 01 Jan 2015 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2015-01-genome_res/ Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq http://www.bx.psu.edu/makova_lab/publication/2014-11-forensic_sci_int_gen/ Sat, 01 Nov 2014 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2014-11-forensic_sci_int_gen/ Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA http://www.bx.psu.edu/makova_lab/publication/2014-10-p_natl_acad_sci_usa/ Tue, 28 Oct 2014 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2014-10-p_natl_acad_sci_usa/ Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations http://www.bx.psu.edu/makova_lab/publication/2014-07-mol_biol_evol/ Tue, 01 Jul 2014 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2014-07-mol_biol_evol/ Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes http://www.bx.psu.edu/makova_lab/publication/2014-07-plos_genet/ Tue, 01 Jul 2014 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2014-07-plos_genet/ The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study http://www.bx.psu.edu/makova_lab/publication/2014-07-bmc_pediatr/ Tue, 01 Jul 2014 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2014-07-bmc_pediatr/ Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach http://www.bx.psu.edu/makova_lab/publication/2014-04-biotechniques/ Tue, 01 Apr 2014 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2014-04-biotechniques/ Segmenting the human genome based on states of neutral genetic divergence http://www.bx.psu.edu/makova_lab/publication/2013-09-p_natl_acad_sci_usa/ Tue, 03 Sep 2013 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2013-09-p_natl_acad_sci_usa/ Gene Survival and Death on the Human Y Chromosome http://www.bx.psu.edu/makova_lab/publication/2013-04-mol_biol_evol/ Mon, 01 Apr 2013 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2013-04-mol_biol_evol/ Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells http://www.bx.psu.edu/makova_lab/publication/2013-03-g3_genes_genom_genet/ Fri, 01 Mar 2013 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2013-03-g3_genes_genom_genet/ Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome http://www.bx.psu.edu/makova_lab/publication/2013-01-genome_biol_evol/ Tue, 01 Jan 2013 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2013-01-genome_biol_evol/ The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes http://www.bx.psu.edu/makova_lab/publication/2013-01-genome_res/ Tue, 01 Jan 2013 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2013-01-genome_res/ Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion http://www.bx.psu.edu/makova_lab/publication/2012-08-plos_genet/ Wed, 01 Aug 2012 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2012-08-plos_genet/ A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? http://www.bx.psu.edu/makova_lab/publication/2012-01-genome_res/ Sun, 01 Jan 2012 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2012-01-genome_res/ SMBE Proposal to the Government of Japan http://www.bx.psu.edu/makova_lab/publication/2012-01-mol_biol_evol/ Sun, 01 Jan 2012 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2012-01-mol_biol_evol/ Genome analyses substantiate male mutation bias in many species http://www.bx.psu.edu/makova_lab/publication/2011-12-bioessays/ Thu, 01 Dec 2011 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2011-12-bioessays/ Harnessing cloud computing with Galaxy Cloud http://www.bx.psu.edu/makova_lab/publication/2011-11-nat_biotechnol/ Tue, 08 Nov 2011 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2011-11-nat_biotechnol/ DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES http://www.bx.psu.edu/makova_lab/publication/2011-10-evolution/ Sat, 01 Oct 2011 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2011-10-evolution/ A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis http://www.bx.psu.edu/makova_lab/publication/2011-06-biol_direct/ Wed, 01 Jun 2011 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2011-06-biol_direct/ Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study http://www.bx.psu.edu/makova_lab/publication/2011-06-genome_biol/ Wed, 01 Jun 2011 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2011-06-genome_biol/ A genome-wide view of mutation rate co-variation using multivariate analyses http://www.bx.psu.edu/makova_lab/publication/2011-03-genome_biol/ Tue, 01 Mar 2011 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2011-03-genome_biol/ A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses http://www.bx.psu.edu/makova_lab/publication/2011-01-genome_biol_evol/ Sat, 01 Jan 2011 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2011-01-genome_biol_evol/ A matter of life or death: How microsatellites emerge in and vanish from the human genome http://www.bx.psu.edu/makova_lab/publication/2011-01-genome_res/ Sat, 01 Jan 2011 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2011-01-genome_res/ Strong Purifying Selection at Genes Escaping X Chromosome Inactivation http://www.bx.psu.edu/makova_lab/publication/2010-11-mol_biol_evol/ Mon, 01 Nov 2010 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2010-11-mol_biol_evol/ Complete Khoisan and Bantu genomes from southern Africa http://www.bx.psu.edu/makova_lab/publication/2010-02-nature/ Thu, 18 Feb 2010 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2010-02-nature/ The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important http://www.bx.psu.edu/makova_lab/publication/2010-01-genome_res/ Fri, 01 Jan 2010 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2010-01-genome_res/ What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats http://www.bx.psu.edu/makova_lab/publication/2010-01-genome_biol_evol/ Fri, 01 Jan 2010 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2010-01-genome_biol_evol/ Genomic Analyses of Sex Chromosome Evolution http://www.bx.psu.edu/makova_lab/publication/2009-09-annu_rev_genom_hum_g/ Tue, 01 Sep 2009 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2009-09-annu_rev_genom_hum_g/ Evolution and Survival on Eutherian Sex Chromosomes http://www.bx.psu.edu/makova_lab/publication/2009-07-plos_genet/ Wed, 01 Jul 2009 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2009-07-plos_genet/ Evolution of X-Degenerate Y Chromosome Genes in Greater Apes: Conservation of Gene Content in Human and Gorilla, But Not Chimpanzee http://www.bx.psu.edu/makova_lab/publication/2009-02-j_mol_evol/ Sun, 01 Feb 2009 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2009-02-j_mol_evol/ Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes http://www.bx.psu.edu/makova_lab/publication/2009-01-genome_biol/ Wed, 28 Jan 2009 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2009-01-genome_biol/ Horse Domestication and Conservation Genetics of Przewalski's Horse Inferred from Sex Chromosomal and Autosomal Sequences http://www.bx.psu.edu/makova_lab/publication/2009-01-mol_biol_evol/ Thu, 01 Jan 2009 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2009-01-mol_biol_evol/ Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions http://www.bx.psu.edu/makova_lab/publication/2009-01-genome_res/ Thu, 01 Jan 2009 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2009-01-genome_res/ Human-macaque comparisons illuminate variation in neutral substitution rates http://www.bx.psu.edu/makova_lab/publication/2008-04-genome_biol/ Tue, 01 Apr 2008 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2008-04-genome_biol/ The genome-wide determinants of human and chimpanzee microsatellite evolution http://www.bx.psu.edu/makova_lab/publication/2008-01-genome_res/ Tue, 01 Jan 2008 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2008-01-genome_res/ A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms http://www.bx.psu.edu/makova_lab/publication/2007-09-plos_comput_biol/ Sat, 01 Sep 2007 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2007-09-plos_comput_biol/ Evolutionary and Biomedical Insights from the Rhesus Macaque Genome http://www.bx.psu.edu/makova_lab/publication/2007-04-science/ Fri, 13 Apr 2007 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2007-04-science/ A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly http://www.bx.psu.edu/makova_lab/publication/2007-01-genome_res/ Mon, 01 Jan 2007 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2007-01-genome_res/ Mammalian Male Mutation Bias: Impacts of Generation Time and Regional Variation in Substitution Rates http://www.bx.psu.edu/makova_lab/publication/2006-10-j_mol_evol/ Sun, 01 Oct 2006 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2006-10-j_mol_evol/ Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome http://www.bx.psu.edu/makova_lab/publication/2006-09-plos_genet/ Fri, 01 Sep 2006 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2006-09-plos_genet/ Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison http://www.bx.psu.edu/makova_lab/publication/2006-03-mol_biol_evol/ Wed, 01 Mar 2006 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2006-03-mol_biol_evol/ Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network http://www.bx.psu.edu/makova_lab/publication/2006-01-bmc_bioinformatics/ Fri, 27 Jan 2006 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2006-01-bmc_bioinformatics/ Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans http://www.bx.psu.edu/makova_lab/publication/2005-10-peptides/ Sat, 01 Oct 2005 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2005-10-peptides/ Initial sequence of the chimpanzee genome and comparison with the human genome http://www.bx.psu.edu/makova_lab/publication/2005-09-nature/ Thu, 01 Sep 2005 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2005-09-nature/ Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLαs/ALEX Relay http://www.bx.psu.edu/makova_lab/publication/2005-08-plos_genet/ Mon, 01 Aug 2005 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2005-08-plos_genet/ Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution http://www.bx.psu.edu/makova_lab/publication/2004-12-nature/ Thu, 09 Dec 2004 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2004-12-nature/ COMPARATIVE GENOMICS http://www.bx.psu.edu/makova_lab/publication/2004-09-annu_rev_genom_hum_g/ Wed, 22 Sep 2004 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2004-09-annu_rev_genom_hum_g/ Genome sequence of the Brown Norway rat yields insights into mammalian evolution http://www.bx.psu.edu/makova_lab/publication/2004-04-nature/ Thu, 01 Apr 2004 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2004-04-nature/ Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents http://www.bx.psu.edu/makova_lab/publication/2004-01-genome_res/ Thu, 01 Jan 2004 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2004-01-genome_res/ DNA Polymorphism and Selection at the Melanocortin-1 Receptor Gene in Normally Pigmented Southern African Individuals http://www.bx.psu.edu/makova_lab/publication/2003-06-ann_ny_acad_sci/ Sun, 01 Jun 2003 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2003-06-ann_ny_acad_sci/ Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate Genes http://www.bx.psu.edu/makova_lab/publication/2003-01-genome_res/ Wed, 01 Jan 2003 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2003-01-genome_res/ Tetranucleotide microsatellite markers for the Brown-headed Cowbird Molothrus ater http://www.bx.psu.edu/makova_lab/publication/2001-03-j_avian_biol/ Wed, 01 Jan 2003 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2001-03-j_avian_biol/ Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum http://www.bx.psu.edu/makova_lab/publication/2002-07-nature/ Thu, 18 Jul 2002 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2002-07-nature/ Strong male-driven evolution of DNA sequences in humans and apes http://www.bx.psu.edu/makova_lab/publication/2002-04-nature/ Thu, 11 Apr 2002 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2002-04-nature/ Male-driven evolution http://www.bx.psu.edu/makova_lab/publication/2002-01-curr_opin_genet_dev/ Tue, 01 Jan 2002 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2002-01-curr_opin_genet_dev/ The K A/K S Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study http://www.bx.psu.edu/makova_lab/publication/2002-01-genome_res/ Tue, 01 Jan 2002 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2002-01-genome_res/ Human DNA Sequence Variation in a 6.6-kb Region Containing the Melanocortin 1 Receptor Promoter http://www.bx.psu.edu/makova_lab/publication/2001-07-genetics/ Sun, 01 Jul 2001 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2001-07-genetics/ Episodic Evolution of Growth Hormone in Primates and Emergence of the Species Specificity of Human Growth Hormone Receptor http://www.bx.psu.edu/makova_lab/publication/2001-06-mol_biol_evol/ Fri, 01 Jun 2001 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2001-06-mol_biol_evol/ Evolution of Microsatellite Alleles in Four Species of Mice (Genus Apodemus) http://www.bx.psu.edu/makova_lab/publication/2000-08-j_mol_evol/ Tue, 01 Aug 2000 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2000-08-j_mol_evol/ Isolation of binary species-specific PCR-based markers and their value for diagnostic applications http://www.bx.psu.edu/makova_lab/publication/2000-05-gene/ Tue, 16 May 2000 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/2000-05-gene/ Representational difference analysis to distinguish cryptic species http://www.bx.psu.edu/makova_lab/publication/1999-07-mol_ecol/ Thu, 01 Jul 1999 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/1999-07-mol_ecol/ Microsatellites indicate a high frequency of multiple paternity in Apodemus (Rodentia) http://www.bx.psu.edu/makova_lab/publication/1999-01-a-mol_ecol/ Fri, 01 Jan 1999 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/1999-01-a-mol_ecol/ Microsattelite markers in wood mouse and striped field mouse (genus Apodemus) http://www.bx.psu.edu/makova_lab/publication/1998-02-mol_ecol/ Sun, 01 Feb 1998 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/1998-02-mol_ecol/ Increased Yield of Tri- and Tetranucleotide Heterospecific Microsatellites from Unenriched Small-Insert Libraries http://www.bx.psu.edu/makova_lab/publication/1998-01-biotechniques/ Thu, 01 Jan 1998 00:00:00 +0000 http://www.bx.psu.edu/makova_lab/publication/1998-01-biotechniques/