{"entity": "researcher", "timestamp": "2026-04-12T03:31:33.617Z", "family": "Makova", "given": "Kateryna D", "initials": "KD", "orcid": "0000-0002-6212-9526", "affiliations": ["Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.", "Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802, USA.", "Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1f4ca58ca046e693c89df604c4160b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1f4ca58ca046e693c89df604c4160b"}}, "publications": [{"entity": "publication", "iuid": "bbc07d308f62492d8088127bea304c70", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bbc07d308f62492d8088127bea304c70.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bbc07d308f62492d8088127bea304c70"}}, "title": "Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.", "authors": [{"family": "Tomaszkiewicz", "given": "Marta", "initials": "M", "orcid": "0000-0003-1523-200X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4950e63e7e8d47ea876c82fd1ffc01e0.json"}}, {"family": "Sahlin", "given": "Kristoffer", "initials": "K"}, {"family": "Medvedev", "given": "Paul", "initials": "P", "orcid": "0000-0003-3143-594X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aec0de4e3d414aab8934186cfbe97084.json"}}, {"family": "Makova", "given": "Kateryna D", "initials": "KD", "orcid": "0000-0002-6212-9526", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1f4ca58ca046e693c89df604c4160b.json"}}], "type": "journal article", "published": "2023-11-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes; however, the diversity of splicing variants remains unexplored. Here, we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this data set resulted in several findings. First, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Second, our results suggest that BPY2 transcripts and proteins originate from separate genomic regions in bonobo versus human, which is possibly facilitated by acquiring new promoters. Third, our analysis indicates that the PRY gene family, having the highest representation of noncoding transcripts, has been undergoing pseudogenization. Fourth, we have not detected signatures of selection in the five YAG families shared among great apes, even though we identified many species-specific protein-coding transcripts. Fifth, we predicted consensus disorder regions across most gene families and species, which could be used for future investigations of male infertility. Overall, our work illuminates the YAG isoform landscape and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.", "doi": "10.1093/gbe/evad205", "pmid": "37967251", "labels": {"Kristoffer Sahlin": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10673640"}, {"db": "pii", "key": "7423992"}], "notes": [], "created": "2024-11-25T21:07:55.601Z", "modified": "2024-11-25T21:08:47.859Z"}, {"entity": "publication", "iuid": "d77aaa7b2ff84ad4a05be30d8875a372", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d77aaa7b2ff84ad4a05be30d8875a372.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d77aaa7b2ff84ad4a05be30d8875a372"}}, "title": "DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.", "authors": [{"family": "Rangavittal", "given": "Samarth", "initials": "S"}, {"family": "Stopa", "given": "Natasha", "initials": "N"}, {"family": "Tomaszkiewicz", "given": "Marta", "initials": "M", "orcid": "0000-0003-1523-200X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4950e63e7e8d47ea876c82fd1ffc01e0.json"}}, {"family": "Sahlin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0001-7378-2320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca3f1ebe1b9946a9ad9eb4b3058a911c.json"}}, {"family": "Makova", "given": "Kateryna D", "initials": "KD", "orcid": "0000-0002-6212-9526", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1f4ca58ca046e693c89df604c4160b.json"}}, {"family": "Medvedev", "given": "Paul", "initials": "P", "orcid": "0000-0003-3143-594X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aec0de4e3d414aab8934186cfbe97084.json"}}], "type": "journal article", "published": "2019-08-09", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "20", "issue": "1", "pages": "641", "issn-l": "1471-2164"}, "abstract": "Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly broadly fall into two categories. The first involves retrieving Y-contigs using proportion sharing with a female, but such a strategy is prone to false positives in the absence of a high-quality, complete female reference. A second strategy uses the ratio of depth of coverage from male and female reads to select Y-contigs, but such a method requires high-depth sequencing of a female and cannot utilize existing female references.\n\nWe develop a k-mer based method called DiscoverY, which combines proportion sharing with female with depth of coverage from male reads to classify contigs as Y-chromosomal. We evaluate the performance of DiscoverY on human and gorilla genomes, across different sequencing platforms including Illumina, 10X, and PacBio. In the cases where the male and female data are of high quality, DiscoverY has a high precision and recall and outperforms existing methods. For cases when a high quality female reference is not available, we quantify the effect of using draft reference or even just raw sequencing reads from a female.\n\nDiscoverY is an effective method to isolate Y-specific contigs from a whole-genome assembly. However, regions homologous to the X chromosome remain difficult to detect.", "doi": "10.1186/s12864-019-5996-3", "pmid": "31399045", "labels": {"Kristoffer Sahlin": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6688218"}, {"db": "pii", "key": "10.1186/s12864-019-5996-3"}], "notes": [], "created": "2020-11-07T13:35:19.178Z", "modified": "2025-11-04T14:22:19.807Z"}, {"entity": "publication", "iuid": "6df617783fbc4bb6af894f78d5bd469e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6df617783fbc4bb6af894f78d5bd469e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6df617783fbc4bb6af894f78d5bd469e"}}, "title": "Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon.", "authors": [{"family": "Sahlin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0001-7378-2320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca3f1ebe1b9946a9ad9eb4b3058a911c.json"}}, {"family": "Tomaszkiewicz", "given": "Marta", "initials": "M", "orcid": "0000-0003-1523-200X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4950e63e7e8d47ea876c82fd1ffc01e0.json"}}, {"family": "Makova", "given": "Kateryna D", "initials": "KD", "orcid": "0000-0002-6212-9526", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1f4ca58ca046e693c89df604c4160b.json"}}, {"family": "Medvedev", "given": "Paul", "initials": "P", "orcid": "0000-0003-3143-594X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aec0de4e3d414aab8934186cfbe97084.json"}}], "type": "journal article", "published": "2018-11-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "9", "issue": "1", "pages": "4601", "issn-l": "2041-1723"}, "abstract": "A significant portion of genes in vertebrate genomes belongs to multigene families, with each family containing several gene copies whose presence/absence, as well as isoform structure, can be highly variable across individuals. Existing de novo techniques for assaying the sequences of such highly-similar gene families fall short of reconstructing end-to-end transcripts with nucleotide-level precision or assigning alternatively spliced transcripts to their respective gene copies. We present IsoCon, a high-precision method using long PacBio Iso-Seq reads to tackle this challenge. We apply IsoCon to nine Y chromosome ampliconic gene families and show that it outperforms existing methods on both experimental and simulated data. IsoCon has allowed us to detect an unprecedented number of novel isoforms and has opened the door for unraveling the structure of many multigene families and gaining a deeper understanding of genome evolution and human diseases.", "doi": "10.1038/s41467-018-06910-x", "pmid": "30389934", "labels": {"Kristoffer Sahlin": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6214943"}, {"db": "pii", "key": "10.1038/s41467-018-06910-x"}], "notes": [], "created": "2020-11-07T13:34:26.078Z", "modified": "2025-11-04T14:22:29.908Z"}]}