Search

Your search keyword '"Seidman, Daniel"' showing total 951 results
Start Over Author "Seidman, Daniel"
951 results on '"Seidman, Daniel"'

3. Meltos: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants

Author

Ricketts, Camir, Seidman, Daniel, Popic, Victoria, Hormozdiari, Fereydoun, Batzoglou, Serafim, and Hajirasouliha, Iman

Subjects
Biotechnology, Genetics, Breast Cancer, Human Genome, Cancer, Good Health and Well Being, Genome, Genomic Structural Variation, Genomics, High-Throughput Nucleotide Sequencing, Humans, Neoplasms, Phylogeny, Sequence Analysis, Software, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

MotivationWe propose Meltos, a novel computational framework to address the challenging problem of building tumor phylogeny trees using somatic structural variants (SVs) among multiple samples. Meltos leverages the tumor phylogeny tree built on somatic single nucleotide variants (SNVs) to identify high confidence SVs and produce a comprehensive tumor lineage tree, using a novel optimization formulation. While we do not assume the evolutionary progression of SVs is necessarily the same as SNVs, we show that a tumor phylogeny tree using high-quality somatic SNVs can act as a guide for calling and assigning somatic SVs on a tree. Meltos utilizes multiple genomic read signals for potential SV breakpoints in whole genome sequencing data and proposes a probabilistic formulation for estimating variant allele fractions (VAFs) of SV events.ResultsIn order to assess the ability of Meltos to correctly refine SNV trees with SV information, we tested Meltos on two simulated datasets with five genomes in both. We also assessed Meltos on two real cancer datasets. We tested Meltos on multiple samples from a liposarcoma tumor and on a multi-sample breast cancer data (Yates et al., 2015), where the authors provide validated structural variation events together with deep, targeted sequencing for a collection of somatic SNVs. We show Meltos has the ability to place high confidence validated SV calls on a refined tumor phylogeny tree. We also showed the flexibility of Meltos to either estimate VAFs directly from genomic data or to use copy number corrected estimates.Availability and implementationMeltos is available at https://github.com/ih-lab/Meltos.Supplementary informationSupplementary data are available at Bioinformatics online.

Published
2020

5. Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population

Author

Kivisild, Toomas, Saag, Lehti, Hui, Ruoyun, Biagini, Simone Andrea, Pankratov, Vasili, D’Atanasio, Eugenia, Pagani, Luca, Saag, Lauri, Rootsi, Siiri, Mägi, Reedik, Metspalu, Ene, Valk, Heiki, Malve, Martin, Irdt, Kadri, Reisberg, Tuuli, Solnik, Anu, Scheib, Christiana L., Seidman, Daniel N., Williams, Amy L., Tambets, Kristiina, and Metspalu, Mait

Published
2021
Full Text
View/download PDF

19. Hormonal contraception for female athletes presents special needs and concerns.

Author

Seidman, Liron, Seidman, Daniel S., and Constantini, Naama W.

Subjects
*WOMEN athletes, *BONE health, *ANTERIOR cruciate ligament injuries, *CONTRACEPTION, *PHYSICAL mobility, *CHILDREN with disabilities, *ENDURANCE athletes
Abstract

Oral contraceptives (OCs) are commonly used by female athletes raising concerns regarding the possible adverse effects of OCs on physical performance, musculoskeletal injuries, and bone density. We aimed to review all current studies on the physiological effects of OCs in physically active women. A review of literature in electronic search in PubMed and Google Scholar databases from December 2002 to December 2022 using relevant keywords. The reference lists of the articles found eligible were also reviewed. Out of 344 articles in the initial database, 54 clinical studies were eligible for inclusion in our literature review. OCs are used by about two-thirds of female athletes. Current research suggests that OCs' effects on endurance performance and muscle strength are mostly reassuring. OCs do not seem to have a major negative impact on bone health or sports injuries. In fact, new data suggests that they may even significantly reduce the risk of anterior cruciate ligament (ACL) injury. OCs can be safely used by young female athletes, who may also benefit from better menstrual cycle control. OCs offer newly realised protection from ACL injuries. The use of OCs must be carefully individualised according to their preferences, expectations, and experience. Hormonal contraception can be safely prescribed to active women. The International Olympic Committee advocates a new and wider definition for the 'athlete triad', where low energy availability presents a special challenge for these athletes. New data suggests that the use of oral contraceptives may protect against ACL injury. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results