Article
Microbiology
Hillary A. Craddock, Yair Motro, Bar Zilberman, Boris Khalfin, Svetlana Bardenstein, Jacob Moran-Gilad
Summary: This study investigated and compared short-read, long-read, and hybrid assemblies of Brucella melitensis. The results showed that hybrid assembly provided the most comprehensive data, and stand-alone short-read sequencing provided comparable data to stand-alone long-read sequencing regarding virulence genes. Further refinement is needed for stand-alone ONP sequencing in genomic epidemiology studies.
Article
Veterinary Sciences
Muhammad Nafees Ur Rehman, Farman Ullah Dawar, Jifeng Zeng, Lixia Fan, Wei Feng, Mengqi Wang, Nuo Yang, Guiying Guo, Jiping Zheng
Summary: In this study, the complete genome sequence of a highly virulent isolate Edwardsiella tarda SC002, which was obtained from hatchlings of the Siamese crocodile, was investigated. The genome of SC002 consisted of one circular chromosome and four novel plasmids, and various gene annotations and analyses were performed. The study confirmed that E. tarda SC002 is a potential pathogen with antibiotic resistance and virulence genes, and its open pan-genome may enhance its host range in the future.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Chongjing Xia, Age Qiu, Meinan Wang, Taiguo Liu, Wanquan Chen, Xianming Chen
Summary: This review summarizes the research on the genomics of rust fungi, including findings on genome size and composition variations, pathogen virulence, and population dynamics. The genomics of rust fungi provides insights into their rapid evolution and host adaptation, and contributes to disease management.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Computer Science, Interdisciplinary Applications
M. A. Bouzinier, D. Etin, S. Trifonov, V. N. Evdokimova, V Ulitin, J. Shen, A. Kokorev, A. A. Ghazani, Y. Chekaluk, Z. Albertyn, A. Giersch, C. C. Morton, F. Abraamyan, P. K. Bendapudi, S. Sunyaev, B. Krier
Summary: Despite genomic sequencing becoming routine in hospitals, there is a lack of genomic analysis software that supports both clinical and research work-flows as well as crowdsourcing. Most software packages are not compatible with ever-changing diagnostic rules and lack explainability for clinicians.
JOURNAL OF BIOMEDICAL INFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Yann X. C. Bourgeois, Ben H. Warren
Summary: The continuous improvement of high-throughput sequencing techniques has enabled the production of whole genome data in various species, which in turn provides better tools for integrating selection into historical frameworks. However, the plethora of analytical tools may confuse users and hinder the dissemination of the latest methods.
Article
Plant Sciences
Xuejin Cui, Kehong Liu, Sagheer Atta, Chunhua Zeng, Changyong Zhou, Xuefeng Wang
Summary: Two unique prophages, designated as P-PA19-1 and P-PA19-2, were identified in the CLas strain PA19 from Pakistan, with P-PA19-2 integrated into the PA19 chromosome, indicating the genomic diversity and evolution of CLas prophages.
Article
Entomology
Anna K. Childers, Scott M. Geib, Sheina B. Sim, Monica F. Poelchau, Brad S. Coates, Tyler J. Simmonds, Erin D. Scully, Timothy P. L. Smith, Christopher P. Childers, Renee L. Corpuz, Kevin Hackett, Brian Scheffler
Summary: High-quality genome assemblies are crucial for modern biological research, and advancements in sequencing methods have made it possible to sequence and assemble many insect genomes at scale. The Ag100Pest Initiative aims to assemble reference-quality genomes of important arthropod pest species to advance agricultural research. The project has already made progress in assembling genomes of multiple species and has expanded the original goal to include a total of 158 species in the pipeline.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Oncology
E. Pleasance, A. Bohm, L. M. Williamson, J. M. T. Nelson, Y. Shen, M. Bonakdar, E. Titmuss, V Csizmok, K. Wee, S. Hosseinzadeh, C. J. Grisdale, C. Reisle, G. A. Taylor, E. Lewis, M. R. Jones, D. Bleile, S. Sadeghi, W. Zhang, A. Davies, B. Pellegrini, T. Wong, R. Bowlby, S. K. Chan, K. L. Mungall, E. Chuah, A. J. Mungall, R. A. Moore, Y. Zhao, B. Deol, A. Fisic, A. Fok, D. A. Regier, D. Weymann, D. F. Schaeffer, S. Young, S. Yip, K. Schrader, N. Levasseur, S. K. Taylor, X. Feng, A. Tinker, K. J. Savage, S. Chia, K. Gelmon, S. Sun, H. Lim, D. J. Renouf, S. J. M. Jones, M. A. Marra, J. Laskin
Summary: This study demonstrates the importance of comprehensive whole-genome and transcriptome sequencing and analysis in guiding personalized cancer therapy, resulting in positive clinical benefits for a significant proportion of patients.
ANNALS OF ONCOLOGY
(2022)
Article
Microbiology
Vishal Mevada, Rajesh Patel, Pravin Dudhagara, Rajesh Chaudhari, Mustafa Vohra, Vikram Khan, Douglas J. H. Shyu, Yih-Yuan Chen, Dolatsinh Zala
Summary: This study aims to elucidate the heterogeneity of the sporadic clinical strain of V. cholerae VC01 among patients residing in Silvasa. The investigation demonstrated the existence of various genetic alterations and resistance profiles against multiple drugs. The present study helps to establish a correlation between the mutation and the coexistence of antimicrobial resistance toward current treatment.
Article
Biochemistry & Molecular Biology
Cameron M. Nugent, Tony Kess, Matthew K. Brachmann, Barbara L. Langille, Steven J. Duffy, Sarah J. Lehnert, Brendan F. Wringe, Paul Bentzen, Ian R. Bradbury
Summary: Despite the absence of physical barriers and the presence of pelagic stages in many marine taxa, environmental variation is widely recognized as a significant factor driving diversity in marine species. However, understanding the genomic and ecological processes that shape populations remains inadequate for most marine species, which often hinders management and conservation efforts.
Article
Biochemistry & Molecular Biology
Jefferson F. Paril, David J. Balding, Alexandre Fournier-Level
Summary: Mapping the genetic basis of complex traits in outbreeding species across a landscape is crucial for understanding species adaptation. Sampling more populations across the landscape using pool sequencing can lead to higher power in quantitative trait locus detection and prediction accuracy, compared to individual sequencing. It is recommended to sample populations from areas with high genetic diversity for more effective genetic mapping.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Fisheries
Syed Farhan Ahmad, Maryam Jehangir, Kornsorn Srikulnath, Cesar Martins
Summary: The rapid transformation of fish genomics and the availability of high-quality datasets provide important roadmaps for research, highlighting fish genomes as vital resources for genomic studies.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2022)
Article
Microbiology
Na Liu, Chao Liu, Yajing Song, Xingmin Han, Guwen Zhang, Zhijuan Feng, Bin Wang, Yuanpeng Bu, Jinwen Ou, Yaming Gong
Summary: Ascochyta pisi is identified as a pathogen causing ascochyta blight of pea in China, and its fully annotated genome is reported in this study. Comparative genome analysis reveals the genetic diversity and evolutionary relationship of Ascochyta species. In planta transcriptome analysis provides valuable information for further understanding the interaction between Ascochyta spp. and legumes.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Konstantinos Tegopoulos, Odysseas Sotirios Stergiou, Despoina Eugenia Kiousi, Margaritis Tsifintaris, Ellie Koletsou, Aristotelis C. Papageorgiou, Anthoula A. Argyri, Nikos Chorianopoulos, Alex Galanis, Petros Kolovos
Summary: Lactiplantibacillus plantarum is a diverse species with potential probiotic traits, as shown by the genomic analysis and functional studies of strain L125.
Article
Genetics & Heredity
Jason L. Vassy, Annjanette Stone, John T. Callaghan, Margaret Mendes, Laurence J. Meyer, Victoria M. Pratt, Ronald M. Przygodzki, Maren T. Scheuner, Jessica Wang-Rodriguez, Steven A. Schichman
GENETICS IN MEDICINE
(2019)
Review
Pharmacology & Pharmacy
Jason L. Vassy, Sojeong Chun, Sanjay Advani, Sophie A. Ludin, Jason G. Smith, Elaine C. Alligood
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2019)
Editorial Material
Medicine, General & Internal
Jason L. Vassy
ANNALS OF INTERNAL MEDICINE
(2019)
Letter
Genetics & Heredity
Jason L. Vassy, Annjanette Stone, John T. Callaghan, Margaret Mendes, Laurence J. Meyer, Victoria M. Pratt, Ronald M. Przygodzki, Maren T. Scheuner, Jessica Wang-Rodriguez, Steven A. Schichman
GENETICS IN MEDICINE
(2019)
Letter
Health Care Sciences & Services
Leland E. Hull, Kevin G. Lynch, David W. Oslin
JOURNAL OF GENERAL INTERNAL MEDICINE
(2019)
Article
Nutrition & Dietetics
Rachel E. Ward, Kelly Cho, Xuan-Mai T. Nguyen, Jason L. Vassy, Yuk-Lam Ho, Rachel M. Quaden, David R. Gagnon, Peter W. F. Wilson, J. Michael Gaziano, Luc Djousse
CLINICAL NUTRITION
(2020)
Article
Cardiac & Cardiovascular Systems
Sridharan Raghavan, Jason L. Vassy, Yuk-Lam Ho, Rebecca J. Song, David R. Gagnon, Kelly Cho, Peter W. F. Wilson, Lawrence S. Phillips
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2019)
Review
Genetics & Heredity
Yvonne Bombard, Kyle B. Brothers, Sara Fitzgerald-Butt, Nanibaa' A. Garrison, Leila Jamal, Cynthia A. James, Gail P. Jarvik, Jennifer B. McCormick, Tanya N. Nelson, Kelly E. Ormond, Heidi L. Rehm, Julie Richer, Emmanuelle Souzeau, Jason L. Vassy, Jennifer K. Wagner, Howard P. Levy
AMERICAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Nutrition & Dietetics
Jacqueline P. Honerlaw, Yuk-Lam Ho, Xuan-Mai T. Nguyen, Kelly Cho, Jason L. Vassy, David R. Gagnon, Christopher J. O'Donnell, J. Michael Gaziano, Peter W. F. Wilson, Luc Djousse
CLINICAL NUTRITION
(2020)
Article
Multidisciplinary Sciences
Mary K. Rhee, Vuk-Lam Ho, Sridharan Raghavan, Jason L. Vassy, Kelly Cho, David Gagnon, Lisa R. Staimez, Christopher N. Ford, Peter W. F. Wilson, Lawrence S. Phillips
Article
Pharmacology & Pharmacy
Leland E. Hull, Catherine Chanfreau-Coffinier, Sony Tuteja, Dan Berlowitz, Lisa S. Lehmann, David W. Oslin, Jeffrey M. Pyne, Scott L. DuVall, Julie A. Lynch
Article
Pathology
Leland E. Hull, Jason L. Vassy, Annjanette Stone, Catherine C. Chanfreau-Coffinier, Craig W. Heise, Victoria M. Pratt, Ronald Przygodzki, Corrine Voils, Deepak Voora, Jessica Wang-Rodriguez, Steven A. Schichman, Maren T. Scheuner
JOURNAL OF MOLECULAR DIAGNOSTICS
(2020)
Article
Genetics & Heredity
Leland E. Hull, Pradeep Natarajan
Summary: This study examined the self-rated family health history knowledge among participants and identified disparities in knowledge levels based on different characteristics. Individuals assigned male sex at birth, those identifying as possible gender and sexual minorities, individuals of non-White race, individuals with lower household income, and those with lower educational attainment were more likely to have less or no family health history knowledge.
GENETICS IN MEDICINE
(2022)
Review
Medicine, General & Internal
Hannah G. Kirby, Heidi L. Rehm, Leland E. Hull
Summary: As patient access to lab testing outside the clinic increases, healthcare providers will face more questions about the usefulness and interpretation of consumer-initiated genetic testing for health risks. This study aimed to understand the variety of consumer-initiated germline genetic testing options available in the market. The researchers conducted an environmental scan to identify companies offering germline genetic tests for diagnosable health conditions, which could be purchased by consumers in the US without consulting healthcare providers. They found 21 companies offering 74 distinct test products that met their criteria, and only a minority of them assessed the presence of CDC Tier 1 conditions that have evidence-based guidelines for detection and management.
MAYO CLINIC PROCEEDINGS
(2023)
Article
Genetics & Heredity
Leland E. Hull, Kelsey Flannery, Anjali Kaimal, Karen Sepucha, Heidi L. Rehm, Jennifer S. Haas
Summary: In this study, the multilevel barriers to the widespread adoption of preconception reproductive genetic carrier screening (RGCS) in the United States were explored through key informant interviews. The barriers were identified at different levels, including test characteristics, patients and couples, clinicians and care teams, and the external health care and policy environments. Potential solutions were discussed by the informants, which may help to alleviate the obstacles.
GENETICS IN MEDICINE
(2023)