Article
Genetics & Heredity
Hila Fridman, Helger G. Yntema, Reedik Magi, Reidar Andreson, Andres Metspalu, Massimo Mezzavila, Chris Tyler-Smith, Yali Xue, Shai Carmi, Ephrat Levy-Lahad, Christian Gilissen, Han G. Brunner
Summary: Genome sequencing revealed that each individual in the European population carries at least 2 pathogenic variants, with nearly 1% of European couples facing the risk of having a child with a severe genetic disorder. The risk is significantly higher for first cousins and particularly increased for skeletal disorders and intellectual disabilities due to their unique genetic architecture.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Tzahi Gabzi, Yitzhak Pilpel, Tamar Friedlander
Summary: This article investigates the fitness landscape of a yeast tRNA gene and finds that the wild type allele is sub-optimal. It also rules out the possibility that the wild type is the fittest on average or located on a local fitness maximum under four different conditions. The study further reveals that the wild type is mutationally robust, while more fit variants are typically mutationally fragile. Similar observations have been made in viral genomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Oncology
Isabelle A. van Zeventer, Aniek O. de Graaf, Jonas B. Salzbrunn, Ilja M. Nolte, Priscilla Kamphuis, Avinash Dinmohamed, Bert A. van der Reijden, Jan Jacob Schuringa, Joop H. Jansen, Gerwin Huls
Summary: Knowledge about the evolution of clonal hematopoiesis is crucial for clinical decision-making. This study investigated clonal evolution in a large cohort and found that spliceosome and JAK2 mutations have the highest growth rates, while DNMT3A and TP53 mutations show minimal growth, regardless of cytosis or cytopenia. Individual variability suggests modulation by non-mutation-related factors. The risk for myeloid malignancy is highest for JAK2, spliceosome, or TP53 mutations and is preceded by cytosis or cytopenia. These findings provide important insights for monitoring and managing clonal hematopoiesis and related disorders.
Article
Ecology
Scott A. Martin, William E. Peterman, Gregory J. J. Lipps Jr, H. Lisle Gibbs
Summary: Assessing environmental factors for species movement is crucial for identifying conservation actions that connect isolated populations. However, direct observations are limited, so alternate approaches like landscape genetic analyses are necessary. This study uses such analysis to assess the impact of landscape features on the movement of the eastern massasauga rattlesnake. The findings highlight the importance of land-cover and inherent landscape features on current connectivity, and provide valuable information for guiding future habitat modification and land acquisition actions to connect isolated populations.
ECOLOGICAL APPLICATIONS
(2023)
Article
Genetics & Heredity
Line Kenborg, Cristina Boschini, Pernille E. Bidstrup, Susanne O. Dalton, Karoline Doser, Thomas T. Nielsen, Anja Kroyer, Christoffer Johansen, Kirsten Frederiksen, Sven Asger Sorensen, Hanne Hove, John R. Ostergaard, John J. Mulvihill, Jeanette F. Winther
Summary: The cumulative incidence of a first pregnancy at age 50 was slightly lower in women with NF1 compared to the population comparison, but the hazard of pregnancy was similar between the two groups after adjusting for potential medical consequences of NF1. Women with NF1 had higher rates of spontaneous abortions and stillbirths compared to the population comparison.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Biology
Robson Rodrigues da Silva, Osias Baptista de Souza Filho, Jose Wilson Magalhaes Bassani, Rosana Almada Bassani
Summary: Mathematical models are valuable tools in studying physiological phenomena, but discrepancies may arise due to differences in assumptions and formulations. This study developed a computational tool, ForceLAB, to implement and compare different contraction models for cardiomyocyte contraction. Comparisons between NL and RWH models revealed variations in the simulation results, particularly in response to modifications of the equilibrium Ca2+-troponin C dissociation constant.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Computer Science, Artificial Intelligence
Yaxin Li, Kunjie Yu, Jing Liang, Caitong Yue, Kangjia Qiao
Summary: Photovoltaic systems have the ability to convert solar energy into electricity directly, and the accuracy and stability of their conversion performance depend on the parameters of the photovoltaic model. The landscape-aware particle swarm optimization algorithm (LaPSO) proposed in this study provides an effective solution for parameter identification of photovoltaic systems, offering accurate and stable estimation results under various practical conditions.
APPLIED SOFT COMPUTING
(2022)
Article
Physics, Multidisciplinary
Kenji Okubo, Kunihiko Kaneko
Summary: The fitness landscape is a critical concept in biology that visualizes the relationship between genotype and fitness. This study adopts gene regulatory networks to analyze how genotype shapes phenotype and fitness, and investigates the population distribution and evolution under sexual reproduction in the obtained landscape.
NEW JOURNAL OF PHYSICS
(2022)
Review
Microbiology
Jose Carlos Ramon Hernandez-Beltran, Alvaro San Millan, Ayari Fuentes-Hernandez, Rafael Pena-Miller
Summary: This review explores theoretical models of plasmid dynamics, ranging from the molecular mechanisms of plasmid partition and copy-number control at a cellular level, to their consequences in the population dynamics of complex microbial communities.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Claribel Tian Yu Foo, Yi Hui To, Astrid Irwanto, Alvin Yu-Jin Ng, Benedict Yan, Sophia Tsong Huey Chew, Jianjun Liu, Lian Kah Ti
Summary: This study describes the variant landscape of the RYR1 gene in Singapore, identifying pathogenic and likely pathogenic variants that are mainly missense mutations and occur at higher frequencies in Asians than globally. These findings will facilitate genetic screening for RYR1-related conditions.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Julia Leme Pablos, Ana Kristina Silva, Noemy Seraphim, Luiza de Moraes Magaldi, Anete Pereira de Souza, Andre Victor Lucci Freitas, Karina Lucas Silva-Brandao
Summary: The study on Atlantic Forest White Morpho butterflies shows that there is no clear species diversification and population structure among the populations, suggesting that the current distinction between the two species is unreasonable. Northern samples exhibit more intragroup structure, and clustering tests indicate the existence of three genetic clusters, with turnover between the states of Paran ' a and Sa similar to o Paulo.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Dave W. Anderson, Florian Baier, Gloria Yang, Nobuhiko Tokuriki
Summary: This study characterizes the catalytic activity of a recently evolved bacterial enzyme under various laboratory conditions, revealing that adaptive landscapes may shift due to genotype-by-environment interactions and environment-dependent epistasis, impacting the fitness of functional mutations.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
William E. Peterman, Nathaniel S. Pope
Summary: The field of landscape genetics is rapidly evolving and using regression-based frameworks to infer the contributions of landscape and habitat variables to genetic differentiation. It is important to model a single conductance or resistance surface as a parameterized function of spatial covariates and estimate parameters by linking resistance distances to genetic dissimilarity. Nuisance parameters in regression models should not be confused with the mapping between spatial covariates and conductance/resistance.
Article
Physics, Multidisciplinary
Shamreen Iram, Emily Dolson, Joshua Chiel, Julia Pelesko, Nikhil Krishnan, Ozenc Gungor, Benjamin Kuznets-Speck, Sebastian Deffner, Efe Ilker, Jacob G. Scott, Michael Hinczewski
Summary: The study proposes using quantum methods to control potential evolutionary outcomes to address the unpredictability of evolution. By manipulating the speed and trajectories of evolution, this approach has diverse applications in disease treatment, climate change adaptation, agriculture, and bioengineering.
Article
Health Care Sciences & Services
Yingzhao Huang, Bowen Liu, Jile Shi, Sen Zhao, Kexin Xu, Liying Sun, Na Chen, Wen Tian, Jianguo Zhang, Nan Wu
Summary: Clinical exome sequencing has proven to be useful in diagnosing Mendelian disorders and can reveal secondary findings unrelated to the primary diagnosis. This study evaluated genetic data from 2987 individuals in the Chinese population and found that 5.3% of them had reportable variants associated with cancer, cardiovascular, metabolic, and other phenotypes. Additionally, 1.5% of the individuals carried secondary findings in newly added genes.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Review
Physics, Multidisciplinary
Uri Obolski, Yoav Ram, Lilach Hadany
REPORTS ON PROGRESS IN PHYSICS
(2018)
Article
Ecology
Yoav Ram, Uri Liberman, Marcus W. Feldman
THEORETICAL POPULATION BIOLOGY
(2019)
Article
Ecology
Yoav Ram, Lilach Hadany
AMERICAN NATURALIST
(2019)
Article
Multidisciplinary Sciences
Yoav Ram, Eynat Dellus-Gur, Maayan Bibi, Kedar Karkare, Uri Obolski, Marcus W. Feldman, Tim F. Cooper, Judith Berman, Lilach Hadany
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Eyal Zinger, Ariel Gueijman, Uri Obolski, Yoav Ram, Eliya Ruby, Mor Binder, Nivi Yechieli, Nir Ohad, Lilach Hadany
SCIENTIFIC REPORTS
(2019)
Letter
Multidisciplinary Sciences
Yoav Ram, Uri Obolski, Marcus W. Feldman, Judith Berman, Lilach Hadany
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Ecology
Uri Liberman, Yoav Ram, Lee Altenberg, Marcus W. Feldman
THEORETICAL POPULATION BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Kaleda Krebs Denton, Yoav Ram, Uri Liberman, Marcus W. Feldman
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Oren Kolodny, Michael Berger, Marcus W. Feldman, Yoav Ram
Article
Biochemical Research Methods
Ronan F. Arthur, James H. Jones, Matthew H. Bonds, Yoav Ram, Marcus W. Feldman
Summary: Epidemics pose challenging dilemmas for governments and individuals, requiring a delicate balance between economic and personal health considerations. Adaptive social contact plays a key role in epidemic outcomes, yet the complexity of human-nature epidemic systems remains poorly understood.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biology
Dor Cohen, Ohad Lewin-Epstein, Marcus W. Feldman, Yoav Ram
Summary: The study examines the cultural evolution of cooperation under vertical and non-vertical cultural transmission, finding conditions for fixation and coexistence of cooperation and defection. Cooperation evolution is facilitated by horizontal transmission and an association between social interactions and horizontal transmission. When stable polymorphism occurs, reduced association between social interactions and horizontal transmission leads to lower cooperation frequency and population mean fitness.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Infectious Diseases
Ilia Kohanovski, Uri Obolski, Yoav Ram
Summary: This study analyzes the differences between the official and effective start dates of non-pharmaceutical interventions (NPIs) and finds that neglecting these differences can lead to underestimation of the impact of NPIs. The study reveals that the effective start dates of NPIs are often later than the official dates in various regions.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Ecology
Kaleda K. Denton, Yoav Ram, Marcus W. Feldman
Summary: The evolution of altruism has been extensively studied under genetic transmission, but less is known about its dynamics under cultural transmission. Previous research has shown that cultural transmission can facilitate the evolution of altruism by increasing the probability of adopting altruistic behavior and promoting assortment among altruists. This study incorporates vertical and oblique transmission, and explores the effects of conformist and anti-conformist transmission on the evolution of altruism in different scenarios. It also investigates the invasion of an allele that increases individuals' content bias for altruism in the absence of other forms of cultural transmission.
THEORETICAL POPULATION BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Grace Avecilla, Julie N. Chuong, Fangfei Li, Gavin Sherlock, David Gresham, Yoav Ram
Summary: The rate of adaptive evolution depends on the rate at which beneficial mutations are introduced into a population and their fitness effects. This study estimates the rate at which beneficial copy number variants (CNVs) are introduced and their fitness effects using CNV adaptation dynamics and simulation-based likelihood-free inference approaches. The results demonstrate the importance of CNVs in rapid adaptive evolution and validate the use of neural network-based likelihood-free inference methods for inferring evolutionary rates and effects.
Correction
Multidisciplinary Sciences
Yoav Ram, Eynat Dellus-Gur, Maayan Bibi, Kedar Karkare, Uri Obolski, Marcus W. Feldman, Tim F. Cooper, Judith Berman, Lilach Hadany
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Ecology
Jorge Pena, Aviad Heifetz, Georg Noldeke
Summary: Cooperation usually becomes harder to sustain as groups become larger, but in some cases, increasing group size can increase the probability of cooperation. The expected payoff and the probability of provision of the public good vary with the cost of cooperation.
THEORETICAL POPULATION BIOLOGY
(2024)