Article
Biotechnology & Applied Microbiology
Junfeng Liu, Xianchao Ji, Hua Chen
Summary: This study introduced a new method called Beta-PSMC, which refines population history in each time interval by incorporating a beta distribution into the Pairwise Sequentially Markovian Coalescent model. Compared to traditional methods, Beta-PSMC achieved more detailed results and demonstrated higher accuracy and resolution in simulation experiments. It was also successfully applied to infer the population history of Adelie penguin, showing contrasting population size fluctuations with temperature changes 15-27 thousand years ago.
Article
Biochemistry & Molecular Biology
Zeqi Yao, Kehui Liu, Shanjun Deng, Xionglei He
Summary: The study introduces a new coalescent method, i-coalescent analysis, which computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles. It accurately reconstructs population size dynamics of highly structured populations, although larger sample sizes are often required for structured populations.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
James B. Dorey, Scott V. C. Groom, Alejandro Velasco-Castrillon, Mark I. Stevens, Michael S. Y. Lee, Michael P. Schwarz
Summary: There is substantial debate on the roles of climate change and human activities on biodiversity and species demographies over the Holocene. Molecular approaches can be used to disentangle the impacts of humans and climate change on tropical pollinators.
Article
Biochemical Research Methods
Gautam Upadhya, Matthias Steinrucken
Summary: This article presents a novel method for inferring the size history of a population using full-genome sequencing data. The method is based on a Coalescent Hidden Markov model framework and can uncover past migration events and population size changes, which are of anthropological and disease-related genetic variation interest. The method is applicable in situations with limited data quality and has potential applications for pseudo-haploid data.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Donna Henderson, Sha (Joe) Zhu, Christopher B. Cole, Gerton Lunter
Summary: This study introduces a coalescent-with-recombination model to connect demography and genetics, using particle filters and Variational Bayes to infer unobserved genealogies in the genome. Through real and simulated genomes, it shows improved accuracy in inferring past population sizes and the potential for jointly analyzing multiple genomes under complex demographic models.
Article
Biochemistry & Molecular Biology
Nathan W. Byer, Matthew L. Holding, Miranda M. Crowell, Todd W. Pierson, Thomas E. Dilts, Eveline S. Larrucea, Kevin T. Shoemaker, Marjorie D. Matocq
Summary: The study revealed that spatially separated populations of pygmy rabbits exhibit local adaptation, potentially driven by genetic loci with functional annotations related to plant secondary compound metabolism. Additionally, populations in the Mono Basin of California likely diverged from other Great Basin populations during late Pleistocene climate oscillations, demonstrating adaptive differentiation despite limited gene flow and small effective population size.
Article
Cell Biology
Nicola F. Mueller, Cassia Wagner, Chris D. Frazar, Pavitra Roychoudhury, Jover Lee, Louise H. Moncla, Benjamin Pelle, Matthew Richardson, Erica Ryke, Hong Xie, Lasata Shrestha, Amin Addetia, Victoria M. Rachleff, Nicole A. P. Lieberman, Meei-Li Huang, Romesh Gautom, Geoff Melly, Brian Hiatt, Philip Dykema, Amanda Adler, Elisabeth Brandstetter, Peter D. Han, Kairsten Fay, Misja Llcisin, Kristen Lacombe, Thomas R. Sibley, Melissa Truong, Caitlin R. Wolf, Michael Boeckh, Janet A. Englund, Michael Famulare, Barry R. Lutz, Mark J. Rieder, Matthew Thompson, Jeffrey S. Duchin, Lea M. Starita, Helen Y. Chu, Jay Shendure, Keith R. Jerome, Scott Lindquist, Alexander L. Greninger, Deborah A. Nickerson, Trevor Bedford
Summary: The study analyzed the spread of SARS-CoV-2 in Washington State in early 2020, finding that factors influencing transmission included the timing of mitigation measures and repeated introductions of viral lineages. Additionally, the increase in frequency of the 614G variant may be related to regional mobility differences and multiple introductions, but no evidence was found that this variant affects clinical severity or patient outcomes.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Mathieu Siol, Thomas Coudoux, Sebastien Ravel, Stephane De Mita
Summary: The egglib software package has been massively updated and optimized into a Python package to accommodate modern-sized datasets for population genetics analysis.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Geography, Physical
Kunhui Ye, Yanming Lyu, Rong Chen
Summary: This study uses China's urban population data to investigate the dynamic adjustment and correlation at the urban hierarchy level. The findings show that the spatial distribution of urban population size is gradually becoming more even within the same urban hierarchy, while the distribution across the entire urban system is becoming more uneven. The study outcomes provide valuable references for Chinese policy-makers and practitioners and have potential benefits for future studies on spatial population size distribution in international communities.
INTERNATIONAL JOURNAL OF DIGITAL EARTH
(2023)
Article
Biochemistry & Molecular Biology
Laurence Gagnon, Claudia Moreau, Catherine Laprise, Helene Vezina, Simon L. Girard
Summary: Using genealogy, researchers studied the demographic history of Quebec's population over the last 400 years. The study showed that the Quebec population structure began forming in the St. Lawrence valley as early as 1750, with distinct groups like the Saguenay and Gaspesian groups. Ancestors of these groups experienced increased kinship and inbreeding levels, leading to the contemporary population structure. Regional founder effects resulted in differences in genetic sharing among these groups, with Gaspe and North Shore groups sharing more large segments and the Sagueneans sharing more short segments.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Plant Sciences
N. N. Mhlongo, M. F. Pfab, E. T. F. Witkowski
Summary: Many succulent Euphorbia species in South Africa are endangered due to human activities such as habitat loss and illegal harvesting. This study focuses on the formerly widespread Euphorbia bupleurifolia and documents its distribution, abundance, and population biology in South Africa. The study reveals a decline in the species' distribution, with only nine populations still remaining. The study also provides important demographic data and highlights the threats and potential conservation strategies for E. bupleurifolia.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Article
Statistics & Probability
Fernando Cordero, Jason Schweinsberg, Adrian Gonzalez Casanova, Maite Wilke-Berenguer
Summary: This article considers the evolution of a population in three seasons: spring, summer, and winter. The wake-up and reproduction processes of individuals are studied, and it is shown that the genealogy of the population can be described by a specific coalescent process under certain parameter choices.
ELECTRONIC JOURNAL OF PROBABILITY
(2022)
Article
Agronomy
Haiyan Yu, Juan Yang, Hailan Cui, Adeel Abbas, Shouhui Wei, Xiangju Li
Summary: Aegilops tauschii, a noxious grass weed affecting wheat quality and yield, was found in wheat fields across various provinces in China. Genetic diversity was moderately high with no clear geographic patterns. Structure analysis divided the populations into three groups, with majority of variation occurring within population groups.
Article
Biochemistry & Molecular Biology
Zhi Yan, Huw A. Ogilvie, Luay Nakhleh
Summary: Accurate inference of population parameters is crucial for understanding evolutionary histories, but modeling recombination exactly remains challenging. This study evaluates three different methods (StarBEAST2, SNAPP, and diCal2) for population parameter estimation. Whole-genome simulations with varying recombination rates, mutation rates, and incomplete lineage sorting levels were conducted. The results show that StarBEAST2 is robust to realistic recombination rates, SNAPP is generally unaffected by recombination events, and surprisingly, diCal2 performs considerably worse than other methods.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Ecology
Degu Abate, Zerihun Girma
Summary: A study was conducted in northern Ethiopia to investigate the population size, structure, and distribution of geladas in Kotu forest and associated grasslands. The study found that the population size was 229, with a male to female ratio of 1:1.178. Geladas were mainly distributed in grassland habitats, emphasizing the need for special attention to the conservation of these habitats for sustainable conservation of the species in the area.
ECOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshoj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andres Lanzos, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, Andre Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uuskula-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Juri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Nuria Lopez-Bigas, Joachim Weischenfeldt, Rameen Beroukhim, Inigo Martincorena, Jakob Skou Pedersen, Gad Getz, Gary D. Bader, Jonathan Barenboim, Soren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti-Passerini, Dale W. Garsed, Ivo G. Gut, David Haan, Arif O. Harmanci, Mohamed Helmy, Ermin Hodzic, Jose M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Alexander Martinez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muinos, Marta Paczkowska, Kiejung Park, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, S. Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro CortesCiriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff Macintyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John Pearson, Montserrat Puiggros, Karsten Rippe, Steven A. Roberts, Bernardo RodriguezMartin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Lixing Yang, Sung-Soo Yoon, Jorge Zamora
Article
Physics, Multidisciplinary
Celia Anteneodo, Lucianno Defaveri, Eli Barkai, David A. Kessler
Summary: This study investigates the overdamped Langevin motion in a deep potential well, where a regularized BG statistics equation can predict the values of dynamical and thermodynamic observables in a non-normalizable quasi-equilibrium state. By eigenfunction expansion of the Fokker-Planck equation, an approximate time-independent solution in BG form valid for long time intervals but short compared to the escape time is obtained. The escaped particles follow a general free-particle statistics with an error function solution shifted due to initial potential well barriers. The validity of regularized BG statistics in describing the time-independent regime despite the non-normalizable quasi-stationary state is demonstrated.
Article
Oncology
Jiil Chung, Yosef E. Maruvka, Sumedha Sudhaman, Jacalyn Kelly, Nicholas J. Haradhvala, Vanessa Bianchi, Melissa Edwards, Victoria J. Forster, Nuno M. Nunes, Melissa A. Galati, Martin Komosa, Shriya Deshmukh, Vanja Cabric, Scott Davidson, Matthew Zatzman, Nicholas Light, Reid Hayes, Ledia Brunga, Nathaniel D. Anderson, Ben Ho, Karl P. Hodel, Robert Siddaway, A. Sorana Morrissy, Daniel C. Bowers, Valerie Larouche, Annika Bronsema, Michael Osborn, Kristina A. Cole, Enrico Opocher, Gary Mason, Gregory A. Thomas, Ben George, David S. Ziegler, Scott Lindhorst, Magimairajan Vanan, Michal Yalon-Oren, Alyssa T. Reddy, Maura Massimino, Patrick Tomboc, An Van Damme, Alexander Lossos, Carol Durno, Melyssa Aronson, Daniel A. Morgenstern, Eric Bouffet, Annie Huang, Michael D. Taylor, Anita Villani, David Malkin, Cynthia E. Hawkins, Zachary F. Pursell, Adam Shlien, Thomas A. Kunkel, Gad Getz, Uri Tabori
Summary: This study identified a new association between loss of polymerase proofreading and MSI, especially when both components are lost. Analysis of indels in microsatellites revealed five distinct signatures, providing insight into the mechanism of indel formation. The research demonstrates that MS-sigs can be a powerful clinical tool for diagnosing replication repair deficiency and predicting immunotherapy response.
Article
Biology
Megan Shand, Jose Soto, Lee Lichtenstein, David Benjamin, Yossi Farjoun, Yehuda Brody, Yosef Maruvka, Paul C. Blainey, Eric Banks
COMMUNICATIONS BIOLOGY
(2020)
Article
Physics, Multidisciplinary
Felix Thiel, Itay Mualem, David Kessler, Eli Barkai
Summary: A classical random walker on a finite graph will always reach any other node, while quantum walks may exhibit non-ergodic features due to destructive interference. The final detection of the system is not guaranteed under repeated projective local measurements, as the Hilbert space is split into bright and dark subspaces. An uncertainty relation for detection probability deviations from the classical counterpart is found in terms of energy fluctuations.
Article
Physics, Multidisciplinary
Lior Zarfaty, Eli Barkai, David A. Kessler
Summary: This paper discusses the classic problem of extreme value statistics, showing that the distribution of maxima converges to one of three limiting forms through the Fisher-Tippett-Gnedenko theorem. Utilizing the Gumbel limit allows for accurate approximation of the extreme value distribution, with parameters represented as power series and the underlying distribution transformed. Functional corrections to the Gumbel limit are considered, obtainable through Taylor expansion, which also helps characterize extreme value statistics in cases where the underlying distribution is unknown.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Multidisciplinary Sciences
Lindsay M. Morton, Danielle M. Karyadi, Chip Stewart, Tetiana Bogdanova, Eric T. Dawson, Mia K. Steinberg, Jieqiong Dai, Stephen W. Hartley, Sara J. Schonfeld, Joshua N. Sampson, Yosef E. Maruvka, Vidushi Kapoor, Dale A. Ramsden, Juan Carvajal-Garcia, Charles M. Perou, Joel S. Parker, Marko Krznaric, Meredith Yeager, Joseph F. Boland, Amy Hutchinson, Belynda D. Hicks, Casey L. Dagnall, Julie M. Gastier-Foster, Jay Bowen, Olivia Lee, Mitchell J. Machiela, Elizabeth K. Cahoon, Alina Brenner, Kiyohiko Mabuchi, Vladimir Drozdovitch, Sergii Masiuk, Mykola Chepurny, Liudmyla Yu Zurnadzhy, Maureen Hatch, Amy Berrington de Gonzalez, Gerry A. Thomas, Mykola D. Tronko, Gad Getz, Stephen J. Chanock
Summary: The 1986 Chernobyl nuclear power plant accident resulted in an increase in papillary thyroid carcinoma (PTC) incidence in surrounding regions, especially in children exposed to radioactive iodine (I-131). Analysis of 440 PTCs from Ukraine showed radiation dose-dependent genomic alterations, with fusion drivers being enriched in individuals who were younger at exposure. Transcriptomic and epigenomic features were strongly associated with driver events, but not radiation dose, indicating DNA double-strand breaks as early carcinogenic events after environmental radiation exposure.
Article
Biochemistry & Molecular Biology
Eial Teomy, David A. Kessler, Herbert Levine
Summary: This study explores the use of notch-delta signaling in constructing ordered patterns of cellular differentiation in biology. Through a mathematical model, it analyzes the process of pattern formation and identifies different types of cellular patterns that can be produced under varying parameter conditions.
Article
Physics, Fluids & Plasmas
David A. Kessler, Nadav M. Shnerb
Summary: This study aims to provide a comprehensive survey by examining a range of scenarios to understand the time distribution and fluctuations of population extinction. The researchers consider the impact of individual stochasticity on the extinction process and propose several generic criteria for classifying different experimental and empirical systems, thereby enhancing our understanding of the mechanisms governing extinction dynamics.
Article
Mathematics
David A. Kessler, Jeremy Schiff
Summary: This article presents a variety of not-well-known asymptotic series for factorials, binomial coefficients, and Catalan numbers, all of which only have even or odd powers. The significance of this property is discussed in terms of the asymptotic evenness or oddness of the underlying quantities.
JOURNAL OF INTEGER SEQUENCES
(2021)
Article
Optics
David A. Kessler, Eli Barkai, Klaus Ziegler
Summary: The study focuses on the detection of quantum systems at random time intervals, deriving statistical results such as probabilities and mean values. It is proven that the mean detection time is related to the average number of attempts and average time intervals. The study also explores various interval distributions and Hamiltonians in the detection process.
Article
Biochemistry & Molecular Biology
Karsten Krug, Eric J. Jaehnig, Shankha Satpathy, Lili Blumenberg, Alla Karpova, Meenakshi Anurag, George Miles, Philipp Mertins, Yifat Geffen, Lauren C. Tang, David Heiman, Song Cao, Yosef E. Maruvka, Jonathan T. Lei, Chen Huang, Ramani B. Kothadia, Antonio Colaprico, Chet Birger, Jarey Wang, Yongchao Dou, Bo Wen, Zhiao Shi, Yuxing Liao, Maciej Wiznerowicz, Matthew A. Wyczalkowski, Xi Steven Chen, Jacob J. Kennedy, Amanda G. Paulovich, Mathangi Thiagarajan, Christopher R. Kinsinger, Tara Hiltke, Emily S. Boja, Mehdi Mesri, Ana Robles, Henry Rodriguez, Thomas F. Westbrook, Li Ding, Gad Getz, Karl R. Clauser, David Fenyo, Kelly Ruggles, Bing Zhang, D. R. Mani, Steven A. Carr, Matthew J. Ellis, Michael A. Gillette
Article
Optics
Felix Thiel, David A. Kessler
Article
Optics
Felix Thiel, David A. Kessler, Eli Barkai
Article
Oncology
Oksana Zavidij, Nicholas J. Haradhvala, Tarek H. Mouhieddine, Romanos Sklavenitis-Pistofidis, Songjie Cai, Mairead Reidy, Mahshid Rahmat, Abdallah Flaifel, Benjamin Ferland, Nang K. Su, Michael P. Agius, Jihye Park, Salomon Manier, Mark Bustoros, Daisy Huynh, Marzia Capelletti, Brianna Berrios, Chia-Jen Liu, Meng Xiao He, Esteban Braggio, Rafael Fonseca, Yosef Maruvka, Jennifer L. Guerriero, Melissa Goldman, Eliezer van Allen, Steven A. McCarroll, Jamil Azzi, Gad Getz, Irene M. Ghobrial
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
