Latest recommendations
Id | Title * | Authors * | Abstract * | Picture * | Thematic fields * | Recommender | Reviewers▼ | Submission date | |
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26 Feb 2024
A workflow for processing global datasets: application to intercroppingRémi Mahmoud, Pierre Casadebaig, Nadine Hilgert, Noémie Gaudio https://hal.science/hal-04145269Collecting, assembling and sharing data in crop sciencesRecommended by Eric Tannier based on reviews by Christine Dillmann and 2 anonymous reviewersIt is often the case that scientific knowledge exists but is scattered across numerous experimental studies. Because of this dispersion in different formats, it remains difficult to access, extract, reproduce, confirm or generalise. This is the case in crop science, where Mahmoud et al [1] propose to collect and assemble data from numerous field experiments on intercropping. It happens that the construction of the global dataset requires a lot of time, attention and a well thought-out method, inspired by the literature on data science [2] and adapted to the specificities of crop science. This activity also leads to new possibilities that were not available in individual datasets, such as the detection of full factorial designs using graph theory tools developed on top of the global dataset. The study by Mahmoud et al [1] has thus multiple dimensions:
I was particularly interested in the promotion of the FAIR principles, perhaps used a little too uncritically in my view, as an obvious solution to data sharing. On the one hand, I am admiring and grateful for the availability of these data, some of which have never been published, nor associated with published results. This approach is likely to unearth buried treasures. On the other hand, I can understand the reluctance of some data producers to commit to total, definitive sharing, facilitating automatic reading, without having thought about a certain reciprocity on the part of users and use by artificial intelligence. Reciprocity in terms of recognition, as is discussed by Mahmoud et al [1], but also in terms of contribution to the commons [5] or reading conditions for machine learning. References [1] Mahmoud R., Casadebaig P., Hilgert N., Gaudio N. A workflow for processing global datasets: application to intercropping. 2024. ⟨hal-04145269v2⟩ ver. 2 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://hal.science/hal-04145269 [2] Wickham, H. 2014. Tidy data. Journal of Statistical Software 59(10) https://doi.org/10.18637/jss.v059.i10 [3] Gaudio, N., R. Mahmoud, L. Bedoussac, E. Justes, E.-P. Journet, et al. 2023. A global dataset gathering 37 field experiments involving cereal-legume intercrops and their corresponding sole crops. https://doi.org/10.5281/zenodo.8081577 [4] Mahmoud, R., Casadebaig, P., Hilgert, N. et al. Species choice and N fertilization influence yield gains through complementarity and selection effects in cereal-legume intercrops. Agron. Sustain. Dev. 42, 12 (2022). https://doi.org/10.1007/s13593-022-00754-y [5] Bernault, C. « Licences réciproques » et droit d'auteur : l'économie collaborative au service des biens communs ?. Mélanges en l'honneur de François Collart Dutilleul, Dalloz, pp.91-102, 2017, 978-2-247-17057-9. https://shs.hal.science/halshs-01562241 | A workflow for processing global datasets: application to intercropping | Rémi Mahmoud, Pierre Casadebaig, Nadine Hilgert, Noémie Gaudio | <p>Field experiments are a key source of data and knowledge in agricultural research. An emerging practice is to compile the measurements and results of these experiments (rather than the results of publications, as in meta-analysis) into global d... | Agricultural Science | Eric Tannier | 2023-06-29 15:38:28 | View | ||
28 Jun 2024
Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome OrganizationThéotime Grohens, Sam Meyer, Guillaume Beslon https://doi.org/10.1101/2022.09.23.509185Understanding the impact of the transcription-supercoiling coupling on bacterial genome evolutionRecommended by Nelle Varoquaux based on reviews by Ivan Junier and 1 anonymous reviewerDNA supercoiling, the under or overwinding of DNA, is known to strongly impact gene expression, as changes in levels of supercoiling directly influence transcription rates. In turn, gene transcription generates DNA supercoiling on each side of an advancing RNA polymerase. This coupling between DNA supercoiling and transcription may result in different outcomes, depending on neighboring gene orientations: divergent genes tend to increase transcription levels, convergent genes tend to inhibit each other, while tandem genes may exhibit more intricate relationships. While several works have investigated the relationship between transcription and supercoiling, Grohens et al [1] address a different question: how does transcription-supercoiling coupling drive genome evolution? To this end, they consider a simple model of gene expression regulation where transcription level only depends on the local DNA supercoiling and where the transcription of one gene generates a linear profile of positive and negative DNA supercoiling on each side of it. They then make genomes evolve through genomic inversions only considering a fitness that reflects the ability of a genome to cope with two distinct environments for which different genes have to be activated or repressed. Using this simple model, the authors illustrate how evolutionary adaptation via genomic inversions can adjust expression levels for enhanced fitness within specific environments, particularly with the emergence of relaxation-activated genes. Investigating the genomic organization of individual genomes revealed that genes are locally organized to leverage the transcription-supercoiling coupling for activation or inhibition, but larger-scale networks of genes are required to strongly inhibit genes (sometimes up to networks of 20 genes). Thus, supercoiling-mediated interactions between genes can implicate more than just local genes. Finally, they construct an "effective interaction graph" between genes by successively simulating gene knock-outs for all of the genes of an individual and observing the effect on the expression level of other genes. They observe a densely connected interaction network, implying that supercoiling-based regulation could evolve concurrently with genome organization in bacterial genomes. References [1] Théotime Grohens, Sam Meyer, Guillaume Beslon (2024) Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization. bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology https://doi.org/10.1101/2022.09.23.509185 | Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization | Théotime Grohens, Sam Meyer, Guillaume Beslon | <p>DNA supercoiling -- the level of twisting and writhing of the DNA molecule around itself -- plays a major role in the regulation of gene expression in bacteria by modulating promoter activity. The level of DNA supercoiling is a dynamic property... | Biophysics, Evolutionary Biology, Systems biology | Nelle Varoquaux | 2023-06-30 10:34:28 | View | ||
10 Jan 2024
An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorillaNicolas Galtier https://doi.org/10.1101/2023.07.06.547897Aphid: A Novel Statistical Method for Dissecting Gene Flow and Lineage Sorting in Phylogenetic ConflictRecommended by Alan Rogers based on reviews by Richard Durbin and 2 anonymous reviewersGaltier [1] introduces “Aphid,” a new statistical method that estimates the contributions of gene flow (GF) and incomplete lineage sorting (ILS) to phylogenetic conflict. Aphid is based on the observation that GF tends to make gene genealogies shorter, whereas ILS makes them longer. Rather than fitting the full likelihood, it models the distribution of gene genealogies as a mixture of several canonical gene genealogies in which coalescence times are set equal to their expectations under different models. This simplification makes Aphid far faster than competing methods. In addition, it deals gracefully with bidirectional gene flow—an impossibility under competing models. Because of these advantages, Aphid represents an important addition to the toolkit of evolutionary genetics. In the interest of speed, Aphid makes several simplifying assumptions. Yet even when these were violated, Aphid did well at estimating parameters from simulated data. It seems to be reasonably robust. Aphid studies phylogenetic conflict, which occurs when some loci imply one phylogenetic tree and other loci imply another. This happens when the interval between successive speciation events is fairly short. If this interval is too short, however, Aphid’s approximations break down, and its estimates are biased. Galtier suggests caution when the fraction of discordant phylogenetic trees exceeds 50–55%. Thus, Aphids will be most useful when the interval between speciation events is short, but not too short. Galtier applies the new method to three sets of primate data. In two of these data sets (baboons and African apes), Aphid detects gene flow that would likely be missed by competing methods. These competing methods are primarily sensitive to gene flow that is asymmetric in two senses: (1) greater flow in one direction than the other, and (2) unequal gene flow connecting an outgroup to two sister species. Aphid finds evidence of symmetric gene flow in the ancestry of baboons and also in that of African apes. The data suggest that ancestral humans and chimpanzees both interbred with ancestral gorillas, and at about the same rate. Aphid’s ability to detect this signature sets it apart from competing methods. References [1] Nicolas Galtier (2023) “An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla”. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.1101/2023.07.06.547897 | An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla | Nicolas Galtier | <p>Gene flow and incomplete lineage sorting are two distinct sources of phylogenetic conflict, i.e., gene trees that differ in topology from each other and from the species tree. Distinguishing between the two processes is a key objective of curre... | Evolutionary Biology, Genetics and population Genetics, Genomics and Transcriptomics | Alan Rogers | 2023-07-06 18:41:16 | View | ||
22 Jul 2024
Genetic Evidence for Geographic Structure within the Neanderthal PopulationAlan R. Rogers https://doi.org/10.1101/2023.07.28.551046Decline in Neanderthal effective population size due to geographic structure and gene flowRecommended by Raquel Assis based on reviews by David Bryant and Guillaume AchazPublished PSMC estimates of Neanderthal effective population size (𝑁e) show an approximately five-fold decline over the past 20,000 years [1]. This observation may be attributed to a true decline in Neanderthal 𝑁e, statistical error that is notorious with PSMC estimation, or geographic subdivision and gene flow that has been hypothesized to occur within the Neanderthal population. Determining which of these factors contributes to the observed decline in Neanderthal 𝑁e is an important question that can provide insight into human evolutionary history. Though it is widely believed that the decline in Neanderthal 𝑁e is due to geographic subdivision and gene flow, no prior studies have theoretically examined whether these evolutionary processes can yield the observed pattern. In this paper [2], Rogers tackles this problem by employing two mathematical models to explore the roles of geographic subdivision and gene flow in the Neanderthal population. Results from both models show that geographic subdivision and gene flow can indeed result in a decline in 𝑁e that mirrors the observed decline estimated from empirical data. In contrast, Rogers argues that neither statistical error in PSMC estimates nor a true decline in 𝑁e are expected to produce the consistent decline in estimated 𝑁e observed across three distinct Neanderthal fossils. Statistical error would likely result in variation among these curves, whereas a true decline in 𝑁e would produce shifted curves due to the different ages of the three Neanderthal fossils. In summary, Rogers provides convincing evidence that the most reasonable explanation for the observed decline in Neanderthal 𝑁e is geographic subdivision and gene flow. Rogers also provides a basis for understanding this observation, suggesting that 𝑁e declines over time because coalescence times are shorter between more recent ancestors, as they are more likely to be geographic neighbors. Hence, Rogers’ theoretical findings shed light on an interesting aspect of human evolutionary history. References [1] Fabrizio Mafessoni, Steffi Grote, Cesare de Filippo, Svante Pääbo (2020) “A high-coverage Neandertal genome from Chagyrskaya Cave”. Proceedings of the National Academy of Sciences USA 117: 15132- 15136. https://doi.org/10.1073/pnas.2004944117 [2] Alan Rogers (2024) “Genetic evidence for geographic structure within the Neanderthal population”. bioRxiv, version 4 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.1101/2023.07.28.551046 | Genetic Evidence for Geographic Structure within the Neanderthal Population | Alan R. Rogers | <p>PSMC estimates of Neanderthal effective population size (N<sub>e</sub>)exhibit a roughly 5-fold decline across the most recent 20 ky before the death of each fossil. To explain this pattern, this article develops new theory relating... | Evolutionary Biology, Genetics and population Genetics | Raquel Assis | 2023-10-17 18:06:38 | View | ||
27 Aug 2024
Impact of a block structure on the Lotka-Volterra modelMaxime Clenet, François Massol, Jamal Najim https://doi.org/10.48550/arXiv.2311.09470Equlibrium of communities in the Lotka-Volterra modelRecommended by Loïc Paulevé based on reviews by 3 anonymous reviewersThis article by Clenet et al. [1] tackles a fundamental mathematical model in ecology to understand the impact of the architecture of interactions on the equilibrium of the system. The authors consider the classical Lotka-Volterra model, depicting the effect of interactions between species on their abundances. They focus on the case whenever there are numerous species, and where their interactions are compartmentalized in a block structure. Each block has a strength coefficient, applied to a random Gaussian matrix. This model aims at capturing the structure of interacting communities, with blocks describing the interactions within a community, and other blocks the interactions between communities. In this general mathematical framework, the authors demonstrate sufficient conditions for the existence and uniqueness of a stable equilibrium, and conditions for which the equilibrium is feasible. Moreover, they derive statistical heuristics for the proportion, mean, and distribution of abundance of surviving species. Overall, the article constitutes an original and solid contribution to the study of mathematical models in ecology. It combines mathematical analysis, dynamical system theory, numerical simulations, grounded with relevant hypothesis for the modeling of ecological systems. References [1] Maxime Clenet, François Massol, Jamal Najim (2023) Impact of a block structure on the Lotka-Volterra model. arXiv, ver.3 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.48550/arXiv.2311.09470 | Impact of a block structure on the Lotka-Volterra model | Maxime Clenet, François Massol, Jamal Najim | <p>The Lotka-Volterra (LV) model is a simple, robust, and versatile model used to describe large interacting systems such as food webs or microbiomes. The model consists of $n$ coupled differential equations linking the abundances of $n$ differen... | Dynamical systems, Ecology, Probability and statistics | Loïc Paulevé | 2023-11-17 21:44:38 | View | ||
23 Jul 2024
Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algoCyprien Borée, Mathieu Giraud, Mikaël Salson https://hal.science/hal-04361907An accelerated Vidjil algorithm: up to 30X faster identification of V(D)J recombinations via spaced seeds and Aho-Corasick pattern matchingRecommended by Giulio Ermanno Pibiri based on reviews by Sven Rahmann and 1 anonymous reviewerVDJ recombination is a crucial process in the immune system, where a V (variable) gene, a D (diversity) gene, and a J (joining) gene are randomly combined to create unique antigen receptor genes. This process generates a vast diversity of antibodies and T-cell receptors, essential for recognizing and combating a wide array of pathogens. By identifying and quantifying these VDJ recombinations, we can gain a deeper and more precise understanding of the immune response, enhancing our ability to monitor and manage immune-related conditions. It is therefore important to develop efficient methods to identify and extract VDJ recombinations from large sequences (e.g., several millions/billions of nucleotides). The work by Borée, Giraud, and Salson [2] contributes one such algorithm. As in previous work, the proposed algorithm employs the Aho-Corasick automaton to simultaneously match several patterns against a string but, differently from other methods, it also combines the efficiency of spaced seeds. Working with seeds rather than the original string has the net benefit of speeding up the algorithm and reducing its memory usage, sometimes at the price of a modest loss in accuracy. Experiments conducted on five different datasets demonstrate that these features grant the proposed method excellent practical performance compared to the best previous methods, like Vidjil [3] (up to 5X faster) and MiXCR [1] (up to 30X faster), with no quality loss. The method can also be considered an excellent example of a more general trend in scalable algorithmic design: adapt "classic" algorithms (in this case, the Aho-Corasick pattern matching algorithm) to work in sketch space (e.g., the spaced seeds used here), trading accuracy for efficiency. Sometimes, this compromise is necessary for the sake of scaling to very large datasets using modest computing power. References [1] D. A. Bolotin, S. Poslavsky, I. Mitrophanov, M. Shugay, I. Z. Mamedov, E. V. Putintseva, and D. M. Chudakov (2015). "MiXCR: software for comprehensive adaptive immunity profiling." Nature Methods 12, 380–381. ISSN: 1548-7091. https://doi.org/10.1038/nmeth.3364 [2] C. Borée, M. Giraud, M. Salson (2024) "Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algo". https://hal.science/hal-04361907v2, version 2, peer-reviewed and recommended by Peer Community In Mathematical and Computational Biology. [3] M. Giraud, M. Salson, M. Duez, C. Villenet, S. Quief, A. Caillault, N. Grardel, C. Roumier, C. Preudhomme, and M. Figeac (2014). "Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing". BMC Genomics 15, 409. https://doi.org/10.1186/1471-2164-15-409. | Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algo | Cyprien Borée, Mathieu Giraud, Mikaël Salson | <p>The diversity of the immune repertoire is grounded on V(D)J recombinations in several loci. Many algorithms and software detect and designate these recombinations in high-throughput sequencing data. To improve their efficiency, we propose a mul... | Combinatorics, Computational complexity, Design and analysis of algorithms, Genomics and Transcriptomics, Immunology | Giulio Ermanno Pibiri | 2023-12-28 18:03:42 | View | ||
02 Oct 2024
HairSplitter: haplotype assembly from long, noisy readsRoland Faure, Dominique Lavenier, Jean-François Flot https://doi.org/10.1101/2024.02.13.580067Accurate Haplotype Reconstruction from Long, Error-Prone, Reads with HairSplitterRecommended by Giulio Ermanno Pibiri based on reviews by Dmitry Antipov and 1 anonymous reviewerA prominent challenge in computational biology is to distinguish microbial haplotypes -- closely related organisms with highly similar genomes -- due to small genomic differences that can cause significant phenotypic variations. Current genome assembly tools struggle with distinguishing these haplotypes, especially for long-read sequencing data with high error rates, such as PacBio or Oxford Nanopore Technology (ONT) reads. While existing methods work well for either viral or bacterial haplotypes, they often fail with low-abundance haplotypes and are computationally intensive. This work by Faure, Lavenier, and Flot [1] introduces a new tool -- HairSplitter -- that offers a solution for both viral and bacterial haplotype separation, even with error-prone long reads. It does this by efficiently calling variants, clustering reads into haplotypes, creating new separated contigs, and resolving the assembly graph. A key advantage of HairSplitter is that it is entirely parameter-free and does not require prior knowledge of the organism's ploidy. HairSplitter is designed to handle both metaviromes and bacterial metagenomes, offering a more versatile and efficient solution than existing tools, like stRainy [2], Strainberry [3], and hifiasm-meta [4]. References [1] Roland Faure, Dominique Lavenier, Jean-François Flot (2024) HairSplitter: haplotype assembly from long, noisy reads. bioRxiv, ver.3 peer-reviewed and recommended by PCI Math Comp Biol https://doi.org/10.1101/2024.02.13.580067 [2] Kazantseva E, A Donmez, M Pop, and M Kolmogorov (2023). stRainy: assembly-based metagenomic strain phasing using long reads. Bioinformatics. https://doi.org/10.1101/2023.01.31.526521 [3] Vicedomini R, C Quince, AE Darling, and R Chikhi (2021). Strainberry: automated strain separation in low complexity metagenomes using long reads. Nature Communications, 12, 4485. ISSN: 2041-1723. https://doi.org/10.1038/s41467-021-24515-9 [4] Feng X, H Cheng, D Portik, and H Li (2022). Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature Methods, 19, 1–4. https://doi.org/10.1038/s41592-022-01478-3 | HairSplitter: haplotype assembly from long, noisy reads | Roland Faure, Dominique Lavenier, Jean-François Flot | <p>Long-read assemblers face challenges in discerning closely related viral or<br>bacterial strains, often collapsing similar strains in a single sequence. This limitation has<br>been hampering metagenome analysis, where diverse strains may harbor... | Design and analysis of algorithms, Development, Genomics and Transcriptomics, Probability and statistics | Giulio Ermanno Pibiri | 2024-02-15 10:17:04 | View | ||
13 Aug 2024
Phenotype control and elimination of variables in Boolean networksElisa Tonello, Loïc Paulevé https://doi.org/10.48550/arXiv.2406.02304Disclosing effects of Boolean network reduction on dynamical properties and control strategiesRecommended by Claudine Chaouiya based on reviews by Tomas Gedeon and David SafranekBoolean networks stem from seminal work by M. Sugita [1], S. Kauffman [2] and R. Thomas [3] over half a century ago. Since then, a very active field of research has been developed, leading to theoretical advances accompanied by a wealth of work on modelling genetic and signalling networks involved in a wide range of cellular processes. Boolean networks provide a successful formalism for the mathematical modelling of biological processes, with a qualitative abstraction particularly well adapted to handle the modelling of processes for which precise, quantitative data is barely available. Nevertheless, these abstract models reveal fundamental dynamical properties, such as the existence and reachability of attractors, which embody stable cellular responses (e.g. differentiated states). Analysing these properties still faces serious computational complexity. Reduction of model size was proposed as a mean to cope with this issue. Furthermore, to enhance the capacity of Boolean networks to produce relevant predictions, formal methods have been developed to systematically identify control strategies enforcing desired behaviours. In their paper, E. Tonello and L. Paulevé [4] assess the most popular reduction that consists in eliminating a model component. Considering three typical update schemes (synchronous, asynchronous and general asynchronous updates), they thoroughly study the effects of the reduction on attractors, minimal trap spaces (minimal subspaces from which the model dynamics cannot leave), and on phenotype controls (interventions which guarantee that the dynamics ends in a phenotype defined by specific component values). Because they embody potential behaviours of the biological process under study, these are all properties of great interest for a modeller. The authors show that eliminating a component can significantly affect some dynamical properties and may turn a control strategy ineffective. The different update schemes, targets of phenotype control and control strategies are carefully handled with useful supporting examples. Overall, E. Tonello and L. Paulevé’s contribution underlines the need for caution when defining a regulatory network and characterises the consequences on critical model properties when discarding a component [4]. References [1] Motoyosi Sugita (1963) Functional analysis of chemical systems in vivo using a logical circuit equivalent. II. The idea of a molecular automation. Journal of Theoretical Biology, 4, 179–92. https://doi.org/10.1016/0022-5193(63)90027-4 [2] Stuart Kauffman (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology, 22, 437–67. https://doi.org/10.1016/0022-5193(69)90015-0 [3] René Thomas (1973) Boolean formalization of genetic control circuits. Journal of Theoretical Biology, 42, 563–85. https://doi.org/10.1016/0022-5193(73)90247-6 [4] Elisa Tonello, Loïc Paulevé (2024) Phenotype control and elimination of variables in Boolean networks. arXiv, ver.2 peer-reviewed and recommended by PCI Math Comp Biol https://arxiv.org/abs/2406.02304 | Phenotype control and elimination of variables in Boolean networks | Elisa Tonello, Loïc Paulevé | <p>We investigate how elimination of variables can affect the asymptotic dynamics and phenotype control of Boolean networks. In particular, we look at the impact on minimal trap spaces, and identify a structural condition that guarantees their pre... | Dynamical systems, Systems biology | Claudine Chaouiya | 2024-06-05 10:12:39 | View |
MANAGING BOARD
Caroline Colijn
Christophe Dessimoz
Barbara Holland
Hirohisa Kishino
Anita Layton
Wolfram Liebermeister
Christian Robert
Celine Scornavacca
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