GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 91 to 120 publications on 1308 in total

Assessing Human Genome-wide Variation in the Massim Region of Papua New Guinea and Implications for the Kula Trading Tradition

Dang Liu, Benjamin M Peter, Wulf Schiefenhövel, Manfred Kayser, Mark Stoneking

Molecular Biology and Evolution . 39

DOI: 10.1093/molbev/msac165

Journal article

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Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Sandra Oliveira, Kathrin Nägele, Selina Carlhoff, Irina Pugach, Toetik Koesbardiati, Alexander Hübner...

Nature Ecology & Evolution . 6 : 1024 - 1034

DOI: 10.1038/s41559-022-01775-2

Journal article

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A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size

Rebekka Müller, Ingemar Kaj, Carina Mugal

Genome Biology and Evolution . 14 ( 5 )

DOI: 10.1093/gbe/evac058

Journal article

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Hydrogen isotope measurements of bone and dental tissues from archaeological human and animal samples and their use as climatic and diet proxies

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Journal of Archaeological Science . 147 : 105676

DOI: 10.1016/j.jas.2022.105676

Journal article

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Climate conditions and dietary practices during the Second Iron Age studied through the multi-isotope analysis of bones and teeth from individuals of Thézy-Glimont, Picardie, France

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Archaeological and Anthropological Sciences . 14 ( 4 ) : 61

DOI: 10.1007/s12520-022-01534-1

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Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

Rasa Muktupavela, Martin Petr, Laure Ségurel, Thorfinn Korneliussen, John Novembre, Fernando Racimo

eLife . 11

DOI: 10.7554/eLife.73767

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Polynomial Delay Algorithm for Minimal Chordal Completions

Caroline Brosse, Vincent Limouzy, Arnaud Mary

49th International Colloquium on Automata, Languages, and Programming (ICALP) .

DOI: 10.4230/LIPIcs.ICALP.2022.33

Conference paper

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Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex

Fatimat Almentina Ramos Shidi, Audric Cologne, Marion Delous, Alicia Besson, Audrey Putoux, Anne-Louise Leutenegger...

Nucleic Acids Research .

DOI: 10.1093/nar/gkac1182

Journal article

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Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling

Sabine Peres, Marc Dinh, Vincent Fromion

International Conference on System Biology .

Conference paper

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Special Issue on “Frontiers in Connecting Steady-State and Dynamic Approaches for Modelling Cell Metabolic Behavior”

Sabine Peres, Mario Jolicoeur

Processes . 10 ( 8 ) : 1612

DOI: 10.3390/pr10081612

Journal article

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Hybrid metabolic modeling to identify new control strategies of living organisms

Sabine Peres

Hybrid models and methods in systems medicine .

Conference paper

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Mod ́elisation m ́etabolique pour identifier de nouvelles strat ́egies de contrˆole des organismes vivants

Sabine Peres

Meetochondrie .

Conference paper

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BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

Carol Moraga, Evelyn Sanchez, Mariana Galvão Ferrarini, Rodrigo A Gutierrez, Elena A Vidal, Marie-France Sagot

GigaScience . 11

DOI: 10.1093/gigascience/giac093

Journal article

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Codiversification of gut microbiota with humans

Taichi Suzuki, J. Liam Fitzstevens, Victor Schmidt, Hagay Enav, Kelsey Huus, Mirabeau Mbong Ngwese...

Science . 377 ( 6612 ) : 1328-1332

DOI: 10.1126/science.abm7759

Journal article

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Protein conformational space at the edge of allostery: turning a nonallosteric malate dehydrogenase into an “allosterized” enzyme using evolution-guided punctual mutations

Antonio Iorio, Céline Brochier-Armanet, Caroline Mas, Fabio Sterpone, Dominique Madern

Molecular Biology and Evolution . 39 ( 9 ) : msac186

DOI: 10.1093/molbev/msac186

Journal article

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GOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements

Alexandre Laverré, Eric Tannier, Philippe Veber, Anamaria Necsulea

DOI: 10.1101/2022.06.13.495495

Preprint

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An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias

Thibault Latrille, Nicolas Lartillot

Molecular Biology and Evolution . 39

DOI: 10.1093/molbev/msac005

Journal article

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Efficiently sparse listing of classes of optimal cophylogeny reconciliations

Yishu Wang, Marie-France Sagot, Arnaud Mary, Blerina Sinaimeri

Algorithms for Molecular Biology . 17 ( 1 ) : 1-16

DOI: 10.1186/s13015-022-00206-y

Journal article

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Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations

Mariana Galvão Ferrarini, Irene Ziska, Ricardo Andrade, Alice Julien-Laferrière, Louis Duchemin, Roberto Marcondes César...

Frontiers in Genetics . 13 : 1-12

DOI: 10.3389/fgene.2022.815476

Journal article

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CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

Hector Roux de Bézieux, Leandro Lima, Fanny Perraudeau, Arnaud Mary, Sandrine Dudoit, Laurent Jacob

Bioinformatics .

DOI: 10.1093/bioinformatics/btac238

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A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Monique Aouad, Jean-Pierre Flandrois, Frédéric Jauffrit, Manolo Gouy, Simonetta Gribaldo, Celine Brochier-Armanet

BMC Ecology and Evolution . 22 ( 1 ) : 1-12

DOI: 10.1186/s12862-021-01952-0

Journal article

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Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

Alexandre Laverré, Eric Tannier, Anamaria Necsulea

Genome Research . 32 ( 2 ) : 280-296

DOI: 10.1101/gr.275901.121

Journal article

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Exploring correlations in genetic and cultural variation across language families in northeast Asia

Hiromi Matsumae, Peter Ranacher, Patrick Savage, Damián Blasi, Thomas Currie, Kae Koganebuchi...

Science Advances . 7 ( 34 )

DOI: 10.1126/sciadv.abd9223

Journal article

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Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn

Song Guo, Shuyun Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S Moreno...

BMC Genomics . 22 : 286

DOI: 10.1186/s12864-021-07542-0

Journal article

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Reconstructing the Human Genetic History of Mainland Southeast Asia: Insights from Genome-Wide Data from Thailand and Laos

Wibhu Kutanan, Dang Liu, Jatupol Kampuansai, Metawee Srikummool, Suparat Srithawong, Rasmi Shoocongdej...

Molecular Biology and Evolution . 38 ( 8 ) : 3459 - 3477

DOI: 10.1093/molbev/msab124

Journal article

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Genomic insights into population history and biological adaptation in Oceania

Jeremy Choin, Javier Mendoza-Revilla, Lara R Arauna, Sebastian Cuadros-Espinoza, Olivier Cassar, Maximilian Larena...

Nature . 592 ( 7855 ) : 583-589

DOI: 10.1038/s41586-021-03236-5

Journal article

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The genomic prehistory of peoples speaking Khoisan languages

Brigitte Pakendorf, Mark Stoneking

Human Molecular Genetics . 30 ( 2 ) : R49-R55

DOI: 10.1093/hmg/ddaa221

Journal article

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Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs

Madeline Chase, Hans Ellegren, Carina Mugal

Evolution - International Journal of Organic Evolution . 75 ( 9 ) : 2179-2196

DOI: 10.1111/evo.14234

Journal article

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The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes

Jesper Boman, Carina Mugal, Niclas Backström

Genome Biology and Evolution . 13 ( 5 )

DOI: 10.1093/gbe/evab064

Journal article

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