Publications
Highlighted
![Practical guidelines and the <scp>EMLN</scp> R package for handling ecological multilayer networks](/images/projects/emln_pic.jpg)
Practical guidelines and the EMLN R package for handling ecological multilayer networks
Methods in Ecology and Evolution
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18 Oct 2023
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doi:10.1111/2041-210X.14225
EMLN package and guidelines
![Conceptualizing microbe–plasmid communities as complex adaptive systems](/images/publications/pic_conceptualizing_microbeplasmid_1.png)
Conceptualizing microbe–plasmid communities as complex adaptive systems
Trends in Microbiology
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01 Jul 2023
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doi:10.1016/j.tim.2023.01.007
![The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification](/images/publications/pic_the_network_structure_and_eco_evol_CRISPR.webp)
The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification
Nature Ecology & Evolution
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19 Oct 2020
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doi:10.1038/s41559-020-01312-z
![The multilayer nature of ecological networks](/images/publications/pic_the_multilayer_nature_of_ecological_net.webp)
The multilayer nature of ecological networks
Nature Ecology & Evolution
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23 Mar 2017
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doi:10.1038/s41559-017-0101
All
2024
![Inductive link prediction boosts data availability and enables cross-community link prediction in ecological networks](/images/publications/pic_inductive_link_prediction_in_ecological_net.png)
Inductive link prediction boosts data availability and enables cross-community link prediction in ecological networks
California Digital Library (CDL)
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02 Aug 2024
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doi:10.32942/X2JS75
![Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases](/images/publications/pic_plasmids_in_the_human_gut.jpeg)
Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases
Nature Communications
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11 Apr 2024
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doi:10.1038/s41467-024-47272-x
2023
![Local and regional processes drive distance decay in structure in a spatial multilayer plant-pollinator network](/images/publications/pic_local_and_regional_processes.png)
Local and regional processes drive distance decay in structure in a spatial multilayer plant-pollinator network
California Digital Library (CDL)
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21 Nov 2023
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doi:10.32942/X28G7K
![Scale-dependent signatures of microbial co-occurrence revealed via multilayer network analysis](/images/publications/pic_scale_dependent_signatures.png)
Scale-dependent signatures of microbial co-occurrence revealed via multilayer network analysis
California Digital Library (CDL)
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01 Nov 2023
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doi:10.32942/X2161C
![Practical guidelines and the <scp>EMLN</scp> R package for handling ecological multilayer networks](/images/projects/emln_pic.jpg)
Practical guidelines and the EMLN R package for handling ecological multilayer networks
Methods in Ecology and Evolution
·
18 Oct 2023
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doi:10.1111/2041-210X.14225
EMLN package and guidelines
![Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness](/images/publications/pic_ecological_network_analysis_reveals_cancer.png)
Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness
Nature Communications
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07 Oct 2023
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doi:10.1038/s41467-023-41906-2
![Conceptualizing microbe–plasmid communities as complex adaptive systems](/images/publications/pic_conceptualizing_microbeplasmid_1.png)
Conceptualizing microbe–plasmid communities as complex adaptive systems
Trends in Microbiology
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01 Jul 2023
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doi:10.1016/j.tim.2023.01.007
![Invasive species modulate the structure and stability of a multilayer mutualistic network](/images/publications/pic_invasive_species_modulate_the_structure.jpeg)
Invasive species modulate the structure and stability of a multilayer mutualistic network
Proceedings of the Royal Society B: Biological Sciences
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28 Jun 2023
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doi:10.1098/rspb.2023.0132
![Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission](/images/publications/pic_multilayer_networks_of_plasmid_genetics.png)
Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission
The ISME Journal
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09 Feb 2023
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doi:10.1038/s41396-023-01373-5
2021
![The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes](/images/publications/pic_the_inerplay_between_vaccination_and_COVID19.jpeg)
The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes
PLOS Computational Biology
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20 Aug 2021
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doi:10.1371/journal.pcbi.1009319
![Frequency-Dependent Competition Between Strains Imparts Persistence to Perturbations in a Model of Plasmodium falciparum Malaria Transmission](https://www.frontiersin.org/files/Articles/633263/fevo-09-633263-HTML-r2/image_m/fevo-09-633263-g001.jpg)
Frequency-Dependent Competition Between Strains Imparts Persistence to Perturbations in a Model of Plasmodium falciparum Malaria Transmission
Frontiers in Ecology and Evolution
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26 May 2021
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doi:10.3389/fevo.2021.633263
![Identifying flow modules in ecological networks using Infomap](/images/publications/pic_identifying_flow_modules_in_ec_net_infomap.jpeg)
Identifying flow modules in ecological networks using Infomap
Methods in Ecology and Evolution
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24 Feb 2021
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doi:10.1111/2041-210X.13569
2020
Frequency-dependent competition between strains imparts resilience to perturbations in a model ofPlasmodium falciparummalaria transmission
Cold Spring Harbor Laboratory
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22 Dec 2020
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doi:10.1101/2020.12.22.423749
![The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification](/images/publications/pic_the_network_structure_and_eco_evol_CRISPR.webp)
The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification
Nature Ecology & Evolution
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19 Oct 2020
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doi:10.1038/s41559-020-01312-z
Identifying flow modules in ecological networks using Infomap
Cold Spring Harbor Laboratory
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14 Apr 2020
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doi:10.1101/2020.04.14.040519
![Pan-Cancer Analysis of Mitochondria Chaperone-Client Co-Expression Reveals Chaperone Functional Partitioning](/images/publications/pic_pan_cancer_analysis_of_mitochondria_chaperone.png)
Pan-Cancer Analysis of Mitochondria Chaperone-Client Co-Expression Reveals Chaperone Functional Partitioning
Cancers
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30 Mar 2020
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doi:10.3390/cancers12040825
2019
![Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum](/images/publications/pic_comp_for_hosts_Plasmodium.jpg)
Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum
PLOS Biology
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24 Jun 2019
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doi:10.1371/journal.pbio.3000336
2018
![Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum](/images/publications/pic_net_of_genetics_similaruty_Plasmodium_falciparum.webp)
Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum
Nature Communications
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08 May 2018
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doi:10.1038/s41467-018-04219-3
2017
Networks of genetic similarity reveal non-neutral processes shape strain structure inPlasmodium falciparum
Cold Spring Harbor Laboratory
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03 Oct 2017
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doi:10.1101/197954
![Asymmetric disease dynamics in multihost interconnected networks](/images/publications/pic_asymmetric_disease_dynamics.jpeg)
Asymmetric disease dynamics in multihost interconnected networks
Journal of Theoretical Biology
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01 Oct 2017
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doi:10.1016/j.jtbi.2017.07.020
Temporal dynamics of direct reciprocal and indirect effects in a host--parasite network
Journal of Animal Ecology
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25 Mar 2017
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:
![The multilayer nature of ecological networks](/images/publications/pic_the_multilayer_nature_of_ecological_net.webp)
The multilayer nature of ecological networks
Nature Ecology & Evolution
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23 Mar 2017
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doi:10.1038/s41559-017-0101
2014
![Multiple effects of host‐species diversity on coexisting host‐specific and host‐opportunistic microbes](https://esajournals.onlinelibrary.wiley.com/cms/asset/fef9467a-1eba-4403-ba9b-9a83f870ae05/ecy20149551173-fig-0001-m.jpg)
Multiple effects of host‐species diversity on coexisting host‐specific and host‐opportunistic microbes
Ecology
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01 May 2014
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doi:10.1890/13-0678.1
![Effects of sewage-water contamination on the immune response of a desert bat](/images/publications/pic_effects_of_sewage_water_desert_bat.jpg)
Effects of sewage-water contamination on the immune response of a desert bat
Mammalian Biology
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01 Apr 2014
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doi:10.1016/j.mambio.2013.10.005
2013
![A trade‐off between quantity and quality of offspring in haematophagous ectoparasites: the effect of the level of specialization](/images/publications/pic_tradeoff_between_quantity_and_quality_2.jpeg)
A trade‐off between quantity and quality of offspring in haematophagous ectoparasites: the effect of the level of specialization
Journal of Animal Ecology
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23 Sep 2013
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doi:10.1111/1365-2656.12134
![Phylogenetic structure of host spectra in Palaearctic fleas: stability versus spatial variation in widespread, generalist species](/images/publications/pic_phylogenrtic_structure_of_host_spectra_in_palaearctic_fleas_2.gif)
Phylogenetic structure of host spectra in Palaearctic fleas: stability versus spatial variation in widespread, generalist species
Parasitology
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04 Sep 2013
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doi:10.1017/s0031182013001376
![Spatial variation in the phylogenetic structure of flea assemblages across geographic ranges of small mammalian hosts in the Palearctic](https://ars.els-cdn.com/content/image/1-s2.0-S0020751913001434-fx1_lrg.jpg)
Spatial variation in the phylogenetic structure of flea assemblages across geographic ranges of small mammalian hosts in the Palearctic
International Journal for Parasitology
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01 Aug 2013
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doi:10.1016/j.ijpara.2013.05.001
![Phylogeny determines the role of helminth parasites in intertidal food webs](/images/publications/pic_phylogeny_determines_the_role_food_webs_2.png)
Phylogeny determines the role of helminth parasites in intertidal food webs
Journal of Animal Ecology
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25 Jun 2013
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doi:10.1111/1365-2656.12101
![Co‐occurrence and phylogenetic distance in communities of mammalian ectoparasites: limiting similarity versus environmental filtering](/images/publications/pic_coocurrence_and_phylogenetic_distance_2.jpeg)
Co‐occurrence and phylogenetic distance in communities of mammalian ectoparasites: limiting similarity versus environmental filtering
Oikos
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21 Jun 2013
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doi:10.1111/j.1600-0706.2013.00646.x
![FOREWORD: Evolution of culture](/images/publications/pic_evolution_of_culture.jpg)
FOREWORD: Evolution of culture
Israel Journal of Ecology and Evolution
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18 May 2013
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doi:10.1080/15659801.2013.865338
![Temporal dynamics of direct reciprocal and indirect effects in a host–parasite network](/images/publications/pic_temporal_dynamics_host_parasite_network_2.png)
Temporal dynamics of direct reciprocal and indirect effects in a host–parasite network
Journal of Animal Ecology
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14 May 2013
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doi:10.1111/1365-2656.12090
2012
![Host body microcosm and ectoparasite infracommunities: arthropod ectoparasites are not spatially segregated](/images/publications/pic_host_body_microcosm.gif)
Host body microcosm and ectoparasite infracommunities: arthropod ectoparasites are not spatially segregated
Parasitology
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05 Sep 2012
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doi:10.1017/s0031182012001205
![Effects of Anthropogenic Disturbance and Climate on Patterns of Bat Fly Parasitism](/images/publications/pic_effects_of_anthropogenic_disturbance.jpg)
Effects of Anthropogenic Disturbance and Climate on Patterns of Bat Fly Parasitism
PLoS ONE
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19 Jul 2012
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doi:10.1371/journal.pone.0041487
2010
![Variability in urine concentration and fecal water content of bats in a tropical deciduous forest](/images/publications/pic_variability_in_urine_concentration.jpg)
Variability in urine concentration and fecal water content of bats in a tropical deciduous forest
Journal of Mammalogy
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16 Jun 2010
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doi:10.1644/09-mamm-a-370.1