Ecological Complexity Lab Elucidating the complexity of ecological systems

Publications

Highlighted

Inductive link prediction facilitates the discovery of missing links and enables cross-community inference in ecological networks
Inductive link prediction facilitates the discovery of missing links and enables cross-community inference in ecological networks
Barry Biton, Rami Puzis, Shai Pilosof
Nature Ecology & Evolution   ·   04 Jun 2025   ·   doi:10.1038/s41559-025-02715-6
Website
software link prediction machine learning ecological networks
Practical guidelines and the <scp>EMLN</scp> R package for handling ecological multilayer networks
Practical guidelines and the EMLN R package for handling ecological multilayer networks
Noa Frydman, Shirly Freilikhman, Itamar Talpaz, Shai Pilosof
Methods in Ecology and Evolution   ·   18 Oct 2023   ·   doi:10.1111/2041-210X.14225
EMLN package and guidelines
Website
software multilayer networks
Conceptualizing microbe–plasmid communities as complex adaptive systems
Conceptualizing microbe–plasmid communities as complex adaptive systems
Shai Pilosof
Trends in Microbiology   ·   01 Jul 2023   ·   doi:10.1016/j.tim.2023.01.007
microbial ecology perspective
The multilayer nature of ecological networks
The multilayer nature of ecological networks
Shai Pilosof, Mason A. Porter, Mercedes Pascual, Sonia Kéfi
Nature Ecology & Evolution   ·   23 Mar 2017   ·   doi:10.1038/s41559-017-0101
perspecrive multilayer networks

All

2025

The structure of pairwise competition is responsible for sudden regime shifts in a microbe-plasmid model
The structure of pairwise competition is responsible for sudden regime shifts in a microbe-plasmid model
Ying-Jie Wang, Alberto Megías, José A. Capitán, Leonardo Aguirre, Shai Pilosof, David Alonso
Cold Spring Harbor Laboratory   ·   12 Sep 2025   ·   doi:10.1101/2025.09.08.674846
Infection profiles in a wild rat–protozoan network are shaped by host traits and environmental factors
Infection profiles in a wild rat–protozoan network are shaped by host traits and environmental factors
Matan Markfeld, Itamar Talpaz, Barry Biton, Toky Randriamoria, Voahangy Soarimalala, Steven Goodman, Charles Nunn, Georgia Titcomb, Shai Pilosof
California Digital Library (CDL)   ·   18 Aug 2025   ·   doi:10.32942/X2MP9H
Metabolite correlation networks reveal complex phenotypes of adaptation-driving mutations
Metabolite correlation networks reveal complex phenotypes of adaptation-driving mutations
Sharon Samuel, Weronika Jasinska, Ezra Sternlicht, Matvey Nikelshparg, Daniel Kleiner, Shai Pilosof, Shimon Bershtein
Cold Spring Harbor Laboratory   ·   20 Jun 2025   ·   doi:10.1101/2025.06.17.660120
Inductive link prediction facilitates the discovery of missing links and enables cross-community inference in ecological networks
Inductive link prediction facilitates the discovery of missing links and enables cross-community inference in ecological networks
Barry Biton, Rami Puzis, Shai Pilosof
Nature Ecology & Evolution   ·   04 Jun 2025   ·   doi:10.1038/s41559-025-02715-6
Website
software link prediction machine learning ecological networks
Species interactions determine plasmid persistence in a 3-member bacterial community
Species interactions determine plasmid persistence in a 3-member bacterial community
Kaitlin A. Schaal, Ying-Jie Wang, Johannes Nauta, Manlio De Domenico, Shai Pilosof, James P. J. Hall
Cold Spring Harbor Laboratory   ·   03 Jun 2025   ·   doi:10.1101/2025.05.31.657151
microbial ecology plasmid
Differential assembly of core and non-core host-microbe network structures along a land-use change gradient
Differential assembly of core and non-core host-microbe network structures along a land-use change gradient
Matan Markfeld, Georgia Titcomb, Toky Randriamoria, Garima Sehgal, Nuzha Baksh, Ashley Kerrigan, Voahangy Soarimalala, Charles Nunn, Shai Pilosof
California Digital Library (CDL)   ·   12 May 2025   ·   doi:10.32942/X2PP94
microbial ecology land-use change
Indirect effects dominate ecosystem service losses in response to agricultural intensification
Indirect effects dominate ecosystem service losses in response to agricultural intensification
Agustin Vitali, Darren Evans, Fredric Windsor, Laura Dee, Anna Eklöf, Michael Pocock, Shai Pilosof
California Digital Library (CDL)   ·   05 Mar 2025   ·   doi:10.32942/X2F33T
ecosystem services food security

2024

Demography-based management of a lake meta-population network boosts food security in Amazonian fisheries
Demography-based management of a lake meta-population network boosts food security in Amazonian fisheries
Carine Emer, Miguel Lurgi, Sérgio Timóteo, João Vitor Campos-Silva, Shai Pilosof
California Digital Library (CDL)   ·   08 Oct 2024   ·   doi:10.32942/X2HC9G
metapopulation network food security
Local and regional processes drive distance decay in structure in a spatial multilayer plant‐pollinator network
Local and regional processes drive distance decay in structure in a spatial multilayer plant‐pollinator network
Agustin Vitali, Maya Goldstein, Matan Markfeld, Shai Pilosof
Journal of Animal Ecology   ·   09 Sep 2024   ·   doi:10.1111/1365-2656.14174
mutualistic interactions multilayer networks space
Regional processes shape the structure of rumen microbial co‐occurrence networks
Regional processes shape the structure of rumen microbial co‐occurrence networks
Geut Galai, Dafna Arbel, Keren Klass, Ido Grinshpan, Itzhak Mizrahi, Shai Pilosof
Ecography   ·   05 Sep 2024   ·   doi:10.1111/ecog.07430
microbial ecology multilayer networks population genetics
Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases
Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases
Alvah Zorea, David Pellow, Liron Levin, Shai Pilosof, Jonathan Friedman, Ron Shamir, Itzhak Mizrahi
Nature Communications   ·   11 Apr 2024   ·   doi:10.1038/s41467-024-47272-x
plasmid inflammatory diseases human gut

2023

Practical guidelines and the <scp>EMLN</scp> R package for handling ecological multilayer networks
Practical guidelines and the EMLN R package for handling ecological multilayer networks
Noa Frydman, Shirly Freilikhman, Itamar Talpaz, Shai Pilosof
Methods in Ecology and Evolution   ·   18 Oct 2023   ·   doi:10.1111/2041-210X.14225
EMLN package and guidelines
Website
software multilayer networks
Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness
Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness
Geut Galai, Xie He, Barak Rotblat, Shai Pilosof
Nature Communications   ·   07 Oct 2023   ·   doi:10.1038/s41467-023-41906-2
Podcast
cancer multilayer networks not our typical paper
Conceptualizing microbe–plasmid communities as complex adaptive systems
Conceptualizing microbe–plasmid communities as complex adaptive systems
Shai Pilosof
Trends in Microbiology   ·   01 Jul 2023   ·   doi:10.1016/j.tim.2023.01.007
microbial ecology perspective
Invasive species modulate the structure and stability of a multilayer mutualistic network
Invasive species modulate the structure and stability of a multilayer mutualistic network
Agustin Vitali, Sofía Ruiz-Suarez, Diego P. Vázquez, Matthias Schleuning, Mariano A. Rodríguez-Cabal, Yamila Sasal, Shai Pilosof
Proceedings of the Royal Society B: Biological Sciences   ·   28 Jun 2023   ·   doi:10.1098/rspb.2023.0132
mutualistic interactions multilayer networks
Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission
Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission
Julie Teresa Shapiro, Alvah Zorea, Aya Brown Kav, Vicente J Ontiveros, Itzhak Mizrahi, Shai Pilosof
The ISME Journal   ·   09 Feb 2023   ·   doi:10.1038/s41396-023-01373-5
microbial ecology multilayer networks dynamics

2021

The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes
The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes
Sharon Guerstein, Victoria Romeo-Aznar, Ma’ayan Dekel, Oren Miron, Nadav Davidovitch, Rami Puzis, Shai Pilosof
PLOS Computational Biology   ·   20 Aug 2021   ·   doi:10.1371/journal.pcbi.1009319
dynamics not our typical paper disease
Frequency-Dependent Competition Between Strains Imparts Persistence to Perturbations in a Model of Plasmodium falciparum Malaria Transmission
Frequency-Dependent Competition Between Strains Imparts Persistence to Perturbations in a Model of Plasmodium falciparum Malaria Transmission
Qixin He, Shai Pilosof, Kathryn E. Tiedje, Karen P. Day, Mercedes Pascual
Frontiers in Ecology and Evolution   ·   26 May 2021   ·   doi:10.3389/fevo.2021.633263
dynamics disease
Identifying flow modules in ecological networks using Infomap
Identifying flow modules in ecological networks using Infomap
Carmel Farage, Daniel Edler, Anna Eklöf, Martin Rosvall, Shai Pilosof
Methods in Ecology and Evolution   ·   24 Feb 2021   ·   doi:10.1111/2041-210X.13569
Website
software multilayer networks

2020

The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification
The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification
Shai Pilosof, Sergio A. Alcalá-Corona, Tong Wang, Ted Kim, Sergei Maslov, Rachel Whitaker, Mercedes Pascual
Nature Ecology & Evolution   ·   19 Oct 2020   ·   doi:10.1038/s41559-020-01312-z
microbial ecology dynamics host-parasite interactions
Pan-Cancer Analysis of Mitochondria Chaperone-Client Co-Expression Reveals Chaperone Functional Partitioning
Pan-Cancer Analysis of Mitochondria Chaperone-Client Co-Expression Reveals Chaperone Functional Partitioning
Geut Galai, Hila Ben-David, Liron Levin, Martin F. Orth, Thomas G. P. Grünewald, Shai Pilosof, Shimon Bershtein, Barak Rotblat
Cancers   ·   30 Mar 2020   ·   doi:10.3390/cancers12040825
cancer not our typical paper

2019

Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum
Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum
Shai Pilosof, Qixin He, Kathryn E. Tiedje, Shazia Ruybal-Pesántez, Karen P. Day, Mercedes Pascual
PLOS Biology   ·   24 Jun 2019   ·   doi:10.1371/journal.pbio.3000336
disease time multilayer networks population genetics

2018

Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum
Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum
Qixin He, Shai Pilosof, Kathryn E. Tiedje, Shazia Ruybal-Pesántez, Yael Artzy-Randrup, Edward B. Baskerville, Karen P. Day, Mercedes Pascual
Nature Communications   ·   08 May 2018   ·   doi:10.1038/s41467-018-04219-3
disease population genetics

2017

Asymmetric disease dynamics in multihost interconnected networks
Asymmetric disease dynamics in multihost interconnected networks
Shai Pilosof, Gili Greenbaum, Boris R. Krasnov, Yuval R. Zelnik
Journal of Theoretical Biology   ·   01 Oct 2017   ·   doi:10.1016/j.jtbi.2017.07.020
disease dynamics multilayer networks
Temporal dynamics of direct reciprocal and indirect effects in a host--parasite network
Temporal dynamics of direct reciprocal and indirect effects in a host--parasite network
[no author info]
Journal of Animal Ecology   ·   25 Mar 2017   ·   :
The multilayer nature of ecological networks
The multilayer nature of ecological networks
Shai Pilosof, Mason A. Porter, Mercedes Pascual, Sonia Kéfi
Nature Ecology & Evolution   ·   23 Mar 2017   ·   doi:10.1038/s41559-017-0101
perspecrive multilayer networks

2014

Multiple effects of host‐species diversity on coexisting host‐specific and host‐opportunistic microbes
Multiple effects of host‐species diversity on coexisting host‐specific and host‐opportunistic microbes
Hadar Kedem, Carmit Cohen, Irit Messika, Monica Einav, Shai Pilosof, Hadas Hawlena
Ecology   ·   01 May 2014   ·   doi:10.1890/13-0678.1
Effects of sewage-water contamination on the immune response of a desert bat
Effects of sewage-water contamination on the immune response of a desert bat
Shai Pilosof, Carmi Korine, Marianne S. Moore, Boris R. Krasnov
Mammalian Biology   ·   01 Apr 2014   ·   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
A trade‐off between quantity and quality of offspring in haematophagous ectoparasites: the effect of the level of specialization
Irina S. Khokhlova, Shai Pilosof, Laura J. Fielden, A. Allan Degen, Boris R. Krasnov
Journal of Animal Ecology   ·   23 Sep 2013   ·   doi:10.1111/1365-2656.12134
Phylogenetic structure of host spectra in Palaearctic fleas: stability versus spatial variation in widespread, generalist species
Phylogenetic structure of host spectra in Palaearctic fleas: stability versus spatial variation in widespread, generalist species
BORIS R. KRASNOV, SHAI PILOSOF, GEORGY I. SHENBROT, IRINA S. KHOKHLOVA, A. ALLAN DEGEN
Parasitology   ·   04 Sep 2013   ·   doi:10.1017/s0031182013001376
space
Spatial variation in the phylogenetic structure of flea assemblages across geographic ranges of small mammalian hosts in the Palearctic
Spatial variation in the phylogenetic structure of flea assemblages across geographic ranges of small mammalian hosts in the Palearctic
Boris R. Krasnov, Shai Pilosof, Georgy I. Shenbrot, Irina S. Khokhlova
International Journal for Parasitology   ·   01 Aug 2013   ·   doi:10.1016/j.ijpara.2013.05.001
space host-parasite interactions
Phylogeny determines the role of helminth parasites in intertidal food webs
Phylogeny determines the role of helminth parasites in intertidal food webs
Robert Poulin, Boris R. Krasnov, Shai Pilosof, David W. Thieltges
Journal of Animal Ecology   ·   25 Jun 2013   ·   doi:10.1111/1365-2656.12101
food webs
Co‐occurrence and phylogenetic distance in communities of mammalian ectoparasites: limiting similarity versus environmental filtering
Co‐occurrence and phylogenetic distance in communities of mammalian ectoparasites: limiting similarity versus environmental filtering
Boris R. Krasnov, Shai Pilosof, Michal Stanko, Serge Morand, Natalia P. Korallo‐Vinarskaya, Maxim V. Vinarski, Robert Poulin
Oikos   ·   21 Jun 2013   ·   doi:10.1111/j.1600-0706.2013.00646.x
FOREWORD: Evolution of culture
FOREWORD: Evolution of culture
Reut Berger-Tal, Elsita Kiekebusch, Iara Sandomirsky, Shai Pilosof
Israel Journal of Ecology and Evolution   ·   18 May 2013   ·   doi:10.1080/15659801.2013.865338
Temporal dynamics of direct reciprocal and indirect effects in a host–parasite network
Temporal dynamics of direct reciprocal and indirect effects in a host–parasite network
Shai Pilosof, Miguel A. Fortuna, Maxim V. Vinarski, Natalia P. Korallo‐Vinarskaya, Boris R. Krasnov
Journal of Animal Ecology   ·   14 May 2013   ·   doi:10.1111/1365-2656.12090
host-parasite interactions time

2012

Host body microcosm and ectoparasite infracommunities: arthropod ectoparasites are not spatially segregated
Host body microcosm and ectoparasite infracommunities: arthropod ectoparasites are not spatially segregated
SHAI PILOSOF, MARCELA LARESCHI, BORIS R. KRASNOV
Parasitology   ·   05 Sep 2012   ·   doi:10.1017/s0031182012001205
host-parasite interactions
Effects of Anthropogenic Disturbance and Climate on Patterns of Bat Fly Parasitism
Effects of Anthropogenic Disturbance and Climate on Patterns of Bat Fly Parasitism
Shai Pilosof, Carl W. Dick, Carmi Korine, Bruce D. Patterson, Boris R. Krasnov
PLoS ONE   ·   19 Jul 2012   ·   doi:10.1371/journal.pone.0041487
host-parasite interactions bats

2010

Variability in urine concentration and fecal water content of bats in a tropical deciduous forest
Variability in urine concentration and fecal water content of bats in a tropical deciduous forest
Shai Pilosof, L. Gerardo Herrera M.
Journal of Mammalogy   ·   16 Jun 2010   ·   doi:10.1644/09-mamm-a-370.1
bats