News

Better late than never! We finally got the chance to celebrate Sharon’s Master’s degree, delayed due to circumstances beyond our control.  Now, as you continue your PhD studies at the Weizmann Institute, we wish you success. Keep shining!

Last Friday in March, we gathered at Shai’s place to celebrate Ying-Jie’s birthday and warm up his new home! We made falafel together and shared sweet moments. Let’s carry that spirit of togetherness and collaboration into our pursuit of scientific breakthroughs in the lab!

Dr. Shai and Ying-Jie Wang visited the University of Liverpool last week. They spent time in Dr. James Hall’s lab. Their time was marked by fruitful discussions, sharing of project outcomes, and strategic planning. Additionally, Dr. Shai took the stage to present a seminar, ‘A Complex Systems View on Microbial Communities,’ at the Department of Evolution, Ecology, and Behaviour in the Institute of Infection, Veterinary, and Ecological Sciences. The trip provided a valuable opportunity for both teams to synchronize efforts and enhance our collaborative project.

Congratulations to Barry for successfully defending his thesis on January 2, 2024, and completing his Master’s degree! Your work and determination have paid off, marking a significant milestone in your academic journey. We’re proud of your achievement and excited to see the impact of your research in the future. We will be enjoying Barry’s presence in the lab for the near future as he continues working with us on his research on predicting links in ecologicla networks.

The highlight of the week: Dr. Shai Pilosof joined Prof. Debbie Toiber and Prof. Barak Rotblat on the BGU radio show “Biology without Biologists.” In this episode, Shai shares his life journey, marked by critical decisions that shaped his research career and path in life. His message to students is inspiring and practical: “Being a student is an excellent opportunity to open your eyes and mind and discover what you love to do. Stay curious and experiment in different labs.”

Our latest preprint, published on November 21, 2023, in EcoEvoRxiv, explores the intricate spatial dynamics of plant-pollinator communities across the Canary Islands. Using a unique multilayer network approach, we reveal how community structures evolve with geographical distance on a regional scale. Our findings highlight the important influence of local and regional processes in shaping these patterns.

The study uses the rumen microbiome of 1,012 cows in seven European farms as a case study to explore the complex interactions between microbes in highly diverse environments. Through multilayer network analysis, we unveil scale-dependent signatures of microbial co-occurrence, shedding light on the underlying processes that structure these networks. The multilayer network analysis approach used in this study could be applied to other contexts to study microbial communities and their functions. Read the full preprint here: EcoEvoRxiv

Our article “Practical guidelines and the EMLN R package for handling ecological multilayer networks” was published in Methods in Ecology and Evolution on October 18, 2023. We’ve developed the EMLN R package, which simplifies working with ecological multilayer networks. It helps organize your multilayer network to use it with other popular tools. Plus, we’ve included practice data sets and step-by-step examples to help you get started.

Our paper, “Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness, ” was officially published in “Nature Communications” on October 7th, 2023.

Following EcoNet2023, Johannes Nauta (postdoctoral researcher, Dept. of Physics, University of Padua, Italy) extended his stay in our lab for an extra week as part of our HFSP-funded collaboration project. Ying Jie and Johannes led intensive discussions and worked hard to model microbiome population dynamics under perturbations using different approaches. Johannes employed ODE systems in his modeling approach, while Ying Jie explored the domain of agent-based modeling. It was a productive week and we are looking forward to the results.

This year, Shai hosted the EcoNet2023 workshop (Ecological networks from theory to application) at Ben Gurion University, Israel.

In July 2023, our lab had the excellent opportunity to participate in the NetSci 2023 conference, organized by the Network Science Society, in the beautiful city of Vienna, Austria. Our lab made its mark with the excellent talks delivered by Shai, Sharon, Matan, and Tino. The conference was a productive venue for enhancing existing collaborations, initiating new partnerships, extending warm birthday wishes to Matan, and reconnecting with a former lab member.

Our paper titled “Invasive species modulate the structure and stability of a multilayer mutualistic network” published on June 28th, 2023, in “THE ROYAL SOCIETY” under the DOI https://doi.org/10.1098/rspb.2023.0132 Our model system and multilayer network analysis allow us to examine the broader consequences of disturbances, such as invasive species, on the structure and stability of multitrophic networks.

Bravo, Sharon and Itamar! Your exceptional achievements in studies have been awarded honors and appreciation. Congratulations on your well-earned successes. Keep up the incredible work!

Welcome back, Tiño! We’re thrilled to have Tiño back in the Lab as a post-doc. We wish you all the best of luck. We missed you.

Dr. Shai started May to strengthen and foster collaborative ties by visiting Duke University, where the NIH project gathered.

A unique visitor marked the last weekend of April, Prof. Darren Evans from the UK graced the Department of Life Science as a special guest of Dr. Shai Pilosof. Prof. Darren delivered an exceptional seminar, enriching our academic community. It was an extraordinary opportunity for Shai’s students to engage with Prof. Darren, sharing their research and benefiting from his expertise. The Shai family opened their home, hosting a delightful Friday dinner for Prof. Darren and the lab.

Time flies! A year has passed, and it’s time to say goodbye to Vicente, who has completed his internship in our lab. We hope his time in Israel was fulfilling both personally and professionally. We do not doubt that Vicente will continue to make meaningful contributions to the field. Take care, Vicente, and all the best!

We had an incredible lab retreat over the weekend (30-31.03.2023). The retreat started on Thursday with a trip to Nahal Amud, where we had a delightful meal at a local Arab restaurant. Later that night, we stayed at a hostel by the Sea of Galilee and enjoyed a fun-filled social evening. The next day, we went on a scenic hike to Harbel Cliff, which offered breathtaking views of the surrounding landscape. For a small glimpse into the trip, have a look at the pictures below.

Ying Jie Wang, a postdoctoral researcher, has recently joined our lab in March. Originally from Taiwan, she brings a wealth of knowledge in stress ecology, community ecology, and eco-evolutionary feedbacks. Despite being with us for just a month, she has already become a key player in our international collaborative project on agent-based modeling of highly-diverse microbial communities. This project brings together ecology and evolution, microbiology, and statistical physics. We are excited to have Ying Jie with us and wish her the best of luck in her research. Welcome to the Lab, Ying Jie!

We are pleased to welcome Itamar, a second-year undergraduate student at BGU, who has recently joined us. Itamar is already working hard, learning the necessary skills and methods to start his project next year. Hope that Itamar enjoys his time in the lab and look forward to seeing the results of Itamar’s hard work. Welcome to the Lab!

Our paper, ‘Conceptualizing microbe-plasmid communities as complex adaptive systems’ on ScienceDirect, available online starting from February 21, 2023. The article discusses the importance of understanding how plasmids shape microbial communities and proposes a theoretical approach to overcome the challenges of studying this complex system. Click on the link to read the paper.

Our paper titled “Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission” was published on February 9th, 2023, in “The ISME Journall” under the DOI https://doi.org/10.1038/s41396-023-01373-5. The study utilized multilayer networks to analyze the genetic similarity between plasmids in a population of dairy cows and sheds light on the spread of antimicrobial resistance (AMR) genes across animal hosts. For more details, please see our paper here.

Students and researchers from around Israel were invited to participate in a workshop about plasmid biology. The workshop was organized by Shai and Prof. Itzik Mizrahi, with Prof. Alvaro San Millan as a guest teacher. The workshop featured insightful talks and inspiring discussions for all participants, while connecting researchers from a range of backgrounds and knowledge bases. Participants developed research ideas on topics at the forefront of plasmid biology after identifying gaps in knowledge.

We will miss her, but wish her all the best down the road!