2nd annual Greek ERA chair meeting

June 28, 2024 The second Greek ERA chair meeting took place in Athens at the National Hellenic Research Foundation.

Identification of World War II victims in Crete

May 20, 2024 An excellent article by science journalist Vasiliki Michopoulou on the Greek national news portal Dnews about our collaborative work with the ancient DNA lab on identifying victims from a world war II mass execution in Adele village, Crete.

FORTH also published a corresponding press release about this work.

The story was also covered by national state television

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Legend2024: Machine Learning for Evolutionary Genomics Data

May 15, 2024 The conference that we organized as kick-off event for BCG together with several colleagues from abroad attracted approximately 80 researchers from Europe and the US to Crete and was also streamed via Zoom.

At the conference dinner tonight, we will discuss with the co-organizers how to transform it into a conference series based on plans to organize the next instances in France and the US.

The picture shows some participants on top of mount Stroumpoulas, a mountain peak near FORTH.

A comprehensive local newspaper interview

May 15, 2024 An extensive interview with Katerina Mylona covering our bird paper in Nature, the machine learning for evolutionary genomics conference we organized at FORTH from May 13-15, the BCG group set up, necessary reforms for achieving sustained brain gain, and our responsibility as scientists in local communities.

Portrait of all 7 Greek ERA chairs

April 23, 2024 As a side effect of the 1st Greek ERA chair meeting Panos Tsakalides and Alexis organized at FORTH in September 2023, portraits of all 7 Greek ERA chairs were published in the national Greek newspaper Kathimerini.

Interview on Research Policy Issues

April 10, 2024 Alexis gave an interview on local Crtean television channel TV Creta that formed part of a comprehensive report on research policy issues, with an emphasis on the substantial lack of national research funding.


Watch the interview on

In Nature: Bird Evolution Paper

April 2, 2024 Alexis and three members of the BCG sister group at HITS contributed to the largest ever phylogenetic analysis of bird evolution that was just published in Nature. Numerous open-source tools enabling research in evolutionary biology, developed by us, were used for this study.

HITS press release and press portal uptake1 and uptake2. Short on-line news item about bird evolution.

FORTH press release - Greek version. Local Cretan press uptake.

An excellent article by Greek science journalist Vasiliki Michopoulou on the broader context of our research in Heidelberg and Heraklion.

An interview on local Cretan TV channel about Bioinformatics, bird evolution, and quantifying uncertainty.
Watch the interview on

Biodiversity Excursion

March 29, 2024 We encountered two rare and elusive individuals of Dendropithecus Cretensis that live in the trees of the Rouvas forest during our Biodiversity excursion to the Rouvas George.

Field work with the museum

March 13, 2024 Our PhD student Lucia joined researchers from the natural history museum of Crete on a field trip in the Lasithi prefecture to collect beatle samples.

Fulbright Fellowship for Adam Leache

February 22, 2024 Our long term collaborator Prof. Adam Leache from the University of Washington at Seattle, obtained a Fulbright fellowship to visit BCG from February to May 2025.

Outreach on Air Traffic Control

January 31, 2024 Alexis presented the new outreach material on AirTraffic Control to the pupils of the primary school of Sivas located in the south of the Heraklion prefecture.

BCG is complete

January 29, 2024 With the arrival of (from left to right) Franziska, Lucia, and Noah, our three PhD students, the BCG team is complete. All three will officially start on Feb 1st.

The smiles on their faces were produced by asking them to pronounce the word "tzatziki".

More UoC Teaching

January 24, 2024 In spring term, Alexis will be teaching a new graduate seminar on "Reproducibility in Bioinformatics" at the computer science department of the University of Crete.

Unfortunately, this will not be a joint UoC-KIT course this time as the UoC spring semester and the KIT summer semester hardly overlap.

Visit by Prof. Dimitris Paraskevis

January 19, 2024 Dimitris Paraskevis, Professor of Epidemiology and Preventive Medicine at the Medical School of the National and Kapodistrian University of Athens, visited us for two days to discuss challenges and future collaborative projects in the area of virus evolution.

From left to right, Giorgos, Panos, Dimitris, Alexis, and Ben enjoying a warm and sunny winter day on the FORTH terrace.

legend2024 : Machine Learning for Evolutionary Genomics Data Conference at FORTH

January 16, 2024 While initially only a smaller BCG inaugural scientific workshop was planned it evolved (it's a long story...) into a conference that Alexis is now jointly organizing and co-financing together with some colleagues from abroad. Please consult the legend2024 conferenace web-site for all details.

Advisory Board of Data-Driven Life Science Project

January 10, 2024 - Alexis joins the advisory board of the SciLifeLab & Wallenberg National Program for Data-Driven Life Science program in Sweden.

About the program: The future of life science is data-driven, providing major new opportunities to explore and understand biology, human health and changing ecosystems. The SciLifeLab & Wallenberg National Program for Data-Driven Life Science (DDLS) is set up to make use of these opportunities.

Joint UoC-KIT course on Bioinformatics attracts interesting guest hearers

January 8, 2024 - The first teaching cycle of the joint UoC-KIT Master level course on "Introduction to Bioinformatics for Computer Scientsists" was completed in the last week before Christmas.

As the course could always be attended on-line via Zoom, Alexis decided to open it up to a broader audience outside KIT and UoC via his networks.

This attracted interesting and surpising guest hearers, such as, for instance, a PhD student and a staff scientist from the Hellenic Center for Marine Research as well as Ümit Atlamaz, an Assistant Professor in the Department of Linguistics at Boğaziçi University in Istanbul.

Primary School Outreach Material on Air Traffic Control

December 7, 2023 - While studying computer science back at TU Munich, Alexis also took several courses on aeronautical engineering and spent a couple of months as an intern at the Eurocontrol Innovation Hub at Bretigny near Paris.

This is how the idea emerged to design primary school material for explaining the basics of Air Traffic Control and thereby foster the student's enthusiasm about maths, physics, science, and technology.

The slides (in Greek) and the corresponding glossary are freely available.

Kostas Patouras, a Greek Air Traffic Controller, kindly supported this effort and reviewed the material produced.

Panos joins and BCG visits HITS

December 4, 2023 - All current members of the Biodiversity Computing Group at ICS-FORTH are visiting the Computational Molecular Evolution (CME) sister group at the Heidelberg Institute for Theoretical Studies (HITS) these days to tighten the links between the groups.

The picture shows all BCG and almost all CME group members in front of the HITS building. The picture also includes Panos Ioannidis who joined BCG as a PostDoc on December 1st 2023.

3rd School Visit

November 22, 2023 - with his colleagues and friends Iasmi Stathi and Stavroula Christodoulopoulou (left and right of Alexis) from the Natural History Museum of Crete, Alexis visited the primary school in the remote mountain village of Gergeri located on the southern slopes of the Psiloritis mountain range to present the dedicated program on The Aegean Archipelago: a living laboratory of evolutionary biology to pupils and teachers.

Alexis highly cited researcher - 8 years in a row

November 22, 2023 Alexis has been included in the Clarivate analytics highly cited researchers list for the 8th consecutive year.

There is a press release by by ICS-FORTH and a respective press release by HITS as well as the uptake on the AlphaGalileo and idw scientific news portals.

The list has also been mentioned by Greek media.

Ben is here and Julia is back

November 6, 2023 The second BCG PostDoc, Ben Bettisworth arrived in Crete and will offcicially join FORTH in mid November. While originally from Alaska, Ben recently completed his PhD in computer science at the Karlsruhe Institute of Technology and now moved even further south to Crete.

Also, KIT and HITS PhD student Julia Haag is back in Crete for a one month visit at FORTH.

On the picture (from left to right) Giorgos, Ben, and Julia are enjoying the warm autumn weather in Crete on the FORTH terrace.

Giorgos is here

October 2, 2023 The first BCG PostDoc, Giorgos Koutsovoulos joins FORTH. Giorgos spent the largest part of his academic career abroad and has now returned to conduct research in Greece after 14 years.

1st meeting of all Greek ERA chairs at FORTH

September 26, 2023 The inaugural Greek ERA chair meeting that included all 7 Greek ERA chairs (see the respective web page of the General Secretariat for Research and Innovation for an overview) was a great success.

The meeting was attended by the Director of FORTH, Prof. Nektarios Tavernarakis, the Director of the Institute of Computer Science at FORTH, Prof. Dimitris Plexousakis, and the Director of the institute of Molecular Biology and Biotechnology at FORTH, Prof. John Vontas (also the coordinator of one of the ERA chair projects). It was also attended by the following policy makers: Deputy Minister of Development, Mr. Maximos Senetakis, General Secretary for Higher Education, Prof. Em. Odysseas Zoras, and Deputy Regional Governor for the Primary Sector, Mrs. Eirini Giakoumaki.

In terms of actionable items, the 7 Greek ERA Chairs decided to:

  • Establish the “Greek ERA Chair Network” in order to ensure a continuous flow and exchange of ideas with an emphasis on policy issues and reforms (to this end, a mail list was set up, that includes all current and shall include all future ERA Chair holders and coordinators).
  • Hold an annual Greek ERA Chair meeting - the 2024 meeting will be held at the National Hellenic Research Foundation in Athens (P. Kastritis), the 2025 meeting will take place at the Biomedical Sciences Research Center “Alexander Fleming” (G. Skretas).
  • Integrate new Greek ERA Chairs from upcoming calls into the ERA Chair Network
  • Provide support and expertise to upcoming ERA Chair proposals
  • Jointly work on a prioritized list of research policy reforms
  • Intensify contacts with the General Secretariat for Research and Innovation, with the Ministry of Education and the Ministry of Development.

Joint UoC-KIT Bioinformatics course starts

September 25, 2023 The joint simultaenous class on "Introduction to Bioinformatics for Computer Scientists" started today featuring a meet and greet session with the Cretan students. This provided a good opportunity to test the Zoom streaming from Uoc -> KIT which worked smoothly out of the box.

Actual lectures will start on October 23 with the begininng of the winter term at KIT.

More brain circulation

September 22, 2023 Noah Wahl, who is currently writing his Master's thesis at the Karsruhe Institute of Technology in front of the FORTH building.

He spent a week in Crete to intensively discuss the details and directions of his Master's thesis with Alexis.

Outreach talk In Listaros

August 12, 2023 On Sunday, June 12 Alexis and the rest of the executive board of Klimatogi, the Cultural Committe of Listaros village organized an outreach talk by Anastasia Markomichelaki, associate professor at the philology department of the Aristotle University of Thessaloniki on "Poetry and Theatre in Venetian Crete: 14th - 17th century"

Her talk was framed by the musicians: Michalis Staurakakis, Giorgis Zacharioudakis, and Kostas Kyritsakis.

The goal of this event that attracted over 100 citizens to Listaros was to better inform the broad public about the important role of this epoch for modern Greek litterature.

Museum Exhibit - Aerial Collisions

August 1st, 2023 With our collaborators and friends at the Museum of Natural History in Crete, we set up an electronic stand in the museum exhibition that showcases the web game we developed in 2022 for explaining evolution, phylogenetics, and the use of DNA data to identify species.

Greek ERA chairs meeting September 26

July 31, 2023 Together with Panos Tsakalides (Coordinator of the TALOS ERA chair project at ICS-FORTH) and Dimitris Plexousakis (director of ICS-FORTH), we are finalizing the preparations for the first meeting of all 7 Greek ERA chairs that will take place at FORTH in Heraklion on September 26.

The meeting will feature a closed session for establishing an initial network between all 7 ERA chairs and coordinators as well as a public project presentation session with policy makers.

Project Funded: Cretan Population Genomics

July 20, 2023 The project we submitted with the ancient DNA lab at FORTH-IMBB and the medical school of the University of Crete entitled "The Genomics of the Cretan population through History and Time, shaping Inflammation and Immune Homeostasis", to the national research funding agency (Hellenic Foundation for Research and Innovation) got funded.

The collaborating PIs will receive approximately 400K EUR over two years.

Reforms: Gender Issues

July 3, 2023 Alexis gave a talk on "Why Greece needs a dedicated female researchers/professors program" in the context of the hybrid seminar for gender dimension in research @FORTH in Horizon Europe.

Alexis came up with the idea of establishing a dedicated female researcher/professors program in Greece following the example of numerous other EU countries and started discussing this with some of his female academic friends in Greece.

In close collaboration with Maria Klapa, president of the gender equality committee at FORTH, we now strive to prepare a respective policy proposal, ideally involving all gender equality committees in Greek Academia.

Advanced ERC grant for Elena Anagnostopoulou

June 29, 2023 Proud to announce that our collaborator from linguistics, Elena Anagnostopoulou, just received an advanced ERC grant for work on language evolution. We are looking forward to continue the interdisciplinary collaboration that started with the Master Thesis by Luise Häuser via a shared PostDoc that will be funded by her ERC grant.

Outreach talk In Listaros

June 11, 2023 On Sunday, June 11 Alexis and the rest of the executive board of Klimatogi, the Cultural Committe of Listaros village organized an outreach talk by Dr. Charalambos Fassoulas, director of the geodiversity department of the Natural History Museum of Crete on the "Geotectonic conditions and movements in the wider Messara area".

The goal was to better inform the broad public about the tectonic particularities of the Messara region, in light of the May 18, 2023 magnitude 5 earthquake whose epicenter was located approximately 3 km east of Listaros village.

Outreach talk at the Museum

May 29, 2023 On Monday, May 29 at 19:30 Alexis gave a public outreach talk (in Greek) on "The role of Computer Science in Evolutionary Biology" at the Darwinian Monday talk series of the Natural History Museum of Crete. It was also streamed via Zoom and is available on youtube. Finally, it was picked up in two local press reports report 1 and report2.

Luise is back in Crete

May 24, 2023 KIT Master student Luise Häuser is back in Crete to present work on "General and Language-specific Aspects of Phylogenetic Inference" in a joint talk with Alexis at the workshop on "Computational Phylogenetics and language (Pre)history: Achievements, Challenges and Prospects" organized by our collaborator from the linguistics department Prof. Elena Anagnostopoulou.

Natural History Museum: Tighter Collaboration

May 23, 2023 The already very close collaboration between BCG and the Natural History Museum of Crete (NHMC) will be further strengthened via a national grant to NHMC at the University of Crete entitled "High mountains, shallow waters: the effects of climate change on organisms living in 'extreme' and sensitive ecosystems".

NHMC will collaborate with BCG on the Bioinformatics analyses of the data that will be sequenced and on dissemination activities.

EMBO Satellite Workshop on Biodiversity Informatics

May 21, 2023 The two day satellite workshop at the Hellenic Center for Marine Research funded by EMBO in conjunction with the 13th summer school on Computational Molecular Evolution (CoME) was a full success.

The workshop was organized by Tereza Manousaki, Cilia Antoniou (both at HCMR) and Alexandros Stamatakis (FORTH).

Apart from talks contributed by CoME lecturers and teaching assistants (early career scientists) there were contributed talks by members of the local research community in Crete (HCMR, FORTH, NHMC), but also from other parts of Greece as well as from the US (via Zoom).

A substantial fraction of talks was contributed by early career scientists.

Likewise, attendees were not only from Crete, but also from Thessaloniki, Italy, and Germany. Upon popular request the workshop was also streamed via Zoom and we spotted attendees from Austria and Spain.

CoME 2023

May 12, 2023 Picture of the fabulous group of students and lecturers attending the 13th summer school on Computational Molecular Evolution (CoME) in front of the main entrance of the Hellenic Center for Marine Research in Heraklion.

Nick Goldman is in Crete

May 12, 2023 International selection panel member for the ERA chair project as well as project advisory board member Nick Goldman is in Crete to teach at the 13th summer school on computational molecular evolution, but also to chat with Alexis about progress and potential collaborations within the framework of the ERA chair project.

More Brain Circulation

May 10, 2023 Lukas Hübner, shared PhD student between Prof. Peter Sanders at KIT and Alexis at HITS is having a freddo espresso ouside the Crete Aquarium located next to the Hellenic Center for Marie Research, where the 13th summer school on computational molecular evolution is taking place.

Apart from drinking coffee he is substantially contributing to the success of the school as a teaching assistant and will also give a talk at the respective satellite workshop on "Biodiversity Informatics" that will take place immediately after the summer school. He will spend two weeks in Crete.

Talk at BSRC in Athens

April 28, 2023 Reviving old networks and establishing new ones in the framework of a talk at the Biomedical Sciences Research Center (BSRC) Alexander Fleming in Athens, Greece.

In the context of this visit Alexis also met with the BSRC ERA chair George Skretas to discuss potential reforms and synergies and plan a meeting of all 7 Greek ERA chairs.

Joint UoC-KIT Bioinformatics Class

March 31, 2023 - It is official ... Starting in winter term 2023/24 Alexis will be simultaneously teaching his 3 ECTS Master's level Course on "Introduction to Bioinformatics for Computer Scientists" at the computer science departments of the Karlsruhe Institute of Technology (KIT) in Germany and the University of Crete (UoC).

The plan is that Alexis will teach a couple of classes live at KIT and stream them to UoC and the other way around, it will be a bit like the Eurovision song contest (Crete, Karlsruhe, can you hear us?).

2nd School Visit

March 31, 2023 - with his colleague and friend Iasmi Stathi from the Natural History Museum of Crete, Alexis visited the Role Model Gymnasium of Heraklion (Πρότυπο Γυμνάσιο Ηρακλείου) to present the dedicated program on The Aegean Archipelago: a living laboratory of evolutionary biology to pupils and teachers.

Image on the right - Alexis drawing a phylogenetic tree with DNA data on the board in the classroom and counting mutations.

Reforms

March 11, 2023 - Apart from the regular monthly meetings on potential reforms with D. Plexousakis (director of ICS-FORTH) and the quarterly meetings with N. Tavernarakis (director of FORTH) upon a very nice initial meeting, Alexis now also agreed to holding regular joint quarterly meetings with M. Klapa and G. Kaklamani (president and vice-president) as representatives of the gender equality committee at FORTH.

Alexis also had a meeting with a representative of the Researchers in the Prefecture of Heraklion organization that mainly represents Master's thesis students, PhD students, and PostDocs to listen to their concerns.

Image on the left - a Malaise insect trap for insect Biodiversity sampling on Crete.

Guest Lecture at UCSD

March 1st, 2023 - Alexis gave a guest lecture in a graduate level course on "Parallel Computing in Bioinformatics" (ECE 284) at the University of California at San Diego entitled "Optimizing and Parallelizing Phylogenetic Likelihood Calculations".

The lecture was also streamed via Zoom to ICS-FORTH.

1st primary school visit

Feb 22, 2023 - Today, Alexis visited the 3rd primary school of Tympaki (southern Heraklion prefecture) to present the dedicated program on The Aegean Archipelago: a living laboratory of evolutionary biology to 5th and 6th grade students. He covered the "aerial collisions game" and the pupils played the "Aegean Settlers" board game.

On the picture, Alexis together with teachers of the third primary school of Tympaki that took part.

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Software Engineering Fun

Feb 20, 2023 - A Bachelor thesis supervised by Alexis at KIT investigating the question if there is a correlation between code quality and the usage of English swear words in open source code written in C on github (there seems to be a correlation) has stirred some media interest.

The findings of the thesis have been covered in a German, a Greek, a Danish news portal, in the local newspaper of Crete, and in the US based technology-focused news portal Ars Technica.

The Bachelor thesis also made it to a popular science broadcast in German (around minute 41:22).

The code quality score distributions over C source code repositories with and without swearwords are shown on the right.

Brain Circulation - reverse direction

Feb 10, 2023 - Angeliki Papadopoulou, a PhD student of Pavlos Pavlidis at ICS-FORTH circulated to BCG's sister lab, Alexis' Computational Molecular Evolution group at the Heidelberg Institute for Theoretical Studies, for three months.

The SoftWipe Competition

Feb 9, 2023 - SoftWipe is an open source tool for checking the adherence of scientific code written in C/C++ to coding standards by computing an overall quality score that was developed by Alexis' group in Germany.

To raise awareness about the importance of good SW engineering practices and to get to know the programming population (Masters and PhD students as well as PostDocs) at ICS-FORTH better, Alexis initiated the SoftWipe score competition. The programming population can submit their open-source codes for evaluation with SoftWipe and the programmer with the highest score (cleanest code) will then get invited by Alexis for lunch or dinner.

Alexis will also give an informal talk about SoftWipe for the programming population at ICS-FORTH in March 2023.

More brain circulation

Feb 3, 2023 - Julia Haag (MSc in computer science, evidently with a Freddo Capuccino on the FORTH terrace), a first year PhD student at KIT and HITS in Germany arrived at FORTH toward the end of January and will stay for 3 months to work with Alexis and Pavlos Pavlidis on quantifying uncertainties in PCA analyses with a focus on population genetics data.

Satellite Workshop on Biodiversity Computing

Feb 1, 2023 - As in every second year since 2010, we are organizing our summer school on Computational Molecular Evolution in Crete at the Hellenic Center for Marine Research (HCMR).

The European Molecular Biology Organization (EMBO) who is the main sponsor of this course now also offers additional funding for satellite events in conjunction wih the school such that the local research community can profit more from the course. Together with former course participant Dr. Tereza Manousaki (now a junior PI at HCMR) and school co-organizer Dr. Aglaia Antoniou (also at HCMR) we are organizing a two-day satellite workshop on "Biodiversity Computing", immediately after the end of the summer school. Some lecturers of the school will stay to also present their research and interact with the local community at this workshop.

Cretan ERA Chairs

Feb 1, 2023 - Alexis has taken the initiative to organize the first meeting with the other three ERA chair projects (one at the University of Crete and two additional ones at FORTH) that will start in Crete in 2023. This first meeting was to get to know each other and identify synergies in particular with respect to implementing reforms.

Local Community Outreach

Feb 1, 2023 - In December 2022, Alexis Stamatakis got re-elected into the executive board of the Cultural Committee of Listaros village - Klimatogi, the village where he lives. Being part of this board means that there is direct and immediate communication with citizens of the village and neighboring villages in southern Crete (Messara region).

In addition, Klimatogi has initiated a series of summer seminars on science for the broader public. The first talk was given by Prof. Nikos Poulakakis, director of the Natural History Museum of Crete (NHMC), in 2022 on the Importance of Biodiversity.

This close connection to a local community will not only serve the outreach purposes of the Biodiversity Computing Group, but also of other EU-funded projects, as the board of Klimatogi has already received a request by NHMC to organize another such event in summer 2023.

Alexis Honorary Fellow of FORTH

Jan 20, 2023 - Alexis was named a honorary fellow of FORTH by the board of directors of the institute.

Brains start circulating

Jan 16, 2023 - Luise Häuser is the first visitor of BCG. She is a Master's student from KIT working on better understanding and characterizing natural language evolution datasets.

Her work does not only span across borders, but also across disciplines as we are collaborating with Prof. Elena Anagnostopoulou, a theoretical linguist from the University of Crete.

On the photo, Luise is enjoying her first Freddo Capuccino on the terrace of the main building of FORTH.

BCG setup phase starts

Jan 11, 2023 - After a very sunny Christmas break in Crete, the BCG setup phase starts, job advertisments are being prepared, the website setup starts, and Alexandros (Alexis) Stamatakis has moved into the new offices at FORTH.

Projects initiated prior to project start on January 1st 2023, such as the Malaise trap insect sampling in Southern Crete via a citizen science initiative will be continued.

First contacts have been established to present the outreach program entitled "The Aegean Archipelago: a living laboratory of evolutionary biology" that was developed in Collaboration with the Natural History Museum of Crete at additional primary schools.

Radio Interview 2

Dec 20, 2022 - Listen to the interview Alexis did with Campus radio at KIT (in German). It puts the project nicely into context with the 2022 Biodiversity summit in Canada.

Radio Interview 1

Nov 30, 2022 - Listen to the interview Alexis did with Campus report (in German) that is funded by the Klaus Tschira Stiftung that also finances HITS.

Newspaper Article 2

Nov 21, 2022 - An interview with Alexis (in Greek) appeared in the local Cretan newspaper Patris.

Alexis had also previously worked with the journalist who covers scientific topics in Crete.

Newspaper Article 1

Nov 15, 2022 - The press releases resulted in a dedicated and very detailed newspaper article in the national Greek news portal Dikaiologitika.

Alexis has been in regular contact with the journalist who wrote the article for almost 10 years. This was also the first opportunity to publicly outline the necessary reforms in the Greek academic system.

Press Releases

Nov 10, 2022 - As planned, press releases on the ERA chair grant were distributed by the three involved institutions: FORTH, HITS, and KIT.