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.
Kostas Patouras, a Greek Air Traffic Controller, kindly supported this effort and reviewed the material produced.
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.
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.
November 22, 2023 Alexis has been included in the Clarivate analytics highly cited researchers list for the 8th consecutive year.
The list has also been mentioned by Greek media.
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.
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.
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:
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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?).
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.
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.
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.
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..
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 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.
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.
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.
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.
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.
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.
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.
Jan 20, 2023 - Alexis was named a honorary fellow of FORTH by the board of directors of the institute.
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.
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.
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.
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.
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.
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.