2022-12-19 Delighted that the peer-reviewed version of our antibody-antigen simulation framework Absolut! is now online at Nature Computational Science. We now provide additional support for the real-world relevance of Absolut!-data for benchmarking antibody specificity predictions.
Paper link: https://rdcu.be/c1TPr
News and Views by Pieter Meysman: https://t.co/dJ0iIdYDOE
Details on new manuscript additions since the first preprint: https://lnkd.in/dDGpCCMx
Tweetorial on first preprint: https://lnkd.in/eedM3Na
Unbelievable work led by two exceptional postdocs: Philippe Robert and Rahmad Akbar. Great collaboration, as usual, with the Geir Kjetil Sandve lab.
See below our proposal for the Cover that, unfortunately, was not chosen (credits: Rahmad Akbar).
2022-12-12 Philippe and Victor published a News and Views article on the article by Zhang et al. (Predicting unseen antibodies’ neutralizability via adaptive graph neural networks).
2022-12-05 Victor gave a talk at the Antibody Engineering and Therapeutics Conference in San Diego.
2022-12-02 A collaborative piece on The evolutionary and functional significance of germline immunoglobulin gene variation was published in Trends in Immunology. Co-authors: Matt Pennell, Corey Watson, Oscar Rodriguez.
2022-12-02 Victor gave a Short Course on Machine Learning Tools for Protein Engineering at PEGS Europe in Barcelona.
2022-11-13 Victor gave Short Course on Machine Learning Tools for Protein Engineering at PEGS Europe in Barcelona.
2022-10-27 Victor contributed a talk to celebrating launch of the UiO-spinout company Authera (co-founders: Jan Terje Andersen, Inger Sandlie, Simone Mester, Torleif T. Gjølberg).
2022-09-30 Victor was a keynote speaker at the CRIION Inaugural Symposium “Intelligent Oncology – The Potential Of AI To Cure Cancer“.
2022-09-29 Victor co-organized, together with Sandeep Kumar, at TAbS Symposium on Biopharmaceutical Informatics. Speakers: Peter Tessier, Lucy Colwell, Konrad Krawczyk, Charlotte Deane. Link and recordings: https://www.antibodysociety.org/biopharmaceuticalinformaticssymposium/
2022-09-21 Victor contributed a thought piece on a Cell Systems Voices issue on the current driving questions in immune repertoire research.
2022-09-20 Congratulations to Ingvild for passing her Master thesis defense with the best grade! Hurray!!
2022-09-19 Victor was named a Young CAS Fellow and will work on Evolutionary imprints of adaptive immunity.
2022-09-15 It was a pleasure to present the progress of our ImmunoLingo convergence environment at the dScience Lunch Seminar: Deciphering the Immune System Through Linguistics-Inspired Statistical Machine Learning
2022-09-11 Our letter to the editor of Bioinformatics on the importance of simulations in bioinformatics research is finally out. Great collaboration again with Geir Kjetil Sandve.
2022-09-10 The first edition of GREIFFLAB OPEN table tennis tournament has been concluded and the winners are:
1st place: Knut & Ivar of SandveLab, Biomedical Informatics (BMI)
2nd place: Eva & Mat of GreiffLab, Computational Systems Immunology (CSI)
3rd place: Rasmus & Fritdjof of FLJ and RI Labs, Department of Immunology
We thanks once more our sponsor, donators, and a very special patron:
Light chain sponsor: Department of Immunology, UiO
Donators: Javier Freire Gonzalez, Eva Smorodina, Habib Bashour, Puneet Rawat, Khang Le Quy, Finn-Eirik Johansen, Anonymous
Special patron: Brij Buhsan Mehta
See you all on the next edition!!!
2022-07-19 The lab is back on the table tennis track and training hard to prepare for the upcoming GREIFFLAB OPEN table tennis tournament in late summer/early fall 2022.
2022-07-19 Eva Smorodina played a host to a wonderful dinner, master chef Andrei and and Lara put together a fantastic course and we capped the night with the first edition of ImmunoVision (winning countries: Lebanon & Malaysia)!
2022-07-19 Our joint publications with the Sandve lab on ultrafast comparison has been published in Bioinformatics. Congrats, Lonneke!
2022-07-14 Eva Smorodina joined the lab as a research assistant to work on structural biology and machine learning projects.
2022-05-25 Our joint work with the Sandve lab on Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification is now out in GigaScience! Congrats, Chakri, Milena, and Lonneke!
2022-04-16 Christin Elster (University of Düsseldorf) joined the lab for a 3 months visiting PhD research visits to work on TCR-seq projects.
2022-04-01 Our work on the In silico proof of principle of machine learning-based antibody design at unconstrained scale was published at mAbs. Congrats, Mat and Philippe!
2022-03-16 Our giant review on machine-learning-based antibody design is finally online! Congrats to all the co-authors!
2022-03-03 Our Nextflow pipeline for immune repertoire analysis is online in ImmunoInformatics! Congrats, Teresa!
2022-01-27 We are ecstatic to have received a large 20MNOK grant from the Research Council of Norway for working on antibody specificity prediction.
2021-12-10 Christoffer Sørensen (DTU, Denmark) joined the lab as a 3 months guest PhD student from the Andreas Laustsen to work on cool anti-venom antibody research.
2021-12-01 Raphael Förster (University of Würzburg) joined the lab for a 2 months Erasmus-funded internship.
2021-11-06 Our immuneML framework (collaboration with Sandvelab) made it on the cover of Nature Machine Intelligence! Congrats Milena and Lonneke!.
2021-11-01 Dr.Puneet Rawat joined the lab as a UiO Scientia Fellow. He will work on TCR repertoire and antibody design projects. Welcome to the lab, Puneet!
2021-10-01 Jahn Zhong (University of Erlangen) joined the lab for a 2 months Erasmus-funded internship and Habib is back in Oslo for two months!
2021-09-25 Victor gave a talk at Institut Pasteur – the first in-person talk at Pasteur since the lockdown!
2021-09-24 We are delighted to be part of the IMI project inno4Vac Innovations to accelerate vaccine development and manufacture.
2021-09-20 Victor gave a talk at the GSK Network Immunology seminar.
2021-09-18 Victor gave a talk at the Insights in Hematology meeting in Cluj (Romania).
2021-09-01 Philippe and Victor gave talks at the NORA workshop for AlphaFold/RosettaFold.
2021-08-24 Tudor and Ingvild joined the group for a summer internship and Master’s project respectively.
2021-08-20 Another very productive day at the science cabin – this time with furry study assistance.
2021-08-17 Our collaboration with the Helland lab on the changes in the T cell receptor repertoire during treatment with radiotherapy was published in Molecular Oncology.
2021-07-30 Maria gave her first in-person poster session at the Moscow Conference on Computational Molecular Biology (MCCMB).
2021-07-22 Milena and Victor gave tutorial talks at ISCB on immune receptor analysis and immuneML, respectively.
2021-07-06 Lonneke gave a very exciting talk at the Galaxy conference on immuneML.
2021-06-30 Andrei gave a wonderful presentation on his recent work at the WIRM conference.
2021-06-27 Our review on “Immunoglobulin germline gene variation and its impact on human disease“ in collaboration with the Ludvig Sollid lab is on out in Genes and Immunity.
2021-06-25 Very productive work-social event at a Norwegian cabin. Very cozy! And yes, these are grilled bananas filled with chocolate. Yummy (credit goes to Philippe)!!
2021-06-17 Talip joined as via the Erasmus program to study 3D antibody-antigen interaction. Welcome to Norway, Talip!
2021-06-16 Congrats to Khang for defending his Master’s thesis with the best grade!!! Also congrats to Igor as his main supervisor.
2021-06-11 Congrats to Roberta and Maria for their paper entitled “TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood” published in Ebiomedicine. It’s also Maria’s first (co)-first author paper!! Hurrraaaa! The story was also picked up by Italian newspapers. This is the second paper from the very productive collaboration with the Ballerini Lab (Uni Florence)
2021-05-20 The Greiff lab has a reputation to defend for its “gourmet” approach to life (pineapple pizza, ice on yummiest donut in Oslo from here)
2021-05-08 The Greiff and Sandve labs participated in the types-of-papers meme for AIRR and antibody engineering papers. Super fun and funny team effort.
2021-04-23 The Greiff lab participated in the Copenhagen Bioinformatics Hackathon 2021 Protein Edition. Thanks so much to all the teams (Bio-Mutant-Ninja-Turtles, Variational-sLayers, BioCoders) that hacked day and night on our very difficult challenge of trying to cluster antigen-specific antibodies.
2021-04-22 Milena and Lonneke gave a wonderful talk at RSG-Norway on “Building a bioinformatics platform: Lessons learned from immuneml”. Available on youtube.
2021-04-19 Congratulations to Andrei, Maria and Philippe for their paper on VDJ recombination rules.
2021-04-15 Philippe’s paper on the Modeling the Dynamics of T-Cell Development in the Thymus made on the cover!
2021-04-06 Victor gave an AIRR/TABS Webinar on AIRR data analysis. Watch it here.
2021-03-19 The lab acquired a new table tennis table (Butterfly Centrefold 25) to elevate our TT playing experience.
2021-03-16 Our paper on the predictability on antibody-antigen binding is finally out in Cell Reports. And we are on the cover!
2021-03-09 immuneml.uio.no is finally on bioRxiv. immuneML is an ecosystem for machine learning analysis of adaptive immune receptor repertoires.
2021-02-15 Victor presented the lab’s research at the main event of Oslo Life Science 2021 Conference.
2021-02-04 immuneML is now part of the Norwegian bioinformatics services promoted by ELIXIR Norway.
2021-02-01 We welcome Robert Frank , a new PhD student, in the lab. Very much looking forward to his research project on machine learning-based antibody-antigen binding prediction.
2020-12-10 Victor is delighted to be the new Chair-elect of the AIRR Community.
2020-12-02 Victor is very happy to be among the newly appointed NCMM Associate Investigators.
2020-11-09 We are very grateful that the Norwegian Cancer Society decided to fund our research on B-cell and antibody diversity in lung cancer.
2020-09-25 We are very happy that our collaborative paper with the Sepp Hochreiter, Günter Klambauer and Geir Kjetil Sandve lab has been accepted at NeurIPS. The paper was accepted as spotlight talk in the: COVID/Applications/Composition track.
2020-08-05 We are elated to be part of a seminal study by the Andrew Macpherson lab on how mucosal or systemic microbiota exposures shape the B cell repertoire.
2020-08-05 The Hogwards express took Habib to the University of Oslo. We wish him a very productive internship!
2020-08-01 By some curious chance one morning (not so) long ago in the quiet of the world, the lab made an unexpected journey to an Alpaca farm. Victor was skeptical at first because he was sure that alpacas spit like lamas but the alpacas warmed his heart. We had a lovely day walking with our own alpacas, strongly recommended (10/10 for alpacas and 14/10 for baby alpacas)! Alpacas are very interesting from a biotechnology point of view because they make single-domain antibodies. More importantly, though, they are super fluffy and pleasant to interact with.
2020-06-27 Lab members ignored their summer weight loss target and went to enjoy sublime donuts and ice creams at My Ugly Baby.
2020-06-19 Victor gave a virtual seminar at the University of Erlangen (FAU, Germany) invited by Prof. Thomas Winkler.
2020-06-18 Greiff Lab and Sandve Lab organized a surprisingly productive “science at the beach” day at Hvervenbukta.
2020-06-14 Lab members quenched their thirst for modern art at Kistefos Museum.
2020-06-04 The lab enjoyed piping hot ramen, steaming dumpling, cold matcha followed by vegetarian waffles at Koie Ramen.
2020-05-31 Lab members took a stroll around Sognsvann lake.
2020-05-20 The Greiff lab received funding from UNIFOR-FRIMED for performing single-cell BCR-sequencing experiments.
2020-04-15 Victor gave an overview talk in an ELLIS [European Laboratory for Learning and Intelligent Systems] Society virtual workshop on how immune repertoire-based machine learning may be used to identify SARS-CoV-2 therapeutics and diagnostics. The workshop was summarized brilliantly by Jürgen Schmidhuber on his blog.
2020-03-27 Keshav Motwani (University of Florida, co-mentored by Victor) received a 2020 Barry Goldwater scholarship! “The Goldwater Scholarship Program, one of the oldest and most prestigious national scholarships in the natural sciences, engineering and mathematics in the United States, seeks to identify and support college sophomores and juniors who show exceptional promise of becoming this Nation’s next generation of research leaders in these fields.” Congrats, Keshav!
2020-03-26 One more great news in these complex times: Dr Cédric Weber, your colleagues (and friends!) from Oslo thank you for the time you spent here, and the research community thanks you for the enormous job you did during your PhD!
2020-03-13 No quarantine could stop her from having a great defense: the lab congratulates Dr Roberta Amoriello! Roberta’s (whose main supervisor was Clara Ballerini, University of Florence) stay in Oslo was very productive leading to a publication on how TCR repertoires change as a function of multiple sclerosis therapy.
2020-03-10 The GreiffLab published a new article in Bioinformatics on immune receptor simulation (immuneSIM R package) in collaboration with the Reddy and Sandve labs.
2020-02-26 Victor gave a talk at the Center for Infectious Medicine at Karolinska Institutet.
2020-02–21 Work hard, play hard in the Greiff lab.
2020-01-19 Victor and Philippe presented at the MABRA Systems Immunology Workshop.
2020-01-06 The lab welcomes a new PhD student, Maria Chernigovskaya!
2019-12-13 We congratulate Wout van Helvoirt for the successfully defended Master thesis. Thank you, Wout, for implementing immunoProbs.
2019-12-09 Victor is so productive! This Monday he gave his more-than-20th talk this year, at Antwerp TCR Meeting 2019.
2019-11-30 Igor visited the Wellcome Genome Campus in Hinxton, UK to take a course in Single Cell Technologies and Analysis.
2019-11-29 The lab (Victor being the NSI Secretary and the others assisting) hosted 37th Annual General Meeting of the Norwegian Society for Immunology. The meeting included lectures by NSI members, electing new NSI President (welcome, Dr. Inderberg!) and thanking the last President, Pr. Inger Sandlie, who had been running the Society for the last two years.
2019-11-23 Victor and Andrei participated in the SCAIR 2019 conference, and the iReceptor Plus meeting is the sunny and windy city of Haifa.
2019-10-25 Together with the lab of Geir Kjetil Sandve, we wrote a popular science blogpost about our approaches to deciphering the language of immune cells.
2019-10-24 Victor visited IUIS2019 conference in Beijing to give a talk about one of the lab’s projects, chair a session on adoptive cell therapy and meet with collaborators. And he brought wonderful Chinese pastry to the lab!
2019-10-11 Mat and Igor trained to be leaders at Postdoc Leadership seminar.
2019-09-24 Victor, Mat and Andrei visited labs of Prof. René E.M. Toes in Leiden and Prof. Antoine H.C. van Kampen in Amsterdam. Thank you, Prof. Toes and Prof. van Kampen for your hospitality and for the fruitful discussions!
2019-09-12 Together with the lab of Geir Kjetil Sandve, we were awarded a UiO IT-Hub project called immunoHUB. The aim of immunoHUB is to improve the UiO life science and medical researchers’ access to an end-to-end software service and tool ecosystem for immune receptor sequence storage and analysis of immune receptor sequence data (immunomics).
2019-09-12 This week the lab collectively published three preprints, submitted one grant and was awarded one grant. A very successful week!
2019-09–02 Two new members joined the lab. Andrei Slabodkin and Dr. Philippe Robert. Welcome!
2019-07–25 Our review on the analysis of immune receptor analysis and engineering has been published in Molecular Systems Design and Engineering
2019-07-04 Enpicom visited the Greiff lab yesterday.
2019-06-29: Lab members completed the lab’s inaugural Ride n Science bike tour from Oslo to Drøbak. They enjoyed an authentic Norwegian pitstop at Geir-Kjetil’s house including but not limited to: Norwegian waffles, watermelon, Norwegian brown cheese, cream soup, and importantly a team of excellent companions and chefs. Thank you Eiril, Magnus, Odin, Mr and Mrs Sandve! Magnus, please send us the recipe for those excellent waffles 😀
2019-06-27: The lab got together to celebrate Roberta and Keshav at Villa Paradiso. Keshav will return to Florida and Roberta to Italy next week.
2019-06-22: Lab members enjoyed the lab’s inaugural Grill n Science bbq session and a long walk around Sognsvann.
2019-06-20: Rahmad climbed mount Fløya with a bunch of nerds during their Norbis Summer School in Tromsø.
2019-06-17: The équipe of the UiO:LifeScience Convergence Environment Immunolingo kicked off their collaboration with a lovely dinner. Unfortunately Ingrid Hobæk Haff was not able to make it.
2019-06-14: Victor gave a presentation on scientific figure preparation at the Jebsen Center for Celiac Disease retreat in Refsnes Gods.
2019-05-30: Victor strikes again. This time he was featured on the UiO’s medicine blog along side Ruben Gudmundsrud discussing about antibiotic resistance. Read the blog here.
2019-05-29: The lab congratulates Lonneke on her successful Ms thesis defense. She will be joining Greiff and Sandve lab this autumn. Congrats!!!
2019-05-27: The lab received a much needed resupply of Mishka. Thank you and kudos Victor!!!
2019-05-15: Greiff Lab hosted Dr Günter Klambauer, LIT AI lab & Institute for Machine learning, Johannes Kepler University Linz. on May 15–16.
2019-05-15: Victor was elected to be a member of the AIRR Community Executive Sub-Committee.
2019-05-08: Roberta presented her work on TCR profiling in multiple sclerosis at the XXVIII AINI Congress. Congrats!!
2019-04-30: The group celebrated our friend Roberta for completing her first manuscript as a first author.
2019-04-02: The Greiff Lab co-coorganized the 49th SSI Conference in Geilo. Inger Sandlie and Victor, as president and secretary of the Norwegian Society of Immunology, respectively, had the great honor to award Prof. Menna Clatworthy the prestigious EFIS-IL Lecture Award.
2019-03-25: The Greiff Lab has been named project manager of a UiO Convergence Environment (CE) encompassing 5 PIs and 4 funded PhD and Postdoc positions. Our CE is called ImmunoLingo and aims to explore how machine learning, immunology and lingustics may elucidate the principles by which the immune system saves and processes immunological information about pathogens, cancer and autoantigens.
2019-03-21: Victor is co-corresponding author on a paper published in Nature Communications on immune receptor network analysis. The first author is Prof. Enkelejda Miho (Basel, Switzerland).
2019-03-18: Victor hosts Prof. Andrew Macpherson in the context of a FOCIS Center of Excellence Visiting Professorship in Oslo for a entire week.
2019-03-13: Victor presents the lab’s research at the 9th Affinity Proteomics Workshop in Alpbach (Austria).
2019-03-07: Victor presents the lab’s research at the Helmholtz Center for Infection Research (Braunschweig, Germany) in the context of the Workshop for Computational Models in Biology and Medicine.
2019-03-07: Rahmad participated in FOCIS’ Advanced Course in Basic & Clinical Immunology, San Diego, California. With Andrew Lichtman and Shiv Pillai in a not so sunny San Diego.
2019-02-22: Victor gave a seminar at Gothenburg University, invited by Davide Angeletti. Victor returned home full of new scientific inspirations.
2019-01-22: The lab welcomed Jeliazko Jeliazkov for a visit (Gray’s lab, Johns Hopkins University). Jeliazko shared exciting results from his PhD work in the afternoon. In the evening, we enjoyed a really memorable dinner. Kudos to Victor for making this happen!
2018-12-12: Victor talked about Pattern detection in immune repertoires at the Antwerp TCR meeting, University of Antwerp. The talks were held in a 500 years old Antwerp Uni building. Amazing!
2018-12-08: Lab members enjoyed a variety of superb home made cookies, a real taste from home. Thank you (Victor’s) mama!
2018-12-08: Santa came early to the Dept of Immunology! Thank you Lise, Ingunn, Charlotte, Lisbeth, Marte, and Erik for the unparalleled support we received this year.
2018-12-04: Igor participates European Advanced Course in Basic & Clinical Immunology in Berlin.
2018-11-30: Rahmad will talk about Machine learning for predicting antibody recognition in silico and the IT challenges in applying ML on HPC systems @ AI lounge, December 18th.2018-11-30: The group enjoys another superb Christmas dinner this time @ holmenkollen chapel. Some of the group members begin to notice an expanding waist line, it’ll be interesting to revisit the state of the waist in January! Special thanks to the Dept of Immunology, UiO for making this happen and Rasmus for taking this picture.
2018-11-28: The group enjoys a superb Christmas dinner @ Brasserie Ouest. Special thanks to Victor for making this happen. Merry Christmas and happy holidays everyone!!!
2018-11-28: Victor gives a couple of lectures on scientific illustration and representation of numerical data.
2018-11-23: GreiffLab@NSI annual meeting and general assembly 2018. Rahmad presents the lab’s ongoing works and Victor is appointed as NSI’s secretary.
2018-11-12: The lab receives funding as Subcontract-PI from the JDRF/Helmsley Trust with Todd Brusko as main PI.
2018-11-06: Victor visits King’s College, Cambridge and the Babraham Institute as external examiner for the Viva of Peter Chovanec (Anne Corcoran Lab)!
2018-10-30: Rahmad receives a travel grant to participate in FOCIS 2019 Advanced Course in Basic & Clinical Immunology, La Jolla, California. Thank you FOCIS!!!
2018-10-28: Greiff Lab with invited talk and posters @ STOCHASTICITY AND CONTROL IN ADAPTIVE IMMUNE REPERTOIRES 2nd International Meeting – PARIS 2018
2018-10-26: Greiff Lab with invited talk @ the 13th International Conference on Genomics, Shenzhen, 26 October 2018.
2018-10-02: The Faculty of Medicine profiles Victor on its website in light of the successful funding of the ireceptor+ Horizon2020 project on which Victor is a Co-PI. Read the full article here (norwegian).
“The immune system is naturally diagnostic and therapeutic, but we still do not know how to imitate its ability to fight disease or to quickly recognize what is hostile pathogens to the body, and what is not” — Victor Greiff.
2018-10-30: Igor received a travel grant to attend the European Advanced Course in Basic & Clinical Immunology, to be held on December 4 – 7, 2018 at the Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Campus Virchow-Klinikum, Germany.
2018-08-23: Lab members participate in a fire safety course at the hospital.
2018-08-17: Hello world! The lab is up and running!
2018-08-02: Sylt joined the lab. He studies Bioinformatics at Hanze University of Applied Sciences, Groningen (Netherlands). Sylt is funded by an Erasmus+ grant and he will spend the next 6 months working on dissecting the charge distribution patterns in human antibody repertoires.
2018-07-30: Igor got accepted to the 8th NIF (Network of Immunology Frontier) Winter School on Advanced Immunology that is going to be held in Singapore in January 2019 (50 participants have been selected from approx. 250 applicants). He received a travel grant of SGD1200 and complete waiving of course registration fee (SGD500).
2018-07-02: Zi, Edvard and Daniel have started their summer research projects on antibody repertoire deep learning. We are looking forward to their exciting findings!
2018-06-21: Victor is a co-author on High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis, a paper published in NAR
2018-04-11: Received funding for Norbis Workshop on Immune Repertoire analysis
2018-03-14: Received funding from UiO:LifeScience for hosting three summer students