22.12.2022DQBM's roundup of 2022

Founded in 2019, the DQBM's mission is to foster research and education at the interface of biomedical research, bio-technology, and computational biomedicine, to develop the foundations of next-generation precision medicine. Ultimately, our goal is to advance precision medicine for the benefit of patients.

To fulfil our mission, we rely on excellent science done by outstanding scientists. Below, we highlight the DQBM events and academic achievements in 2022.

On 1.1.2022, DQBM welcomed the Joller group. Nicole Joller’s lab studies the impact of the disease history of an individual on their immune system and consequently on susceptibility to infectious and autoimmune diseases. Particular emphasis lies on studying the regulatory arm of the immune system as this controls many immune processes.

After a long covid-related delay, the DQBM finally enjoyed its first joint Retreat in the beautiful Kloster Kappel, Kappel am Albis. Thanks to a well-organized program packed with science and social activities, the members of the DQBM got to know each other - and each other's work - in whole new ways. Our thanks go out to the 2022 DQBM Retreat Organization team!
 

In 2022, we had the pleasure of welcoming the following scientific speakers to the DQBM Special Seminar and the DQBM Junior Scientist Series:

• Prof. Dr. Stefan Feuerriegel, Head of Institute, Institute of Artificial Intelligence (AI) in Management, Ludwig Maximilian University of Munich (Germany)
• Prof. Dr. Paola Picotti, Deputy Head of Institute for Molecular Systems Biology, ETH Zurich
• Prof. Dr. Klaus Eyer, Department of Chemistry and Applied Biosciences, ETH Zurich
• Prof. Dr. Hans Steenackers, Microbial Communities and Antimicrobials (MICA) Lab, Centre of Microbial and Plant Genetics, KU Leuven (Belgium)
• Prof. Dr. Jaime Grutzendler, Dr. Harry M. Zimmerman and Dr. Nicholas and Viola Spinelli Professor of Neurology and Neuroscience; Vice-Chair for Research, Neurology; Director, Center for Experimental Neuroimaging, Yale School of Medicine (USA)
• Uria Mor, Computational Biologist in the Elinav Lab, Weizmann Institute of Science (Israel)

Check out JUSCOR's webpage full of photos of the scientific and social events they organized.

2022 was a successful fundraising year for DQBM's scientists. Notably:

• Bernd Bodenmiller received a Swiss Personalized Oncology National Data Stream grant from the Swiss Personalized Health Network-Personalized Health and Related Technologies (SPHN-PHRT).
  Bernd Bodenmiller received a SNSF Bridge-Discovery Grant on the development of a CE-IVD certified imaging mass cytometry diagnostic test for first to third line metastatic colorectal cancer treatment prediction.
  Bernd Bodenmiller received a SNSF project grant. 
• Michael Krauthammer received support as core team member of the newly funded DIZH innovation structure Zurich Applied Digital Health Center: a practice lab for patient-centered clinical innovation.
• Michael Krauthammer became Co-Lead on the LOOP biomedical informatics platform, establishing a research data ecosystem between the four University hospitals (USZ, Balgrist, PUK, KISPI).
• Michael Krauthammer received a Krebsliga skin cancer grant on "Predictive bio-markers in BCC patients treated with Hedgehog inhibitors and anti-PD1”, together with UZH/USZ Dermatology.
• Rolf Kümmerli was awarded a project grant from the SNSF.
• Bjoern Menze received a 2022 SNSF Sinergia grant with colleagues at the University of Geneva on ‘Illuminating the functions, cellular locations and regulation of inositol pyrophosphate nutrient messengers’.
• Magdalini Polymenidou received the coveted ERC Consolidator Grant for the project “TDP-43 transitions”. 
• Magdalini Polymenidou received a Target ALS and Alzheimer’s Drug Discovery Foundation Award for Biomarker Research.

DQBM's junior scientists also did a fantastic job in securing research funds:

• JUSCOR received a Graduate Campus Scientific Events Grant.
• JUSCOR received a UZH Alumni Scientific Events Grant
• Matthias Rath (Joller lab) was awarded an SAMW MD-PhD Fellowship.
• Ivna Ivankovic (Krauthammer lab) was awarded an UZH Candoc Grant. 
• Ivna Ivankovic (Krauthammer lab) was awarded a Biomed Travel Grant to attend the AACR conference.
• Tamaz Amiranashvili (Menze lab) received a MIDL 2022 Runner-up for Best Paper Award.
• Ruchi Manglunia (Polymenidou lab) was awarded an India Bioscience Outreach Grant.
• Pierre de Rossi (Polymenidou lab) was awarded a Stuart Berry ZNZ Poster Award. 
• Elena Tantardini (Polymenidou lab) was awarded a LS2 Travel Grant.

The following DQBM members were honored for their scientific excellence:

• Zsolt Balazs from the Krauthammer lab won the Pfizer Research Prize 2022.
• Carlo Scialo from the Polymenidou lab won the 2022 Silvia Zucchelli prize for the best PhD thesis from the International School for Advanced Studies (Italy). 

• Bernd Bodenmiller, Stephane Chevrier, Jana Fischer and Andrea Jacobs founded Navignostics AG. 
• Bernd Bodenmiller was listed as ‘Highly Cited Researcher 2022’ by Clarivate.
• Nicole Joller was appointed to the editorial board for Discovery Immunology.
• Bjoern Menze together with Ender Konukoglu (ETHZ) organized the 2022 Medical Imaging with Deep Learning (MIDL) Conference.
• Magdalini Polymenidou was appointed to the Evaluation Committee of the SNSF Careers Division.

The following bright minds completed their PhD thesis in 2022:  

• Priyanikha Jayakumar (Kümmerli lab): 'Collective Decision-Making and the Evolution of Cell-to-Cell Communication System in Pseudomonas aeruginosa'.
• Laura Kuett (Bodenmiller lab): "Studying breast cancer invasion and metastasis with 3D and 2D imaging mass cytometry".
• Manuela Perez-Berlanga (Polymenidou lab): "Roles of TDP-43 oligomerization and RNA binding in physiology and pathology".
• Kyriakos Schwarz (Krauthammer lab): "Deep Learning in Computational Pharmacology".
• Jonas Windhager (Bodenmiller lab): "Multiplexed Tissue Image Processing and Spatial Single-Cell Data Integration".
   

Furthermore, the following MSc student graduated in 2022 with a DQBM MSc thesis: 

• Ruben Rigort (Polymenidou lab): "Identifications and studies of novel nucleotide-binding site of TDP-43".

Bodenmiller lab:

Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation.
Bost P, Schulz D, Engler S, Wasserfall C, Bodenmiller B.
Nat Methods. 2022 Dec 30. 
doi: 10.1038/s41592-022-01692-z. 

Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies.
Wild SA, Cannell IG, Nicholls A, Kania K, Bressan D; CRUK IMAXT Grand Challenge Team, Hannon GJ, Sawicka K.
Elife. 2022 Dec 16;11:e80981.
doi: 10.7554/eLife.80981.

Single-cell genomic variation induced by mutational processes in cancer.
Funnell T, O'Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN; IMAXT Consortium, Shah SP, Aparicio S.
Nature. 2022 Dec;612(7938):106-115.
doi: 10.1038/s41586-022-05249-0. 
 
Vaccination with Designed Neopeptides Induces Intratumoral, Cross-reactive CD4+ T-cell Responses in Glioblastoma.
Wang J, Weiss T, Neidert MC, Toussaint NC, Naghavian R, Sellés Moreno C, Foege M, Tomas Ojer P, Medici G, Jelcic I, Schulz D, Rushing E, Dettwiler S, Schrörs B, Shin JH, McKay R, Wu CJ, Lutterotti A, Sospedra M, Moch H, Greiner EF, Bodenmiller B, Regli L, Weller M, Roth P, Martin R.
Clin Cancer Res. 2022 Dec 15;28(24):5368-5382.
doi: 10.1158/1078-0432.CCR-22-1741.
 
scQUEST: Quantifying tumor ecosystem heterogeneity from mass or flow cytometry data.
Martinelli AL, Wagner J, Bodenmiller B, Rapsomaniki MA.
STAR Protoc. 2022 Jul 20;3(3):101578.
doi: 10.1016/j.xpro.2022.101578. 

 
A shared disease-associated oligodendrocyte signature among multiple CNS pathologies.
Kenigsbuch M, Bost P, Halevi S, Chang Y, Chen S, Ma Q, Hajbi R, Schwikowski B, Bodenmiller B, Fu H, Schwartz M, Amit I.
Nat Neurosci. 2022 Jul;25(7):876-886.
doi: 10.1038/s41593-022-01104-7. 
 
T-cell recovery and evidence of persistent immune activation 12 months after severe COVID-19.
Taeschler P, Adamo S, Deng Y, Cervia C, Zurbuchen Y, Chevrier S, Raeber ME, Hasler S, Bächli E, Rudiger A, Stüssi-Helbling M, Huber LC, Bodenmiller B, Boyman O, Nilsson J.
Allergy. 2022 Aug;77(8):2468-2481.
doi: 10.1111/all.15372. 
 
Single-cell proteomics defines the cellular heterogeneity of localized prostate cancer.
De Vargas Roditi L, Jacobs A, Rueschoff JH, Bankhead P, Chevrier S, Jackson HW, Hermanns T, Fankhauser CD, Poyet C, Chun F, Rupp NJ, Tschaebunin A, Bodenmiller B, Wild PJ.
Cell Rep Med. 2022 Apr 19;3(4):100604.
doi: 10.1016/j.xcrm.2022.100604. 
 
Breast tumor microenvironment structures are associated with genomic features and clinical outcome.
Danenberg E, Bardwell H, Zanotelli VRT, Provenzano E, Chin SF, Rueda OM, Green A, Rakha E, Aparicio S, Ellis IO, Bodenmiller B, Caldas C, Ali HR.
Nat Genet. 2022 May;54(5):660-669.
doi: 10.1038/s41588-022-01041-y. 
 
Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy.
Hoch T, Schulz D, Eling N, Gómez JM, Levesque MP, Bodenmiller B.
Sci Immunol. 2022 Apr;7(70):eabk1692.
doi: 10.1126/sciimmunol.abk1692. 
 
Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines.
Wagner J, Masek M, Jacobs A, Soneson C, Sivapatham S, Damond N, de Souza N, Robinson MD, Bodenmiller B.
Sci Data. 2022 Feb 9;9(1):44.
doi: 10.1038/s41597-022-01137-4.
 
Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment.
Kuett L, Catena R, Özcan A, Plüss A; Cancer Grand Challenges IMAXT Consortium, Schraml P, Moch H, de Souza N, Bodenmiller B.
Nat Cancer. 2022 Jan;3(1):122-133.
doi: 10.1038/s43018-021-00301-w. 

Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients
Mitamura Y, Schulz D, Oro S, Li N, Kolm I, Lang C, Ziadlou R, Tan G, Bodenmiller B, Steiger P, Marzano A, de Prost N, Caudin O, Levesque M, Stoffel C, Schmid-Grendelmeier P, Maverakis E, Akdis CA, Brüggen MC.
Allergy. 2022; 77: 595– 608.
https://doi.org/10.1111/all.14983

Joller lab:

Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity.
Shlesinger D, Hong KL, Shammas G, Page N, Sandu I, Agrafiotis A, Kreiner V, Fonta N, Vincenti I, Wagner I, Piccinno M, Mariotte A, Klimek B, Dizerens R, Manero-Carranza M, Kuhn R, Ehling R, Frei L, Khodaverdi K, Panetti C, Joller N, Oxenius A, Merkler D, Reddy ST, Yermanos A.
Genes Immun. 2022 Sep;23(6):183-195. 
doi: 10.1038/s41435-022-00180-w. 
 
Nematode microRNAs can Individually Regulate Interferon Regulatory Factor 4 and mTOR in Differentiating T Helper 2 Lymphocytes and Modulate Cytokine Production in Macrophages.
Soichot J, Guttmann N, Rehrauer H, Joller N, Tritten L.
Front Mol Biosci. 2022 Jun 28;9:909312. 
doi: 10.3389/fmolb.2022.909312. 
 
Moving to the Outskirts: Interplay Between Regulatory T Cells and Peripheral Tissues.
Estrada Brull A, Panetti C, Joller N.
Front Immunol. 2022 Apr 29;13:864628. 
doi: 10.3389/fimmu.2022.864628. 

Alkali therapy protects renal function, suppresses inflammation, and improves cellular metabolism in kidney disease.
Pastor Arroyo EM, Yassini N, Sakiri E, Russo G, Bourgeois S, Mohebbi N, Amann K, Joller N, Wagner CA, Imenez Silva PH.
Clin Sci (Lond). 2022 Apr 29;136(8):557-577. 
doi: 10.1042/CS20220095.
 

Krauthammer lab:

The Use and Ethics of Digital Twins in Medicine.
Iqbal JD, Krauthammer M, Biller-Andorno N.
J Law Med Ethics. 2022;50(3):583-596.
doi: 10.1017/jme.2022.97.

Vision transformer assisting rheumatologists in screening for capillaroscopy changes in systemic sclerosis: an artificial intelligence model.
Garaiman A, Nooralahzadeh F, Mihai C, Gonzalez NP, Gkikopoulos N, Becker MO, Distler O, Krauthammer M, Maurer B.
Rheumatology (Oxford). 2022 Nov 9:keac541.
doi: 10.1093/rheumatology/keac541. 
 
Live slow-frozen human tumor tissues viable for 2D, 3D, ex vivo cultures and single-cell RNAseq.
Restivo G, Tastanova A, Balázs Z, Panebianco F, Diepenbruck M, Ercan C, Preca BT, Hafner J, Weber WP, Kurzeder C, Vetter M, Soysal SM, Beisel C, Bentires-Alj M, Piscuoglio S, Krauthammer M, Levesque MP.
Commun Biol. 2022 Oct 28;5(1):1144.
doi: 10.1038/s42003-022-04025-0.
 
Prospective observational study of the role of the microbiome in BCG responsiveness prediction (SILENT-EMPIRE): a study protocol.
Bieri U, Scharl M, Sigg S, Szczerba BM, Morsy Y, Rüschoff JH, Schraml PH, Krauthammer M, Hefermehl LJ, Eberli D, Poyet C.
BMJ Open. 2022 Apr 18;12(4):e061421.
doi: 10.1136/bmjopen-2022-061421.

AI support for ethical decision-making around resuscitation: proceed with care
Biller-Andorno N, Ferrario A, Joebges S, Krones T, Massini F, Barth P, Arampatzis G, Krauthammer M.
J Med Ethics 2022;0:1–9.
doi: 10.1136/medethics-2020-106786

Kümmerli lab:

Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution.
Kümmerli R.
Biometals. 2022 Dec 12.
doi: 10.1007/s10534-022-00480-8.

Collective decision-making in Pseudomonasaeruginosa involves transient segregation of quorum-sensing activities across cells.
Jayakumar P, Thomas SA, Brown SP, Kümmerli R.
Curr Biol. 2022 Nov 16:S0960-9822(22)01700-6.
doi: 10.1016/j.cub.2022.10.052. 

Evolution of Quorum Sensing in Pseudomonas aeruginosa Can Occur via Loss of Function and Regulon Modulation.
Jayakumar P, Figueiredo ART, Kümmerli R.  
mSystems. 2022 Oct 26;7(5):e0035422. 
doi: 10.1128/msystems.00354-22. 

Rapid identification of pyoverdines of fluorescent Pseudomonas spp. by UHPLC-IM-MS.
Rehm K, Vollenweider V, Kümmerli R, Bigler L. 
Biometals. 2022 Oct 20. 
doi: 10.1007/s10534-022-00454-w. 

Coordination of siderophore gene expression among clonal cells of the bacterium Pseudomonas aeruginosa.
Mridha S, Kümmerli R.
Commun Biol. 2022 Jun 6;5(1):545.
doi: 10.1038/s42003-022-03493-8.

Enforced specialization fosters mutual cheating and not division of labour in the bacterium Pseudomonas aeruginosa.
Mridha S, Kümmerli R.
J Evol Biol. 2022 May;35(5):719-730.
doi: 10.1111/jeb.14001. 

A comprehensive method to elucidate pyoverdines produced by fluorescent Pseudomonas spp. by UHPLC-HR-MS/MS.
Rehm K, Vollenweider V, Kümmerli R, Bigler L.
Anal Bioanal Chem. 2022 Mar;414(8):2671-2685.
doi: 10.1007/s00216-022-03907-w. 

Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad.
Figueiredo ART, Özkaya Ö, Kümmerli R, Kramer J.
Ecol Lett. 2022 Jan;25(1):138-150.
doi: 10.1111/ele.13912. 

Menze lab:

Spatial proteomics in three-dimensional intact specimens.
Singh Bhatia H, Brunner A-D, Öztürk F, Kapoor S, Rong Z, Mai H, Thielert M, Ali M, Al-Maskari R, Paetzold JC, Kofler F, Todorov MI, Molbay M, Kolabas ZI, Negwer M, Hoeher L, Steinke H, Dima A, Gupta B, Kaltenecker D, Caliskan ÖS, Brandt D, Krahmer N, Müller S, Lichtenthaler SF, Hellal F, Bechmann I, Menze B, Theis F, Mann M, Ertürk A.
Cell, 2022 Volume 185, Issue 26.
https://doi.org/10.1016/j.cell.2022.11.021

The Liver Tumor Segmentation Benchmark (LiTS).
Bilic P, Christ P, Li HB, Vorontsov E, Ben-Cohen A, Kaissis G, Szeskin A, Jacobs C, Mamani GEH, Chartrand G, Lohöfer F, Holch JW, Sommer W, Hofmann F, Hostettler A, Lev-Cohain N, Drozdzal M, Amitai MM, Vivanti R, Sosna J, Ezhov I, Sekuboyina A, Navarro F, Kofler F, Paetzold JC, Shit S, Hu X, Lipková J, Rempfler M, Piraud M, Kirschke J, Wiestler B, Zhang Z, Hülsemeyer C, Beetz M, Ettlinger F, Antonelli M, Bae W, Bellver M, Bi L, Chen H, Chlebus G, Dam EB, Dou Q, Fu CW, Georgescu B, Giró-I-Nieto X, Gruen F, Han X, Heng PA, Hesser J, Moltz JH, Igel C, Isensee F, Jäger P, Jia F, Kaluva KC, Khened M, Kim I, Kim JH, Kim S, Kohl S, Konopczynski T, Kori A, Krishnamurthi G, Li F, Li H, Li J, Li X, Lowengrub J, Ma J, Maier-Hein K, Maninis KK, Meine H, Merhof D, Pai A, Perslev M, Petersen J, Pont-Tuset J, Qi J, Qi X, Rippel O, Roth K, Sarasua I, Schenk A, Shen Z, Torres J, Wachinger C, Wang C, Weninger L, Wu J, Xu D, Yang X, Yu SC, Yuan Y, Yue M, Zhang L, Cardoso J, Bakas S, Braren R, Heinemann V, Pal C, Tang A, Kadoury S, Soler L, van Ginneken B, Greenspan H, Joskowicz L, Menze B.
Med Image Anal. 2022 Nov 17;84:102680.
doi: 10.1016/j.media.2022.102680. 
 
Federated learning enables big data for rare cancer boundary detection.
Pati S, Baid U, Edwards B, Sheller M, Wang SH, Reina GA, Foley P, Gruzdev A, Karkada D, Davatzikos C, Sako C, Ghodasara S, Bilello M, Mohan S, Vollmuth P, Brugnara G, Preetha CJ, Sahm F, Maier-Hein K, Zenk M, Bendszus M, Wick W, Calabrese E, Rudie J, Villanueva-Meyer J, Cha S, Ingalhalikar M, Jadhav M, Pandey U, Saini J, Garrett J, Larson M, Jeraj R, Currie S, Frood R, Fatania K, Huang RY, Chang K, Quintero CB, Capellades J, Puig J, Trenkler J, Pichler J, Necker G, Haunschmidt A, Meckel S, Shukla G, Liem S, Alexander GS, Lombardo J, Palmer JD, Flanders AE, Dicker AP, Sair HI, Jones CK, Venkataraman A, Jiang M, So TY, Chen C, Heng PA, Dou Q, Kozubek M, Lux F, Michálek J, Matula P, Keřkovský M, Kopřivová T, Dostál M, Vybíhal V, Vogelbaum MA, Mitchell JR, Farinhas J, Maldjian JA, Yogananda CGB, Pinho MC, Reddy D, Holcomb J, Wagner BC, Ellingson BM, Cloughesy TF, Raymond C, Oughourlian T, Hagiwara A, Wang C, To MS, Bhardwaj S, Chong C, Agzarian M, Falcão AX, Martins SB, Teixeira BCA, Sprenger F, Menotti D, Lucio DR, LaMontagne P, Marcus D, Wiestler B, Kofler F, Ezhov I, Metz M, Jain R, Lee M, Lui YW, McKinley R, Slotboom J, Radojewski P, Meier R, Wiest R, Murcia D, Fu E, Haas R, Thompson J, Ormond DR, Badve C, Sloan AE, Vadmal V, Waite K, Colen RR, Pei L, Ak M, Srinivasan A, Bapuraj JR, Rao A, Wang N, Yoshiaki O, Moritani T, Turk S, Lee J, Prabhudesai S, Morón F, Mandel J, Kamnitsas K, Glocker B, Dixon LVM, Williams M, Zampakis P, Panagiotopoulos V, Tsiganos P, Alexiou S, Haliassos I, Zacharaki EI, Moustakas K, Kalogeropoulou C, Kardamakis DM, Choi YS, Lee SK, Chang JH, Ahn SS, Luo B, Poisson L, Wen N, Tiwari P, Verma R, Bareja R, Yadav I, Chen J, Kumar N, Smits M, van der Voort SR, Alafandi A, Incekara F, Wijnenga MMJ, Kapsas G, Gahrmann R, Schouten JW, Dubbink HJ, Vincent AJPE, van den Bent MJ, French PJ, Klein S, Yuan Y, Sharma S, Tseng TC, Adabi S, Niclou SP, Keunen O, Hau AC, Vallières M, Fortin D, Lepage M, Landman B, Ramadass K, Xu K, Chotai S, Chambless LB, Mistry A, Thompson RC, Gusev Y, Bhuvaneshwar K, Sayah A, Bencheqroun C, Belouali A, Madhavan S, Booth TC, Chelliah A, Modat M, Shuaib H, Dragos C, Abayazeed A, Kolodziej K, Hill M, Abbassy A, Gamal S, Mekhaimar M, Qayati M, Reyes M, Park JE, Yun J, Kim HS, Mahajan A, Muzi M, Benson S, Beets-Tan RGH, Teuwen J, Herrera-Trujillo A, Trujillo M, Escobar W, Abello A, Bernal J, Gómez J, Choi J, Baek S, Kim Y, Ismael H, Allen B, Buatti JM, Kotrotsou A, Li H, Weiss T, Weller M, Bink A, Pouymayou B, Shaykh HF, Saltz J, Prasanna P, Shrestha S, Mani KM, Payne D, Kurc T, Pelaez E, Franco-Maldonado H, Loayza F, Quevedo S, Guevara P, Torche E, Mendoza C, Vera F, Ríos E, López E, Velastin SA, Ogbole G, Soneye M, Oyekunle D, Odafe-Oyibotha O, Osobu B, Shu'aibu M, Dorcas A, Dako F, Simpson AL, Hamghalam M, Peoples JJ, Hu R, Tran A, Cutler D, Moraes FY, Boss MA, Gimpel J, Veettil DK, Schmidt K, Bialecki B, Marella S, Price C, Cimino L, Apgar C, Shah P, Menze B, Barnholtz-Sloan JS, Martin J, Bakas S.
Nat Commun. 2022 Dec 5;13(1):7346. 
doi: 10.1038/s41467-022-33407-5.
  
The federated tumor segmentation (FeTS) tool: an open-source solution to further solid tumor research.
Pati S, Baid U, Edwards B, Sheller MJ, Foley P, Anthony Reina G, Thakur S, Sako C, Bilello M, Davatzikos C, Martin J, Shah P, Menze B, Bakas S.
Phys Med Biol. 2022 Oct 12;67(20):10.1088/1361-6560/ac9449. 
doi: 10.1088/1361-6560/ac9449.
 
A Unified 3D Framework for Organs-at-Risk Localization and Segmentation for Radiation Therapy Planning.
Navarro F, Sasahara G, Shit S, Sekuboyina A, Ezhov I, Peeken JC, Combs SE, Menze BH.
Annu Int Conf IEEE Eng Med Biol Soc. 2022 Jul;2022:1544-1547. 
doi: 10.1109/EMBC48229.2022.9871680.
 
Self-Supervised Pretext Tasks in Model Robustness & Generalizability: A Revisit from Medical Imaging Perspective.
Navarro F, Watanabe C, Shit S, Sekuboyina A, Peeken JC, Combs SE, Menze BH.
Annu Int Conf IEEE Eng Med Biol Soc. 2022 Jul;2022:5074-5079. 
doi: 10.1109/EMBC48229.2022.9870911.
 

Preoperative Prediction of Lymph Node Metastasis in Colorectal Cancer with Deep Learning.
Liu H, Zhao Y, Yang F, Lou X, Wu F,; Li H, Xing X,; Peng T, Menze B, Huang J, Zhang S, Han A, Yao J, Fan X.  
BME Frontiers 2022:9860179.
https://doi.org/10.34133/2022/9860179

SRflow: Deep learning based super-resolution of 4D-flow MRI data.
Shit S, Zimmermann J, Ezhov I, Paetzold JC, Sanches AF, Pirkl C, Menze BH.
Front Artif Intell. 2022 Aug 12;5:928181. 
doi: 10.3389/frai.2022.928181. 
 
The Medical Segmentation Decathlon.
Antonelli M, Reinke A, Bakas S, Farahani K, Kopp-Schneider A, Landman BA, Litjens G, Menze B, Ronneberger O, Summers RM, van Ginneken B, Bilello M, Bilic P, Christ PF, Do RKG, Gollub MJ, Heckers SH, Huisman H, Jarnagin WR, McHugo MK, Napel S, Pernicka JSG, Rhode K, Tobon-Gomez C, Vorontsov E, Meakin JA, Ourselin S, Wiesenfarth M, Arbeláez P, Bae B, Chen S, Daza L, Feng J, He B, Isensee F, Ji Y, Jia F, Kim I, Maier-Hein K, Merhof D, Pai A, Park B, Perslev M, Rezaiifar R, Rippel O, Sarasua I, Shen W, Son J, Wachinger C, Wang L, Wang Y, Xia Y, Xu D, Xu Z, Zheng Y, Simpson AL, Maier-Hein L, Cardoso MJ.
Nat Commun. 2022 Jul 15;13(1):4128.
doi: 10.1038/s41467-022-30695-9.
 
Application of machine learning to pretherapeutically estimate dosimetry in men with advanced prostate cancer treated with 177Lu-PSMA I&T therapy.
Xue S, Gafita A, Dong C, Zhao Y, Tetteh G, Menze BH, Ziegler S, Weber W, Afshar-Oromieh A, Rominger A, Eiber M, Shi K.
Eur J Nucl Med Mol Imaging. 2022 Oct;49(12):4064-4072. 
doi: 10.1007/s00259-022-05883-w. 
 
Influence of Auditory Cues on the Neuronal Response to Naturalistic Visual Stimuli in a Virtual Reality Setting.
Al Boustani G, Weiß LJK, Li H, Meyer SM, Hiendlmeier L, Rinklin P, Menze B, Hemmert W, Wolfrum B.
Front Hum Neurosci. 2022 Jun 2;16:809293. 
doi: 10.3389/fnhum.2022.809293. 
 
Level-Specific Volumetric BMD Threshold Values for the Prediction of Incident Vertebral Fractures Using Opportunistic QCT: A Case-Control Study.
Dieckmeyer M, Löffler MT, El Husseini M, Sekuboyina A, Menze B, Sollmann N, Wostrack M, Zimmer C, Baum T, Kirschke JS.
Front Endocrinol (Lausanne). 2022 May 20;13:882163. 
doi: 10.3389/fendo.2022.882163. 
 
Automated Opportunistic Osteoporosis Screening in Routine Computed Tomography of the Spine: Comparison With Dedicated Quantitative CT.
Sollmann N, Löffler MT, El Husseini M, Sekuboyina A, Dieckmeyer M, Rühling S, Zimmer C, Menze B, Joseph GB, Baum T, Kirschke JS.
J Bone Miner Res. 2022 Jul;37(7):1287-1296. 
doi: 10.1002/jbmr.4575. 
 
Prediction of multiple pH compartments by deep learning in magnetic resonance spectroscopy with hyperpolarized 13C-labelled zymonic acid.
Fok WR, Grashei M, Skinner JG, Menze BH, Schilling F.
EJNMMI Res. 2022 Apr 23;12(1):24. 
doi: 10.1186/s13550-022-00894-y.

Proposed diagnostic volumetric bone mineral density thresholds for osteoporosis and osteopenia at the cervicothoracic spine in correlation to the lumbar spine.
Rühling S, Scharr A, Sollmann N, Wostrack M, Löffler MT, Menze B, Sekuboyina A, El Husseini M, Braren R, Zimmer C, Kirschke JS.
Eur Radiol. 2022 Sep;32(9):6207-6214. 
doi: 10.1007/s00330-022-08721-7. 
 
Modelling glioma progression, mass effect and intracranial pressure in patient anatomy.
Lipková J, Menze B, Wiestler B, Koumoutsakos P, Lowengrub JS.
J R Soc Interface. 2022 Mar;19(188):20210922. 
doi: 10.1098/rsif.2021.0922. 
 
Anatomy-Aware Inference of the 3D Standing Spine Posture from 2D Radiographs.
Bayat A, Pace DF, Sekuboyina A, Payer C, Stern D, Urschler M, Kirschke JS, Menze BH.
Tomography. 2022 Feb 11;8(1):479-496.

Learning residual motion correction for fast and robust 3D multiparametric MRI.
Pirkl CM, Cencini M, Kurzawski JW, Waldmannstetter D, Li H, Sekuboyina A, Endt S, Peretti L, Donatelli G, Pasquariello R, Costagli M, Buonincontri G, Tosetti M, Menzel MI, Menze BH.
Med Image Anal. 2022 Apr;77:102387. 
doi: 10.1016/j.media.2022.102387. 

Efficient Claustrum Segmentation in T2-weighted Neonatal Brain MRI Using Transfer Learning from Adult Scans.
Neubauer A, Li HB, Wendt J, Schmitz-Koep B, Menegaux A, Schinz D, Menze B, Zimmer C, Sorg C, Hedderich DM.
Clin Neuroradiol. 2022 Sep;32(3):665-676. 
doi: 10.1007/s00062-021-01137-8. 
  
Detection and analysis of cerebral aneurysms based on X-ray rotational angiography - the CADA 2020 challenge.
Ivantsits M, Goubergrits L, Kuhnigk JM, Huellebrand M, Bruening J, Kossen T, Pfahringer B, Schaller J, Spuler A, Kuehne T, Jia Y, Li X, Shit S, Menze B, Su Z, Ma J, Nie Z, Jain K, Liu Y, Lin Y, Hennemuth A.
Med Image Anal. 2022 Apr;77:102333. 
doi: 10.1016/j.media.2021.102333. 

Geometry-Aware Neural Solver for Fast Bayesian Calibration of Brain Tumor Models.
Ezhov I, Mot T, Shit S, Lipkova J, Paetzold JC, Kofler F, Pellegrini C, Kollovieh M, Navarro F, Li H, Metz M, Wiestler B, Menze B.
IEEE Trans Med Imaging. 2022 May;41(5):1269-1278. 
doi: 10.1109/TMI.2021.3136582. 
  
Face Restoration via Plug-and-Play 3D Facial Priors.
Hu X, Ren W, Yang J, Cao X, Wipf D, Menze B, Tong X, Zha H.
IEEE Trans Pattern Anal Mach Intell. 2022 Dec;44(12):8910-8926. 
doi: 10.1109/TPAMI.2021.3123085. 
 
Automated detection of the contrast phase in MDCT by an artificial neural network improves the accuracy of opportunistic bone mineral density measurements.
Rühling S, Navarro F, Sekuboyina A, El Husseini M, Baum T, Menze B, Braren R, Zimmer C, Kirschke JS.
Eur Radiol. 2022 Mar;32(3):1465-1474. 
doi: 10.1007/s00330-021-08284-z.  
 
Tumor Sink Effect in 68Ga-PSMA-11 PET: Myth or Reality?
Gafita A, Wang H, Robertson A, Armstrong WR, Zaum R, Weber M, Yagubbayli F, Kratochwil C, Grogan TR, Nguyen K, Navarro F, Esfandiari R, Rauscher I, Menze B, Elashoff D, Delpassand ES, Herrmann K, Czernin J, Hofman MS, Calais J, Fendler WP, Eiber M.
J Nucl Med. 2022 Feb;63(2):226-232. 
doi: 10.2967/jnumed.121.261906. 

Polymenidou lab:

Comprehensive evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9orf72 disease.
Jambeau M, Meyer KD, Hruska-Plochan M, Tabet R, Lee CZ, Ray-Soni A, Aguilar C, Savage K, Mishra N, Cavegn N, Borter P, Lin CC, Jansen-West KR, Jiang J, Freyermuth F, Li N, De Rossi P, Pérez-Berlanga M, Jiang X, Daughrity LM, Pereira J, Narayanan S, Gu Y, Dhokai S, Dalkilic-Liddle I, Maniecka Z, Weber J, Workman M, McAlonis-Downes M, Berezovski E, Zhang YJ, Berry J, Wainger BJ, Kankel MW, Rushe M, Hock C, Nitsch RM, Cleveland DW, Petrucelli L, Gendron TF, Montrasio F, Grimm J, Polymenidou M, Lagier-Tourenne C.
Proc Natl Acad Sci U S A. 2022 Dec 6;119(49):e2123487119.
doi: 10.1073/pnas.2123487119. 
 
An arrayed genome-wide perturbation screen identifies the ribonucleoprotein Hnrnpk as rate-limiting for prion propagation.
Avar M, Heinzer D, Thackray AM, Liu Y, Hruska-Plochan M, Sellitto S, Schaper E, Pease DP, Yin JA, Lakkaraju AK, Emmenegger M, Losa M, Chincisan A, Hornemann S, Polymenidou M, Bujdoso R, Aguzzi A.
EMBO J. 2022 Dec 1;41(23):e112338.
doi: 10.15252/embj.2022112338. 
 
Tau: a phase in the crowd.
Wiersma VI, Rigort R, Polymenidou M.
EMBO J. 2022 Jun 1;41(11):e111425.
doi: 10.15252/embj.2022111425.
 
Identification of RNA-RBP Interactions in Subcellular Compartments by CLIP-Seq.
Sahadevan S, Pérez-Berlanga M, Polymenidou M.
Methods Mol Biol. 2022;2428:305-323.
doi: 10.1007/978-1-0716-1975-9_19.

FedCostWAvg: A New Averaging for Better Federated Learning.
Mächler L, Ezhov I, Kofler F, Shit S, Paetzold JC, Loehr T, Zimmer C, Wiestler B, Menze BH. (2022).
In: Crimi, Alessandro ; Bakas, Spyridon . Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. Cham: Springer, 383-391.
 

Identification of RNA–RBP Interactions in Subcellular Compartments by CLIP-Seq.
Sahadevan S, Pérez-Berlanga M, Polymenidou M. (2022).
In: Matějů, Daniel ; Chao, Jeffrey A . 2021 The Integrated Stress Response pp 305–323.

Relationformer: A unified framework for image-to-graph generation.
Shit S, et al. Menze BH.
Proc ECCV 2022, 12p

AutoGAN-synthesizer: neural architecture search for cross-modality MRI synthesis.
Hu X, et al., Menze BH.
Proc MICCAI 2022, 8p

Landmark-free statistical shape modeling via neural flow deformations.
Lüdke D, Amiranashvili T, Ambellan F, Ezhov I, Menze BH, Zachow S.
Proc MICCAI 2022, 8p

Physiology-based simulation of the retinal vasculature enables annotation-free segmentation of OCT angiographs.
Menten M, Paetzold J, Dima A, Menze BH, Knier B, Rueckert D.
Proc MICCAI 2022, 8p

Learning shape reconstruction from sparse measurements with neural implicit functions.
Amiranashvili T, Lüdke D, Li H, Menze BH, Zachow S.
Proc MIDL 2022, 8p.

We are excited about and grateful for all our members' achievements, opportunities and successes in 2022. Moreover, we are looking forward to an exciting year ahead with more excellent science. Please stay tuned!