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DQBM was founded on 1.1.2019. Our joint mission is to foster research and education at the interface of biomedical research, biotechnology, and computational biology, to develop the foundations of next generation precision medicine. Ultimately, our goal is to advance precision medicine for the benefit of patients.
To achieve this, we take on the challenge of bridging the gap between basic research, data science and translational / clinical research groups. Specifically, we aim to strengthen quantitative biomedicine in Zurich by combining basic research and the development of novel quantitative methods for the molecular analysis of patient samples, with translational research and the development of medical informatics (Figure 1).
To fulfil our mission, we rely on excellent science done by outstanding scientists. Below, we highlight the academic achievements of DQBM's members in 2019.
The following professorships were established at DQBM in 2019:
2019 was a great fundraising year for DQBM's scientists. Notably:
DQBM's junior scientists also did a fantastic job in securing research funds:
A number of DQBM members were honored for their scientific excellence:
The following bright minds completed their PhD thesis in 2019:
Furthermore, the following MSc students graduated in 2019 with a DQBM MSc thesis:
Bodenmiller lab:
Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy.
Klufa J, Bauer T, Hanson B, Herbold C, Starkl P, Lichtenberger B, Srutkova D, Schulz D, Vujic I, Mohr T, Rappersberger K, Bodenmiller B, Kozakova H, Knapp S, Loy A, Sibilia M. Sci Transl Med. 2019 Dec 11;11(522). pii: eaax2693.
doi: 10.1126/scitranslmed.aax2693.
Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.
Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O.
Cell Rep. 2019 Oct 1;29(1):202-211.e6.
doi: 10.1016/j.celrep.2019.08.077.
Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.
Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B.
Mol Cell. 2019 Jun 6;74(5):1086-1102.e5.
doi: 10.1016/j.molcel.2019.04.021.
A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.
Wagner J, Rapsomaniki MA, Chevrier S, Anzeneder T, Langwieder C, Dykgers A, Rees M, Ramaswamy A, Muenst S, Soysal SD, Jacobs A, Windhager J, Silina K, van den Broek M, Dedes KJ, Rodríguez Martínez M, Weber WP, Bodenmiller B.
Cell. 2019 May 16;177(5):1330-1345.e18.
doi: 10.1016/j.cell.2019.03.005.
IL-8 and CXCR1 expression is associated with cancer stem cell-like properties of clear cell renal cancer.
Corrò C, Healy ME, Engler S, Bodenmiller B, Li Z, Schraml P, Weber A, Frew IJ, Rechsteiner M, Moch H. J Pathol. 2019 Jul;248(3):377-389.
doi: 10.1002/path.5267.
In-Depth Characterization of Monocyte-Derived Macrophages using a Mass Cytometry-Based Phagocytosis Assay.
Schulz D, Severin Y, Zanotelli VRT, Bodenmiller B.
Sci Rep. 2019 Feb 13;9(1):1925.
doi: 10.1038/s41598-018-38127-9.
A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry.
Damond N, Engler S, Zanotelli VRT, Schapiro D, Wasserfall CH, Kusmartseva I, Nick HS, Thorel F, Herrera PL, Atkinson MA, Bodenmiller B.
Cell Metab. 2019 Mar 5;29(3):755-768.e5.
doi: 10.1016/j.cmet.2018.11.014.
Krauthammer lab:
Neural networks versus Logistic regression for 30 days all-cause readmission prediction.
Allam A, Nagy M, Thoma G, Krauthammer M.
Sci Rep. 2019 Jun 26;9(1):9277.
doi: 10.1038/s41598-019-45685-z.
A novel anti-melanoma SRC-family kinase inhibitor.
Halaban R, Bacchiocchi A, Straub R, Cao J, Sznol M, Narayan D, Allam A, Krauthammer M, Mansour TS.
Oncotarget. 2019 Mar 19;10(23):2237-2251.
doi: 10.18632/oncotarget.26787.
Kümmerli lab:
Positive linkage between bacterial social traits reveals that homogeneous rather than specialized behavioral repertoires prevail in natural Pseudomonas communities.
Kramer J, López Carrasco MÁ, Kümmerli R.
FEMS Microbiol Ecol. 2019 Nov 26. pii: fiz185.
doi: 10.1093/femsec/fiz185.
Bacterial siderophores in community and host interactions.
Kramer J, Özkaya Ö, Kümmerli R.
Nat Rev Microbiol. 2019 Nov 20.
doi: 10.1038/s41579-019-0284-4.
Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations.
O'Brien S, Kümmerli R, Paterson S, Winstanley C, Brockhurst MA.
Proc Biol Sci. 2019 Oct 9;286(1912):20191794.
doi: 10.1098/rspb.2019.1794.
Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia.
Sathe S, Mathew A, Agnoli K, Eberl L, Kümmerli R. Evolution Letters.
doi:10.1002/evl3.144
In-vivo microscopy reveals the impact of Pseudomonas aeruginosa social interactions on host colonization.
Rezzoagli C, Granato ET, Kümmerli R.
ISME J. 2019 Oct;13(10):2403-2414.
doi: 10.1038/s41396-019-0442-8.
Individual- versus group-optimality in the production of secreted bacterial compounds.
Schiessl KT, Ross-Gillespie A, Cornforth DM, Weigert M, Bigosch C, Brown SP, Ackermann M, Kümmerli R.
Evolution. 2019 Apr;73(4):675-688.
doi: 10.1111/evo.13701.
Understanding policing as a mechanism of cheater control in cooperating bacteria.
Wechsler T, Kümmerli R, Dobay A.
J Evol Biol. 2019 May;32(5):412-424.
doi: 10.1111/jeb.13423.
Polymenidou lab:
SarkoSpin: A Technique for Biochemical Isolation and Characterization of Pathological TDP-43 Aggregates.
Pérez-Berlanga M, Laferrière F, Polymenidou M. Bio-protocol.
DOI:10.21769/BioProtoc.3424.
Structural Transition, Function and Dysfunction of TDP-43 in Neurodegenerative Diseases.
Afroz T, Pérez-Berlanga M, Polymenidou M. Chimia (Aarau). 2019 May 29;73(6):380-390.
doi: 10.2533/chimia.2019.380.
The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity.
Loughlin FE, Lukavsky PJ, Kazeeva T, Reber S, Hock EM, Colombo M, Von Schroetter C, Pauli P, Cléry A, Mühlemann O, Polymenidou M, Ruepp MD, Allain FH. Mol Cell. 2019 Feb 7;73(3):490-504.e6.
doi: 10.1016/j.molcel.2018.11.012.
TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies and neurotoxic effects reflecting disease progression rates.
Laferrière F, Maniecka Z, Pérez-Berlanga M, Hruska-Plochan M, Gilhespy L, Hock EM, Wagner U, Afroz T, Boersema PJ, Barmettler G, Foti SC, Asi YT, Isaacs AM, Al-Amoudi A, Lewis A, Stahlberg H, Ravits J, De Giorgi F, Ichas F, Bezard E, Picotti P, Lashley T, Polymenidou M. Nat Neurosci. 2019 Jan;22(1):65-77.
doi: 10.1038/s41593-018-0294-y.
Memory Decline and Its Reversal in Aging and Neurodegeneration Involve miR-183/96/182 Biogenesis.
Jawaid A, Woldemichael BT, Kremer EA, Laferriere F, Gaur N, Afroz T, Polymenidou M, Mansuy IM. Mol Neurobiol. 2019 May;56(5):3451-3462.
doi: 10.1007/s12035-018-1314-3.
It is safe to say that DQBM is off to a great start. Our prognosis is that 2020 will be even more exciting, as i) we aim to expand our Faculty with a Professorship for Machine Learning in Precision Medicine, ii) we will proclaim our founding with a celebratory DQBM Founding Symposium on 19 October 2020, and iii) we will be doing more excellent science. Please stay tuned!