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CBBP publications 2020-2021

2021

A community effort to identify and correct mislabeled samples in proteogenomic studies
S. Yoo, Z. Shi, B. Wen, S. Kho, R. Pan, H. Feng, H. Chen, A. Carlsson, P. Edén, W. Ma, M. Raymer, E.J. Maier, Z. Tezak, E. Johansson, D. Hinton, H. Rodriguez, J. Zhu, E. Boja, P. Wang and B. Zhang
Patterns 2, 100245 (2021)
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A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control
Y. Refahi, A. Zardilis, G. Michelin, R. Wightman, B. Leggio, J. Legrand, E. Faure, L. Vachez, A. Armezzani, A.E. Risson, F. Zhao, P. Das, N. Prunet, E.M. Meyerowitz, C. Godin, G. Malandain, H. Jönsson and J. Traas
Developmental Cell 56 540-556.e8 (2021)
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A predictive model of antibody binding in the presence of IgG-interacting bacterial surface proteins
V. Kumra Ahnlide, T. de Neergaard, M. Sundwall, T. Ambjörnsson and P. Nordenfelt
Frontiers in Immunology 12, 629103 (2021)
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Combining dense and sparse labeling in optical DNA mapping
E. Torstensson, G. Goyal, A. Johnning, F. Westerlund and T. Ambjörnsson
PLoS ONE 16, e0260489 (2021)
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Deep learning for inverse problems in quantum mechanics
V. Lantz, N. Abiri, G. Carlsson and M.E Pistol
International Journal of Quantum Chemistry 121, e26599 (2021)
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Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach
A. Dvirnas, C. Stewart, V. Müller, S.K. Bikkarolla, K. Frykholm, L. Sandegren, E. Kristiansson, F. Westerlund and T. Ambjörnsson
PLoS ONE 16, e0259670 (2021)
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Finite-size shifts in simulated protein droplet phase diagrams
D. Nilsson and A. Irbäck
Journal of Chemical Physics 154, 235101 (2021)
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KATANIN and CLASP function at different spatial scales to mediate microtubule response to mechanical stress in Arabidopsis cotyledons
R.C. Eng, R. Schneider, T.W. Matz, R. Carter, D.W. Ehrhardt, H. Jönsson, Z. Nikoloski and A. Sampathkumar
Current Biology 31, 3262-3274.e6 (2021)
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Machine learning compared with rule-in/rule-out algorithms and logistic regression to predict acute myocardial infarction based on troponin T concentrations
A. Björkelund, M. Ohlsson, J. Lundager Forberg, A. Mokhtari, P. Olsson de Capretz, U. Ekelund and J. Björk
Journal of the American College of Emergency Physicians Open 2, e12363 (2021)
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Mapping archeological signs from airborne lidar data using deep neural networks: Primary results
M. Küçükdemirci, G. Landeschi, N. Dell'Unto and M. Ohlsson
14th International Conference of Archaeological Prospection, vol. 45, 291-293 (2021)
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Modeling protein target search in human chromosomes
M. Nyberg, T. Ambjörnsson, P. Stenberg and L. Lizana
Physical Review Research 3, 013055 (2021)
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Molecular mechanism of cytokinin-activated cell division in Arabidopsis
W. Yang, S. Cortijo, N. Korsbo, P. Roszak, K. Schiessl, A. Gurzadyan, R. Wightman, H. Jönsson and E. Meyerowitz
Science 371, 1350-1355 (2021)
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Neural tube patterning: from a minimal model for rostrocaudal patterning toward an integrated 3D model
M. Brambach, A. Ernst, S. Nolbrant, J. Drouin-Ouellet, A. Kirkeby, M. Parmar and V. Olariu
iScience 24, 102559 (2021)
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Proteomic data analysis for differential profiling of the autoimmune diseases SLE, RA, SS, and ANCA-associated vasculitis
M. Ohlsson, T. Hellmark, A.A. Bengtsson, E. Theander, C. Turesson, C. Klint, C. Wingren and A.I. Ekstrand
Journal of Proteome Research 20, 1252-1260 (2021)
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The genetic base for peanut height-related traits revealed by a meta-analysis
J. Wang, C. Yan, D. Shi, X. Zhao, C. Yuan, Q. Sun, Y. Mou, H. Chen, Y. Li, C. Li and S. Shan
Plants 10, 1058 (2021)
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A quantitative model of cellular decision making in direct neuronal reprogramming
A. Merlevede, E. Legault, V. Drugge, R.A. Barker, J. Drouin-Ouellet and V. Olariu
Scientific Reports 11, 1514 (2021)
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Tissue folding at the organ–meristem boundary results in nuclear compression and chromatin compaction
K. Fal, N. Korsbo, J. Alonso-Serra, J. Teles, M. Liu, Y. Refahi, M.E. Chabouté, H. Jönsson and O. Hamant
Proc Natl Acad Sci USA 118, e2017859118 (2021)
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Multi-scale dynamical modeling of T cell development from an early thymic progenitor state to lineage commitment
V. Olariu, M.A. Yui, P. Krupinski, W. Zhou, J. Deichmann, E. Andersson, E.V. Rothenberg and C. Peterson
Cell Reports 34, 108622 (2021)
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2020

When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina
Y. Li, S. Mohanty, D. Nilsson, B. Hansson, K. Mao and A. Irbäck
Scientific Reports 10, 18752 (2020)
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Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts
N. Atabaki-Pasdar, M. Ohlsson, A. Viñuela, F. Frau, H. Pomares-Millan, M. Haid, A.G. Jones, E.L. Thomas, R.W. Koivula, A. Kurbasic, P.M. Mutie, H. Fitipaldi, J. Fernandez, A.Y. Dawed, G.N. Giordano, I.M. Forgie, T.J. McDonald, F. Rutters, H. Cederberg, E. Chabanova, M. Dale, F. De Masi, C.E. Thomas, K.H. Allin, T.H. Hansen, A. Heggie, M.-G. Hong, P.J.M. Elders, G. Kennedy, T. Kokkola, H. Krogh Pedersen, A. Mahajan, D. McEvoy, F. Pattou, V. Raverdy, R.S. Häussler, S. Sharma, H.S. Thomsen, J. Vangipurapu, H. Vestergaard, L.M. 't Hart, J. Adamski, P.B. Musholt, S. Brage, S. Brunak, E. Dermitzakis, G. Frost, T. Hansen, M. Laakso, O. Pedersen, M. Ridderstråle, H. Ruetten, A.T. Hattersley, M. Walker, J.W.J. Beulens, A. Mari, J.M. Schwenk, R. Gupta, M.I. McCarthy, E.R. Pearson, J.D. Bell, I. Pavo and P.W. Franks
PLoS Medicine 17, e1003149 (2020)
[ HTML at journal ] [ medRxiv ]

It's about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology
N. Korsbo and H. Jönsson
PLoS Computational Biology 16, e1007982 (2020)
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Pitfalls of medication adherence approximation through EHR and pharmacy records: Definitions, data and computation
A. Galozy, S. Nowaczyk, A. Sant’Anna, M. Ohlsson and M. Lingman
International Journal of Medical Informatics 136, 104092 (2020)
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Modelling protein target-search in human chromosomes
M. Nyberg, T. Ambjörnsson, P. Stenberg and L. Lizana
arXiv preprint arXiv:1909.09478
arXiv ]

Cultivation-free typing of bacteria using optical DNA mapping
V. Müller, M. Nyblom, A. Johnning, M. Wrande, A. Dvirnas, S. KK, C.G. Giske, T. Ambjörnsson, L. Sandegren, E. Kristiansson and F. Westerlund
ACS Infectious Diseases 6, 1076-1084 (2020)
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Cytoskeletal organization in isolated plant cells under geometry control
P. Durand-Smet, T.A. Spelman, E.M. Meyerowitz and H. Jönsson
Proc Natl Acad Sci USA 117, 17399-17408 (2020)
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Perfect edge-transmitting recombination of permutations
A. Merlevede and C. Troein
arXiv preprint arXiv:2005.01113v1
arXiv ]

Finite-size scaling analysis of protein droplet formation
D. Nilsson and A. Irbäck
Physical Review E 101, 022413 (2020)
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OCTAVVS: A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data
C. Troein, S. Siregar, M. Op De Beeck, C. Peterson, A. Tunlid and P. Persson
Methods and Protocols 3, 34 (2020)
Abstract ] [ BioRxiv ]

Regulation of fungal decomposition at single-cell level
M. Op De Beeck, C. Troein, S. Siregar, L. Gentile, G. Abbondanza, C. Peterson, P. Persson and A. Tunlid
The ISME Journal 14 896-905 (2020)
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