2021
September
Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses
Florian Geiger, Julia Acker, Guido Pap, Xinyu Wang, William E Arter, Kadi L Saar, Nadia A Erkamp, Runzhang Qi, Jack PK Bravo, Sebastian Strauss, Georg Krainer, Oscar R Burrone, Ralf Jungmann, Tuomas PJ Knowles, Hanna Engelke, Alexander Borodavka - The EMBO Journal, 2021
Visualization of individual cell division history in complex tissues using iCOUNT
Annina Denoth-Lippuner, Baptiste N. Jaeger, Tong Liang, Lars N.Royall, Stefanie E.Chie, Kilian Buthey, Diana Machado, Vladislav I. Korobeynyk, Merit Kruse, Clara M. Munz, Alexander Gerbaulet, Benjamin D. Simons, Sebastian Jessberger - Cell Stem Cell, 2021
Lymph node tissue homeostasis and adaptation to immune challenge resolved by fibroblast network mechanics
Horsnell H, Tetley R, De Belly H, Makris S, Millward L, Benjamin A, de Winde C, Paluch E, Mao Y, Acton S
Preprint from Research Square, 13 Aug 2021
Quantitative Measurement of the Affinity of Toxic and Nontoxic Misfolded Protein Oligomers for Lipid Bilayers and of its Modulation by Lipid Composition and …
Silvia ErricoSilvia Errico, Hassan Ramshini, Claudia Capitini, Claudio Canale, Martina Spaziano, Denise Barbut, Martino Calamai, Michael Zasloff, Reinier Oropesa-Nuñez, Michele Vendruscolo, and Fabrizio Chiti - ACS Chemical …, 2021
Myc determines the functional age state of oligodendrocyte progenitor cells
B Neumann, M Segel, T Ghosh, C Zhao… - Nature Aging, 2021
The binding of the small heat-shock protein αB-crystallin to fibrils of α-synuclein is driven by entropic forces
T Scheidt, JA Carozza, CC Kolbe, FA Aprile… - Proceedings of the National …, 2021
An “occlusive thrombosis-on-a-chip” microfluidic device for investigating the effect of anti-thrombotic drugs
J Berry, F Peaudecerf, NA Masters, KB Neeves… - 2021
Geometry of Catenoidal Soap Film Collapse Induced by Boundary Deformation
R Goldstein, A Pesci, C Raufaste, J Shemilt - 2021
Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay
M van der Schaar, AM Alaa, A Floto, A Gimson… - 2021
DNA breathing initiated strand displacement circuits for mimicking ant foraging with nanopore readout
J Zhu, J Kong, U Keyser, E Wang - 2021
The role of pro-domains in human growth factors and cytokines
M Ratcliff, RX Zhou, L Jermutus, M Hyvönen - Biochemical Society Transactions, 2021
Unraveling the Physicochemical Determinants of Protein Liquid-liquid Phase Separation by Nanoscale Infrared Vibrational Spectroscopy
FS Ruggeri, AM Miller, M Vendruscolo, TPJ Knowles - Bio-protocol, 2021
Weakly coupled synthetic antiferromagnetic nanodisks with perpendicular magnetic anisotropy for lab-on-chip devices
EN Welbourne, T Vemulkar, DCMC Petit, RP Cowburn - Applied Physics Letters, 2021
The Amyloid-β Pathway in Alzheimer's Disease
H Hampel, J Hardy, K Blennow, C Chen, G Perry… - Molecular Psychiatry, 2021
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
T Lohoff, S Ghazanfar, A Missarova, N Koulena… - Nature Biotechnology, 2021
Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods
AM Wolf Pérez, N Lorenzen, M Vendruscolo… - Therapeutic Antibodies, 2022
Deep learning for bioimage analysis in developmental biology
A Hallou, HG Yevick, B Dumitrascu, V Uhlmann - Development, 2021
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
T Lohoff, S Ghazanfar, A Missarova, N Koulena… - Nature Biotechnology, 2021
Vinculin is required for neuronal mechanosensing but not for axon outgrowth
DY Wang, C Melero, A Albaraky, P Atherton… - Experimental Cell Research, 2021
Minimal Design Principles for Icosahedral Virus Capsids
M Martín-Bravo, JMG Llorente, J Hernández-Rojas… - ACS nano, 2021
Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory
C Lövkvist, P Mikulski, S Reeck, M Hartley, C Dean… - Elife, 2021
COVID-19 Sounds: A Large-Scale Audio Dataset for Digital COVID-19 Detection
T Xia, D Spathis, J Ch, A Grammenos, J Han… - 2021
New frontiers for machine learning in protein science
AS Morgunov, KL Saar, M Vendruscolo, TPJ Knowles - Journal of Molecular Biology, 2021
August
Sequential Storage and Release of Microdroplets
Z Toprakcioglu, T Knowles - 2021
Aurora B‐dependent polarization of the cortical actomyosin network during mitotic exit
N Ramkumar, JV Patel, J Anstatt, B Baum - EMBO reports
Cut the noise or couple up: coordinating circadian and synthetic clocks
CN Micklem, JCW Locke - iScience, 2021
Conformational Expansion of Tau in Condensates Promotes Irreversible Aggregation
J Wen, L Hong, G Krainer, QQ Yao, TPJ Knowles, S Wu… - Journal of the American …, 2021
Feedback control of protein aggregation
AJ Dear, TCT Michaels, TPJ Knowles, L Mahadevan - The Journal of Chemical …, 2021
Evolutionary loss of inflammasomes in the Carnivora and implications for the carriage of zoonotic infections
Z Digby, P Tourlomousis, J Rooney, JP Boyle… - Cell Reports, 2021
Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats
F Hollfelder, L Lindenburg, M Hyvonen, C Kaminski… - 2021
The people behind the papers: Toby Andrews and
E Benito-Gutierrez - 2021
Logic Explained Networks
G Ciravegna, P Barbiero, F Giannini, M Gori, P Lió… - arXiv preprint arXiv …, 2021
Improving Protein Function Annotation via Unsupervised Pre-training: Robustness, Efficiency, and Insights
D Dohan, A Gane, ML Bileschi, D Belanger, L Colwell - Proceedings of the 27th ACM …, 2021
Lymph node tissue homeostasis and adaptation to immune challenge resolved by fibroblast network mechanics
H Horsnell, R Tetley, H De Belly, S Makris, L Millward… - 2021
Noisy transcription under the spotlight
K Abley, JCW Locke - Nature Plants, 2021
Responsive core-shell DNA particles trigger lipid-membrane disruption and bacteria entrapment
Michal Walczak, Ryan A. Brady, Leonardo Mancini, Claudia Contini, Roger Rubio-Sánchez, William T. Kaufhold, Pietro Cicuta & Lorenzo Di Michele - Nature Communications, 2021
Remote teaching data-driven physical modeling through a COVID-19 open ended data challenge
Lagomarsino MC, Pacifico G, Firmano V, Bella E, Benzoni P, Grilli J, Bassetti F, Capuani F, Cicuta P, Gherardi M - Preprint from arXiv, 05 Aug 2021
Diffusion-mediated HEI10 coarsening can explain meiotic crossover positioning in Arabidopsis
C Morgan, JA Fozard, M Hartley, IR Henderson… - Nature Communications, 2021
A genome-wide screen uncovers multiple roles for mitochondrial nucleoside diphosphate kinase D in inflammasome activation
O Ernst, J Sun, B Lin, B Banoth, MG Dorrington, J Liang… - Science Signaling, 2021
Stochastic Processes in Theoretical Physics and Biology (L16)
R Adhikari, M Bruna
Lipid regulation of NLRP3 inflammasome activity through organelle stress
JJ Liang, IDC Fraser, CE Bryant - Trends in Immunology, 2021
Mutations in two SARS-CoV-2 variants of concern reflect two distinct strategies of antibody escape
S Fiedler, V Denninger, AS Morgunov, A Ilsley, R Worth… - 2021
Structural Biology
Y Itoh, EJ Woods, K Minami, K Maeshima… - Current Opinion in Structural …, 2021
July
Exogenous misfolded protein oligomers can cross the intestinal barrier and cause a disease phenotype in C. elegans
M Perni, B Mannini, CK Xu, JR Kumita, CM Dobson… - Scientific Reports, 2021
Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling?
Y Itoh, EJ Woods, K Minami, K Maeshima… - Current Opinion in Structural …, 2021
Asymmetric nuclear division in neural stem cells generates sibling nuclei that differ in size, envelope composition, and chromatin organization
C Roubinet, IJ White, B Baum - Current Biology, 2021
Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients
J Rene Espinosa, I Sanchez-Burgos… - 2021
Hydroxymethylation profile of cell free DNA is a biomarker for early colorectal cancer
N Walker, M Rashid, S Yu, H Bignell, C Lumby, C Livi… - 2021
Squalamine and Its Derivatives Modulate the Aggregation of Amyloid-β and α-Synuclein and Suppress the Toxicity of Their Oligomers
B Strodel, HV Deutscher, Y Miller, EY Chi, R Limbocker…
Standardizing characterization of membrane active peptides with microfluidics
K Al Nahas, UF Keyser - Biomicrofluidics, 2021
Two human metabolites rescue a C. elegans model of Alzheimer's disease via a cytosolic unfolded protein response
P Joshi, M Perni, R Limbocker, B Mannini, S Casford… - Communications Biology, 2021
Deep learning for bioimage analysis
A Hallou, H Yevick, B Dumitrascu, V Uhlmann - arXiv preprint arXiv:2107.02584, 2021
High Frequency EEG Artifact Detection with Uncertainty via Early Exit Paradigm
L Qendro, A Campbell, P Liò, C Mascolo - arXiv preprint arXiv:2107.10746, 2021
Algorithmic Concept-based Explainable Reasoning
D Georgiev, P Barbiero, D Kazhdan, P Veličković, P Liò - arXiv preprint arXiv …, 2021
Viroplasms: Assembly and Functions of Rotavirus Replication Factories
G Papa, A Borodavka, U Desselberger - Viruses, 2021
Soluble amyloid beta-containing aggregates are present throughout the brain at early stages of Alzheimer's disease
DI Sideris, JSH Danial, D Emin, FS Ruggeri, Z Xia… - Brain Communications, 2021
STEM CELL TECHNOLOGY PROVIDES NOVEL TOOLS TO UNDERSTAND HUMAN VARIATION IN Plasmodium falciparum MALARIA Alena Pance*, Bee Ling, Kioko …
RM Ponstingl, F Law, JC Rayner
Numerical analysis of first-passage processes in finite Markov chains exhibiting metastability
DJ Sharpe, DJ Wales - Physical Review E, 2021
Inverse Decision Modeling: Learning Interpretable Representations of Behavior
D Jarrett, A Hüyük, M Van Der Schaar - International Conference on Machine …, 2021
Hereditary Spastic Paraplegias: At the Crossroads of Molecular Pathways and Clinical Options
A Martinuzzi, C Blackstone, CJ O'Kane, G Stevanin - Frontiers in Neuroscience, 2021
Rotavirus research: 2014-2020
S Caddy, G Papa, A Borodavka, U Desselberger - Virus Research, 2021
Research data in support of: Tailoring interleaflet lipid transfer with a DNA-based synthetic enzyme
D Sobota, A Ohmann, H Joshi, U Keyser… - 2021
Synthetic algal-bacteria consortia for space-efficient microalgal growth in a simple hydrogel system
M Davey, A Smith, D Wangpraseurt, S Vignolini - 2021
Sounds of COVID-19: exploring realistic performance of audio-based digital testing
J Han, T Xia, D Spathis, E Bondareva, C Brown… - arXiv preprint arXiv …, 2021
Weisfeiler and Lehman Go Cellular: CW Networks
C Bodnar, F Frasca, N Otter, YG Wang, P Liò… - arXiv preprint arXiv …, 2021
The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758
D Mead, I Saccheri, CJ Yung, K Lohse, C Lohse… - Wellcome Open Research, 2021
Soluble amyloid beta-containing aggregates are present throughout the brain at early stages of Alzheimer's disease
DI Sideris, JSH Danial, D Emin, FS Ruggeri, Z Xia… - Brain Communications, 2021
Chemical profiling of DNA G-quadruplex-interacting proteins in live cells
X Zhang, J Spiegel, SM Cuesta, S Adhikari… - Nature Chemistry, 2021
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set
J Buhmann, A Sheridan, C Malin-Mayor, P Schlegel… - Nature Methods, 2021
June
Predicting the imagined contents using brain activation
K Prasad Miyapuram, W Schultz, PN Tobler - arXiv e-prints, 2021
Image Encoding Using Multi‐Level DNA Barcodes with Nanopore Readout
J Zhu, N Ermann, K Chen, UF Keyser - Small, 2021
Explaining Time Series Predictions with Dynamic Masks
J Crabbé, M van der Schaar - arXiv preprint arXiv:2106.05303, 2021
Generic nature of the condensed states of proteins
M Fuxreiter, M Vendruscolo - Nature Cell Biology, 2021
Cell size controlled in plants using DNA content as an internal scale
M D'Ario, R Tavares, K Schiessl, B Desvoyes… - Science, 2021
Biomembranes in Bioelectronic Sensing
R Owens, T Knowles, A Jayaram, W Traberg - 2021
Graph transformation and shortest paths algorithms for finite Markov chains
DJ Sharpe, DJ Wales - Physical Review E, 2021
Entropy-based Logic Explanations of Neural Networks
P Barbiero, G Ciravegna, F Giannini, P Lió, M Gori… - arXiv preprint arXiv …, 2021
Dynamics of driven polymer transport through a nanopore
K Chen, I Jou, N Ermann, M Muthukumar, UF Keyser… - 2021
Attentional meta-learners are polythetic classifiers
B Day, R Viñas, N Simidjievski, P Liò - arXiv preprint arXiv:2106.05317, 2021
The Medkit-Learn (ing) Environment: Medical Decision Modelling through Simulation
AJ Chan, I Bica, A Huyuk, D Jarrett, M van der Schaar - arXiv preprint arXiv …, 2021
Embryonic stem cells are devoid of macropinocytosis, a trafficking pathway for activin a in differentiated cells
N Kostopoulou, S Bellou, E Bagli, M Markou… - Journal of Cell Science, 2021
Neural message passing for joint paratope-epitope prediction
A Del Vecchio, A Deac, P Liò, P Veličković - arXiv preprint arXiv:2106.00757, 2021
Research data in support of:" Responsive core-shell DNA particles trigger lipid-membrane disruption and bacteria entrapment"
M Walczak, R Brady, L Mancini, C Contini… - 2021
High proliferation and delamination during skin epidermal stratification
M Damen, L Wirtz, E Soroka, H Khatif, C Kukat… - Nature Communications, 2021
Two human metabolites rescue a C. elegans model of Alzheimer's disease via a cytosolic unfolded protein response
M Vendruscolo, P Joshi, M Perni, R Limbocker… - 2021
Existence and regularity for a system of porous medium equations with small cross-diffusion and nonlocal drifts
L Alasio, M Bruna, S Fagioli, S Schulz - arXiv preprint arXiv:2105.14037, 2021
pH‐Responsive Capsules with a Fibril Scaffold Shell Assembled from an Amyloidogenic Peptide
U Shimanovich, A Levin, D Eliaz, T Michaels… - Small
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits
T Azevedo, GM Dimitri, P Lió, ER Gamazon - npj Systems Biology and Applications, 2021
Reduced hippocampal ten-eleven translocation 3 (Tet3) protein expression in Tet3 conditional knockout mice
C Antunes, JD Da Silva, S Guerra-Gomes, ND Alves… - Molecular psychiatry, 2021
Prediction of major complications and readmission after lumbar spinal fusion: a machine learning-driven approach
AA Shah, SK Devana, C Lee, A Bugarin, EL Lord… - World Neurosurgery, 2021
Developmental bifurcation of human T follicular regulatory cells
S Kumar, VR Fonseca, F Ribeiro, AP Basto… - Science Immunology, 2021
Distinct responses of human peripheral blood cells to different misfolded protein oligomers
M Leal-Lasarte, B Mannini, F Chiti, M Vendruscolo… - Immunology
May
MIASSR: An Approach for Medical Image Arbitrary Scale Super-Resolution
J Zhu, C Tan, J Yang, G Yang, P Lio - arXiv preprint arXiv:2105.10738, 2021
Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides
D Chakraborty, A Banerjee, DJ Wales - The Journal of Physical Chemistry B, 2021
Rapid and Modular DNA Assembly for Transformation of Marchantia Chloroplasts
E Frangedakis, K Markel, S Sauret-Gueto, J Haseloff - Chloroplast Biotechnology, 2021
April
Transient suppression of transplanted spermatogonial stem cell differentiation restores fertility in mice
Nakamura Y, Jörg DJ, Kon Y, Simons BD, Yoshida S.
Cell Stem Cell. 2021 Apr 8:S1934-5909(21)00122-3. doi: 10.1016/j.stem.2021.03.016
March
Compliant Substrates Enhance Macrophage Cytokine Release and NLRP3 Inflammasome Formation During Their Pro-Inflammatory Response
Escolano JC, Taubenberger AV, Abuhattum S, Schweitzer C, Farrukh A, Del Campo A, Bryant CE, Guck J.
Front Cell Dev Biol. 2021 Mar 29;9:639815. doi: 10.3389/fcell.2021.639815. eCollection 2021.
Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitors
Single molecule imaging of protein aggregation in dementia: Methods, insights and prospects.
February
Long-term self-renewing stem cells in the adult mouse hippocampus identified by intravital imaging
Bottes S, Jaeger BN, Pilz GA, Jörg DJ, Cole JD, Kruse M, Harris L, Korobeynyk VI, Mallona I, Helmchen F, Guillemot F, Simons BD, Jessberger S.
Nat Neurosci. 2021 Feb;24(2):225-233. doi: 10.1038/s41593-020-00759-4
Systemic α-synuclein injection triggers selective neuronal pathology as seen in patients with Parkinson's disease
Kuan WL, Stott K, He X, Wood TC, Yang S, Kwok JCF, Hall K, Zhao Y, Tietz O, Aigbirhio FI, Vernon AC, Barker RA.
Membrane Tension Gates ERK-Mediated Regulation of Pluripotent Cell Fate
De Belly H, Stubb A, Yanagida A, Labouesse C, Jones PH, Paluch EK, Chalut KJ.
Cell Stem Cell. 2021 Feb 4;28(2):273-284.e6. doi: 10.1016/j.stem.2020.10.018
Salmonella Flagellin Activates NAIP/NLRC4 and Canonical NLRP3 Inflammasomes in Human Macrophages
Gram AM, Wright JA, Pickering RJ, Lam NL, Booty LM, Webster SJ, Bryant CE.
Chicken cGAS Senses Fowlpox Virus Infection and Regulates Macrophage Effector Functions
Oliveira M, Rodrigues DR, Guillory V, Kut E, Giotis ES, Skinner MA, Guabiraba R, Bryant CE, Ferguson BJ.
Front Immunol. 2021 Feb 1;11:613079. doi: 10.3389/fimmu.2020.613079
Knöckel J, Dundas K, Yang ASP, Galaway F, Metcalf T, Gemert GV, Sauerwein RW, Rayner JC, Billker O, Wright GJ.
Mol Cell Proteomics. 2021 Jan 27;20:100038. doi: 10.1074/mcp.RA120.002432
Systematic Activity Maturation of a Single-Domain Antibody with Non-canonical Amino Acids through Chemical Mutagenesis
Lindstedt PR, Aprile FA, Sormanni P, Rakoto R, Dobson CM, Bernardes GJL, Vendruscolo M.
Cell Chem Biol. 2021 Jan 21;28(1):70-77.e5. doi: 10.1016/j.chembiol.2020.11.002.
Neuromesodermal Progenitors: A Basis for Robust Axial Patterning in Development and Evolution
Sambasivan R, Steventon B.
Front Cell Dev Biol. 2021 Jan 15;8:607516. doi: 10.3389/fcell.2020.607516
Octopaminergic neurons have multiple targets in Drosophila larval mushroom body calyx and can modulate behavioral odor discrimination
Wong JYH, Wan BA, Bland T, Montagnese M, McLachlan AD, O'Kane CJ, Zhang SW, Masuda-Nakagawa LM
Absolute quantification of cerebral tissue oxygen saturation with multidistance broadband NIRS in newborn brain
Kovacsova Z, Bale G, Mitra S, Lange F, Tachtsidis I.
Biomed Opt Express. 2021 Jan 15;12(2):907-925. doi: 10.1364/BOE.412088
A deep learning approach for staging embryonic tissue isolates with small data
Pond AJR, Hwang S, Verd B, Steventon B.
PLoS One. 2021 Jan 8;16(1):e0244151. doi: 10.1371/journal.pone.0244151
Soft Polydimethylsiloxane-Supported Lipid Bilayers for Studying T Cell Interactions
Lippert AH, Dimov IB, Winkel AK, Humphrey J, McColl J, Chen KY, Santos AM, Jenkins E, Franze K, Davis SJ, Klenerman D.
Biophys J. 2021 Jan 5;120(1):35-45. doi: 10.1016/j.bpj.2020.11.021