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Cambridge Centre for Physical Biology






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



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



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



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



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



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



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


Early stem cell aging in the mature brain

Ibrayeva A, Bay M, Pu E, Jörg DJ, Peng L, Jun H, Zhang N, Aaron D, Lin C, Resler G, Hidalgo A, Jang MH, Simons BD, Bonaguidi MA.Cell Stem Cell. 2021 Apr 7:S1934-5909(21)00124-7. doi: 10.1016/j.stem.2021.03.018.




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

Bach K, Pensa S, Zarocsinceva M, Kania K, Stockis J, Pinaud S, Lazarus KA, Shehata M, Simões BM, Greenhalgh AR, Howell SJ, Clarke RB, Caldas C, Halim TYF, Marioni JC, Khaled WT.

Nat Commun. 2021 Mar 9;12(1):1502. doi: 10.1038/s41467-021-21783-3


Single molecule imaging of protein aggregation in dementia: Methods, insights and prospects.

Danial JSH, Klenerman D.

Neurobiol Dis. 2021 Mar 8:105327. doi: 10.1016/j.nbd.2021.105327.






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.

Mol Psychiatry. 2021 Feb;26(2):556-567. doi: 10.1038/s41380-019-0608-9. 


Membrane Tension Gates ERK-Mediated Regulation of Pluripotent Cell Fate

De Belly H, Stubb A, Yanagida A, Labouesse C, Jones PH, Paluch EKChalut 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.

J Immunol. 2021 Feb 1;206(3):631-640. doi: 10.4049/jimmunol.2000382


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

Learn Mem. 2021 Jan 15;28(2):53-71. doi: 10.1101/lm.052159.120. 


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