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March 2024

Post-translational modifications of proteins can have high impact on their structure, function, half-life, and many more. Considering the prediction and design of typical post-translational modifications such as N-linked or O-linked glycosylation during protein design is now possible through our integration of machine learning models in the Rosetta software suite. For N-linked glycosylation, we added structural features to the machine learning model to improve likelihood of glycan presence. Post-translational modifications can now actively be included or removed while designing the proteins sequence. Ertelt et al 2024

Image Credit: Moritz Ertelt

Education Articles

Twelve quick tips for deploying a Beacon

Lauren A. Fromont, Mauricio Moldes, Michael Baudis, Anthony J. Brookes, Arcadi Navarro, Jordi Rambla

Ten simple rules for pushing boundaries of inclusion at academic events

Siobhan Mackenzie Hall, Daniel Kochin, Carmel Carne, Patricia Herterich, Kristen Lenay Lewers, Mohamed Abdelhack, Arun Ramasubramanian, Juno Felecia Michael Alphonse, Visotheary Ung, Sara El-Gebali, Christopher Brian Currin, Esther Plomp, Rachel Thompson, Malvika Sharan

Ten simple rules to leverage large language models for getting grants

Elizabeth Seckel, Brandi Y. Stephens, Fatima Rodriguez

Raising awareness of uncertain choices in empirical data analysis: A teaching concept toward replicable research practices

Maximilian M. Mandl, Sabine Hoffmann, Sebastian Bieringer, Anna E. Jacob, Marie Kraft, Simon Lemster, Anne-Laure Boulesteix

Perspectives

For long-term sustainable software in bioinformatics

Luis Pedro Coelho

Ethical frameworks should be applied to computational modelling of infectious disease interventions

Cameron Zachreson, Julian Savulescu, Freya M. Shearer, Michael J. Plank, Simon Coghlan, Joel C. Miller, Kylie E. C. Ainslie, Nicholas Geard

Research Articles

When do stereotypes undermine indirect reciprocity?

Mari Kawakatsu, Sebastián Michel-Mata, Taylor A. Kessinger, Corina E. Tarnita, Joshua B. Plotkin

Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine

Wencel Valega-Mackenzie, Marisabel Rodriguez Messan, Osman N. Yogurtcu, Ujwani Nukala, Zuben E. Sauna, Hong Yang

How neuronal morphology impacts the synchronisation state of neuronal networks

Robert P. Gowers, Susanne Schreiber

Dimensionality of locomotor behaviors in developing C. elegans

Cera W. Hassinan, Scott C. Sterrett, Brennan Summy, Arnav Khera, Angie Wang, Jihong Bai

Unsupervised learning of perceptual feature combinations

Minija Tamosiunaite, Christian Tetzlaff, Florentin Wörgötter

Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation

Nadin Haase, Wolf Holtkamp, Simon Christ, Dag Heinemann, Marina V. Rodnina, Sophia Rudorf

Tipping points emerge from weak mutualism in metacommunities

Jonas Denk, Oskar Hallatschek

LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies

Tadeusz Satława, Mateusz Tarkowski, Sonia Wróbel, Paweł Dudzic, Tomasz Gawłowski, Tomasz Klaus, Marek Orłowski, Anna Kostyn, Sandeep Kumar, Andrew Buchanan, Konrad Krawczyk

Bifurcations and bursting in the Epileptor

Maria Luisa Saggio, Viktor Jirsa

Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data

Chenyu Wu, Einar Bjarki Gunnarsson, Even Moa Myklebust, Alvaro Köhn-Luque, Dagim Shiferaw Tadele, Jorrit Martijn Enserink, Arnoldo Frigessi, Jasmine Foo, Kevin Leder

Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations

J. Galván Fraile, Franz Scherr, José J. Ramasco, Anton Arkhipov, Wolfgang Maass, Claudio R. Mirasso

Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein

Timothy Hasse, Esra Mantei, Rezvan Shahoei, Shristi Pawnikar, Jinan Wang, Yinglong Miao, Yu-ming M. Huang

Using early detection data to estimate the date of emergence of an epidemic outbreak

Sofía Jijón, Peter Czuppon, François Blanquart, Florence Débarre

Cortical cell assemblies and their underlying connectivity: An in silico study

András Ecker, Daniela Egas Santander, Sirio Bolaños-Puchet, James B. Isbister, Michael W. Reimann

Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers

Kosaku Kitagawa, Kwang Su Kim, Masashi Iwamoto, Sanae Hayashi, Hyeongki Park, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Shinji Nakaoka, Kazuyuki Aihara, Alan S. Perelson, Lena Allweiss, Maura Dandri, Koichi Watashi, Yasuhito Tanaka, Shingo Iwami

AI-Aristotle: A physics-informed framework for systems biology gray-box identification

Nazanin Ahmadi Daryakenari, Mario De Florio, Khemraj Shukla, George Em Karniadakis

It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs

Yang Jiang, Charlotte M. Deane, Garrett M. Morris, Edward P. O’Brien

End-to-end deep learning approach to mouse behavior classification from cortex-wide calcium imaging

Takehiro Ajioka, Nobuhiro Nakai, Okito Yamashita, Toru Takumi

Computational prediction of protein interactions in single cells by proximity sequencing

Junjie Xia, Hoang Van Phan, Luke Vistain, Mengjie Chen, Aly A. Khan, Savaş Tay

CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning network

Jialiang Sun, Jun Guo, Jian Liu

An analytically tractable, age-structured model of the impact of vector control on mosquito-transmitted infections

Emma L. Davis, T. Déirdre Hollingsworth, Matt J. Keeling

Mathematical models of Plasmodium vivax transmission: A scoping review

Md Nurul Anwar, Lauren Smith, Angela Devine, Somya Mehra, Camelia R. Walker, Elizabeth Ivory, Eamon Conway, Ivo Mueller, James M. McCaw, Jennifer A. Flegg, Roslyn I. Hickson

Unlocking ensemble ecosystem modelling for large and complex networks

Sarah A. Vollert, Christopher Drovandi, Matthew P. Adams

Impact on backpropagation of the spatial heterogeneity of sodium channel kinetics in the axon initial segment

Benjamin S. M. Barlow, André Longtin, Béla Joós

Bayesian inference of relative fitness on high-throughput pooled competition assays

Manuel Razo-Mejia, Madhav Mani, Dmitri Petrov

Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study

Pahala Gedara Jayathilake, Pedro Victori, Clara E. Pavillet, Chang Heon Lee, Dimitrios Voukantsis, Ana Miar, Anjali Arora, Adrian L. Harris, Karl J. Morten, Francesca M. Buffa

Ensemble dynamics and information flow deduction from whole-brain imaging data

Yu Toyoshima, Hirofumi Sato, Daiki Nagata, Manami Kanamori, Moon Sun Jang, Koyo Kuze, Suzu Oe, Takayuki Teramoto, Yuishi Iwasaki, Ryo Yoshida, Takeshi Ishihara, Yuichi Iino

Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn

Hao-Ting Wang, Steven L. Meisler, Hanad Sharmarke, Natasha Clarke, Nicolas Gensollen, Christopher J. Markiewicz, François Paugam, Bertrand Thirion, Pierre Bellec

The condition for dynamic stability in humans walking with feedback control

Hendrik Reimann, Sjoerd M. Bruijn

Learning environment-specific learning rates

Jonas Simoens, Tom Verguts, Senne Braem

Enrichment on steps, not genes, improves inference of differentially expressed pathways

Nicholas Markarian, Kimberly M. Van Auken, Dustin Ebert, Paul W. Sternberg

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration

Cecilia Wieder, Juliette Cooke, Clement Frainay, Nathalie Poupin, Russell Bowler, Fabien Jourdan, Katerina J. Kechris, Rachel PJ Lai, Timothy Ebbels

A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment

Yitong Lv, He Gong, Xuechao Liu, Jia Hao, Lei Xu, Zhiwei Sun, Changyuan Yu, Lida Xu

Bias in the arrival of variation can dominate over natural selection in Richard Dawkins’s biomorphs

Nora S. Martin, Chico Q. Camargo, Ard A. Louis

Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects

Peng Liu, Ke Bo, Mingzhou Ding, Ruogu Fang

The multi-dimensional challenges of controlling respiratory virus transmission in indoor spaces: Insights from the linkage of a microscopic pedestrian simulation and SARS-CoV-2 transmission model

Büsra Atamer Balkan, You Chang, Martijn Sparnaaij, Berend Wouda, Doris Boschma, Yangfan Liu, Yufei Yuan, Winnie Daamen, Mart C. M. de Jong, Colin Teberg, Kevin Schachtschneider, Reina S. Sikkema, Linda van Veen, Dorine Duives, Quirine A. ten Bosch

Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1

Tyler Cassidy, Kathryn E. Stephenson, Dan H. Barouch, Alan S. Perelson

Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating

Jakub Svoboda, Soham Joshi, Josef Tkadlec, Krishnendu Chatterjee

Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models

Yucai Shao, Andrew F. Magee, Tetyana I. Vasylyeva, Marc A. Suchard

Active reinforcement learning versus action bias and hysteresis: control with a mixture of experts and nonexperts

Jaron T. Colas, John P. O’Doherty, Scott T. Grafton

Methods

A multiscale computational framework for the development of spines in molluscan shells

Derek E. Moulton, Nathanaël Aubert-Kato, Axel A. Almet, Atsuko Sato

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering

Søren D. Petersen, Lucas Levassor, Christine M. Pedersen, Jan Madsen, Lea G. Hansen, Jie Zhang, Ahmad K. Haidar, Rasmus J. N. Frandsen, Jay D. Keasling, Tilmann Weber, Nikolaus Sonnenschein, Michael K. Jensen

Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

Moritz Ertelt, Vikram Khipple Mulligan, Jack B. Maguire, Sergey Lyskov, Rocco Moretti, Torben Schiffner, Jens Meiler, Clara T. Schoeder

A machine-learning method for biobank-scale genetic prediction of blood group antigens

Kati Hyvärinen, Katri Haimila, Camous Moslemi, Blood Service Biobank, Martin L. Olsson, Sisse R. Ostrowski, Ole B. Pedersen, Christian Erikstrup, Jukka Partanen, Jarmo Ritari

Software

kCSD-python, reliable current source density estimation with quality control

Chaitanya Chintaluri, Marta Bejtka, Władysław Średniawa, Michał Czerwiński, Jakub M. Dzik, Joanna Jędrzejewska-Szmek, Daniel K. Wójcik