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February 2025, Volume 21, Issue 2
- 1-23 Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA
by Eliezyer Fermino de Oliveira & Pranjal Garg & Jens Hjerling-Leffler & Renata Batista-Brito & Lucas Sjulson - 1-23 AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis
by Rui Miao & Hao-Yang Yu & Bing-Jie Zhong & Hong-Xia Sun & Qiang Xia - 1-24 Information transmission in a cell monolayer: A numerical study
by Paweł Nałęcz-Jawecki & Przemysław Szyc & Frederic Grabowski & Marek Kochańczyk & Tomasz Lipniacki - 1-25 Optimal control prevents itself from eradicating stochastic disease epidemics
by Rachel Russell & Nik J Cunniffe - 1-26 Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data
by Xueda Shen & Aaron Rumack & Bryan Wilder & Ryan J Tibshirani - 1-26 Identification of recurrent dynamics in distributed neural populations
by Rodrigo Osuna-Orozco & Edward Castillo & Kameron Decker Harris & Samantha R Santacruz - 1-26 Hexagons all the way down: grid cells as a conformal isometric map of space
by Vemund Sigmundson Schøyen & Kosio Beshkov & Markus Borud Pettersen & Erik Hermansen & Konstantin Holzhausen & Anders Malthe-Sørenssen & Marianne Fyhn & Mikkel Elle Lepperød - 1-26 Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern
by Wenxuan Li & Xu Chen & Suli Liu & Chiyu Zhang & Guyue Liu - 1-27 Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction
by Xianghao Zhan & Qinmei Xu & Yuanning Zheng & Guangming Lu & Olivier Gevaert - 1-33 ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature
by Luca Musella & Alejandro Afonso Castro & Xin Lai & Max Widmann & Julio Vera
January 2025, Volume 21, Issue 1
- 1-10 Ten simple rules to complete successfully a computational MSc thesis project
by Edoardo Saccenti & Cristina Furlan - 1-12 Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning
by Mohammad Neamul Kabir & Li Rong Wang & Wilson Wen Bin Goh - 1-13 Eight quick tips for biologically and medically informed machine learning
by Luca Oneto & Davide Chicco - 1-15 Learning predictive signatures of HLA type from T-cell repertoires
by María Ruiz Ortega & Mikhail V Pogorelyy & Anastasia A Minervina & Paul G Thomas & Thierry Mora & Aleksandra M Walczak - 1-16 A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data
by Lulu Pan & Qian Gao & Kecheng Wei & Yongfu Yu & Guoyou Qin & Tong Wang - 1-18 Extracting the fingerprints of sequences of random rhythmic auditory stimuli from electrophysiological data
by Fernando A Najman & Antonio Galves & Marcela Svarc & Claudia D Vargas - 1-19 Benchmarking uncertainty quantification for protein engineering
by Kevin P Greenman & Ava P Amini & Kevin K Yang - 1-20 Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers
by Kwang Su Kim & Masashi Iwamoto & Kosaku Kitagawa & Hyeongki Park & Sanae Hayashi & Senko Tsukuda & Takeshi Matsui & Masanori Atsukawa & Kentaro Matsuura & Natthaya Chuaypen & Pisit Tangkijvanich & Lena Allweiss & Takara Nishiyama & Naotoshi Nakamura & Yasuhisa Fujita & Eiryo Kawakami & Shinji Nakaoka & Masamichi Muramatsu & Kazuyuki Aihara & Takaji Wakita & Alan S Perelson & Maura Dandri & Koichi Watashi & Shingo Iwami & Yasuhito Tanaka - 1-20 Role and modulation of various spinal pathways for human upper limb control in different gravity conditions
by Alice Bruel & Lina Bacha & Emma Boehly & Constance De Trogoff & Luca Represa & Gregoire Courtine & Auke Ijspeert - 1-21 Ten simple rules for good model-sharing practices
by Ismael Kherroubi Garcia & Christopher Erdmann & Sandra Gesing & Michael Barton & Lauren Cadwallader & Geerten Hengeveld & Christine R Kirkpatrick & Kathryn Knight & Carsten Lemmen & Rebecca Ringuette & Qing Zhan & Melissa Harrison & Feilim Mac Gabhann & Natalie Meyers & Cailean Osborne & Charlotte Till & Paul Brenner & Matt Buys & Min Chen & Allen Lee & Jason Papin & Yuhan Rao - 1-21 Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data
by Xu Shi & Xiao Wang & Lu Jin & Leena Halakivi-Clarke & Robert Clarke & Andrew F Neuwald & Jianhua Xuan - 1-21 Integration of unpaired single cell omics data by deep transfer graph convolutional network
by Yulong Kan & Yunjing Qi & Zhongxiao Zhang & Xikeng Liang & Weihao Wang & Shuilin Jin - 1-22 Bayesian active sound localisation: To what extent do humans perform like an ideal-observer?
by Glen McLachlan & Piotr Majdak & Jonas Reijniers & Michael Mihocic & Herbert Peremans - 1-25 Data-driven discovery and parameter estimation of mathematical models in biological pattern formation
by Hidekazu Hishinuma & Hisako Takigawa-Imamura & Takashi Miura - 1-26 Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model
by Xiaoyi Wang & Zhen Jin - 1-27 Optimal control of agent-based models via surrogate modeling
by Luis L Fonseca & Lucas Böttcher & Borna Mehrad & Reinhard C Laubenbacher - 1-28 HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data
by Evan Gorstein & Rosa Aghdam & Claudia Solís-Lemus - 1-29 Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell
by Julien Laussu & Deborah Michel & Léa Magne & Stephane Segonds & Steven Marguet & Dimitri Hamel & Muriel Quaranta-Nicaise & Frederick Barreau & Emmanuel Mas & Vincent Velay & Florian Bugarin & Audrey Ferrand - 1-29 Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense
by Nicole M Moody & Cole M Williams & Sohini Ramachandran & Matthew J Fuxjager - 1-30 The calcitron: A simple neuron model that implements many learning rules via the calcium control hypothesis
by Toviah Moldwin & Li Shay Azran & Idan Segev - 1-30 Sparse high-dimensional decomposition of non-primary auditory cortical receptive fields
by Shoutik Mukherjee & Behtash Babadi & Shihab Shamma - 1-33 Trajectory inference from single-cell genomics data with a process time model
by Meichen Fang & Gennady Gorin & Lior Pachter - 1-37 Mechanisms for dysregulation of excitatory-inhibitory balance underlying allodynia in dorsal horn neural subcircuits
by Alexander G Ginsberg & Scott F Lempka & Bo Duan & Victoria Booth & Jennifer Crodelle
December 2024, Volume 20, Issue 12
- 1-9 Hands-on training about data clustering with orange data mining toolbox
by Janez Demšar & Blaž Zupan - 1-10 Randomness as a driver of inactivity in social groups
by Abel Bernadou & Raphaël Jeanson - 1-11 ClustAll: An R package for patient stratification in complex diseases
by Asier Ortega-Legarreta & Sara Palomino-Echeverria & Estefania Huergo & Vincenzo Lagani & Narsis A Kiani & Pierre-Emmanuel Rautou & Nuria Planell Picola & Jesper Tegner & David Gomez-Cabrero - 1-17 Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity
by Alexandre Guet-McCreight & Frank Mazza & Thomas D Prevot & Etienne Sibille & Etay Hay - 1-17 Mechanical network equivalence between the katydid and mammalian inner ears
by Emine Celiker & Charlie Woodrow & Òscar Guadayol & Leonidas-Romanos Davranoglou & Christian M Schlepütz & Beth Mortimer & Graham K Taylor & Stuart Humphries & Fernando Montealegre-Z - 1-18 Optimisation strategies for directed evolution without sequencing
by Jessica James & Sebastian Towers & Jakob Foerster & Harrison Steel - 1-19 Properties of winning Iterated Prisoner’s Dilemma strategies
by Nikoleta E Glynatsi & Vincent Knight & Marc Harper - 1-19 Machine learning mathematical models for incidence estimation during pandemics
by Oscar Fajardo-Fontiveros & Mattia Mattei & Giulio Burgio & Clara Granell & Sergio Gómez & Alex Arenas & Marta Sales-Pardo & Roger Guimerà - 1-19 Adapting to time: Why nature may have evolved a diverse set of neurons
by Karim G Habashy & Benjamin D Evans & Dan F M Goodman & Jeffrey S Bowers - 1-20 Preserving friendships in school contacts: An algorithm to construct synthetic temporal networks for epidemic modelling
by Lucille Calmon & Elisabetta Colosi & Giulia Bassignana & Alain Barrat & Vittoria Colizza - 1-20 A mathematical model of plasmin-mediated fibrinolysis of single fibrin fibers
by Roukayatou R Ouedraogo & Hannah K Sowers & Spencer R Lynch & Nathan E Hudson & Brittany E Bannish - 1-21 scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum
by Yuqian Liu & Yan Chen & Huanwen Wu & Xuanping Zhang & Yuqi Wang & Xin Yi & Zhiyong Liang & Jiayin Wang - 1-22 Mapping genes for human face shape: Exploration of univariate phenotyping strategies
by Meng Yuan & Seppe Goovaerts & Michiel Vanneste & Harold Matthews & Hanne Hoskens & Stephen Richmond & Ophir D Klein & Richard A Spritz & Benedikt Hallgrimsson & Susan Walsh & Mark D Shriver & John R Shaffer & Seth M Weinberg & Hilde Peeters & Peter Claes - 1-22 Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform
by Xavier Escriba-Montagut & Yannick Marcon & Augusto Anguita-Ruiz & Demetris Avraam & Jose Urquiza & Andrei S Morgan & Rebecca C Wilson & Paul Burton & Juan R Gonzalez - 1-22 The Burr distribution as a model for the delay between key events in an individual’s infection history
by Nyall Jamieson & Christiana Charalambous & David M Schultz & Ian Hall - 1-22 Estimating the distribution of parameters in differential equations with repeated cross-sectional data
by Hyeontae Jo & Sung Woong Cho & Hyung Ju Hwang - 1-24 A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
by Henri Schmidt & Benjamin J Raphael - 1-24 A multi-scale study of thalamic state-dependent responsiveness
by Jorin Overwiening & Federico Tesler & Domenico Guarino & Alain Destexhe - 1-25 Estimating the time-varying effective reproduction number via Cycle Threshold-based Transformer
by Xin-Yu Zhang & Lan-Lan Yu & Wei-Yi Wang & Gui-Quan Sun & Jian-Cheng Lv & Tao Zhou & Quan-Hui Liu - 1-26 Evolution of cooperation in multichannel games on multiplex networks
by Amit Basak & Supratim Sengupta - 1-27 A framework for modelling desert locust population dynamics and large-scale dispersal
by Renata Retkute & William Thurston & Keith Cressman & Christopher A Gilligan - 1-29 Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling
by Jiyoung Kang & Hae-Jeong Park - 1-31 Marked point process variational autoencoder with applications to unsorted spiking activities
by Ryohei Shibue & Tomoharu Iwata - 1-31 Mathematical basis and toolchain for hierarchical optimization of biochemical networks
by Nisha Ann Viswan & Alexandre Tribut & Manvel Gasparyan & Ovidiu Radulescu & Upinder S Bhalla - 1-32 Neuro-cognitive multilevel causal modeling: A framework that bridges the explanatory gap between neuronal activity and cognition
by Moritz Grosse-Wentrup & Akshey Kumar & Anja Meunier & Manuel Zimmer - 1-37 Parallel development of object recognition in newborn chicks and deep neural networks
by Lalit Pandey & Donsuk Lee & Samantha M W Wood & Justin N Wood - 1-39 Uncovering population contributions to the extracellular potential in the mouse visual system using Laminar Population Analysis
by Atle E Rimehaug & Anders M Dale & Anton Arkhipov & Gaute T Einevoll - 1-43 Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework
by Máté Mohácsi & Márk Patrik Török & Sára Sáray & Luca Tar & Gábor Farkas & Szabolcs Káli - 1-44 Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction
by Akash Bahai & Chee Keong Kwoh & Yuguang Mu & Yinghui Li - 1-46 Extracting interpretable signatures of whole-brain dynamics through systematic comparison
by Annie G Bryant & Kevin Aquino & Linden Parkes & Alex Fornito & Ben D Fulcher
November 2024, Volume 20, Issue 11
- 1-10 Eleven quick tips for properly handling tabular data
by Marla I Hertz & Ashley S McNeill - 1-17 MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm
by Chao Wang & Quan Zou - 1-17 Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function
by Yuanchen Zhao & Otto X Cordero & Mikhail Tikhonov - 1-17 Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models
by Wyatt G Madden & Wei Jin & Benjamin Lopman & Andreas Zufle & Benjamin Dalziel & C Jessica E. Metcalf & Bryan T Grenfell & Max S Y Lau - 1-18 The evolutionary cost of homophily: Social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens
by Shuanger Li & Davorka Gulisija & Oana Carja - 1-19 Socially driven negative feedback regulates activity and energy use in ant colonies
by Maurizio Porfiri & Nicole Abaid & Simon Garnier - 1-21 A new look at TFPI inhibition of factor X activation
by Fabian Santiago & Amandeep Kaur & Shannon Bride & Dougald Monroe & Karin Leiderman & Suzanne Sindi - 1-21 Approximate planning in spatial search
by Marta Kryven & Suhyoun Yu & Max Kleiman-Weiner & Tomer Ullman & Joshua Tenenbaum - 1-21 scGRN-Entropy: Inferring cell differentiation trajectories using single-cell data and gene regulation network-based transfer entropy
by Rui Sun & Wenjie Cao & ShengXuan Li & Jian Jiang & Yazhou Shi & Bengong Zhang - 1-23 A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors
by Alireza Rezvani-Sharif & Hadi Lioe & Steven K Dower & Matthias Pelzing & Con Panousis & Dalton J E Harvie & Ineke L Muir - 1-23 Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
by Robert van Dijk & John Arevalo & Mehrtash Babadi & Anne E Carpenter & Shantanu Singh - 1-23 GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies
by Lin Lin & Rachel L Spreng & Kelly E Seaton & S Moses Dennison & Lindsay C Dahora & Daniel J Schuster & Sheetal Sawant & Peter B Gilbert & Youyi Fong & Neville Kisalu & Andrew J Pollard & Georgia D Tomaras & Jia Li - 1-23 Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing
by Sven B Gould & Jonas Magiera & Carolina García García & Parth K Raval - 1-24 Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics
by Alexandria M Jensen & Peter DeWitt & Brianne M Bettcher & Julia Wrobel & Katerina Kechris & Debashis Ghosh - 1-25 Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion
by Aaron R Allred & Caroline R Austin & Lanna Klausing & Nicholas Boggess & Torin K Clark - 1-25 Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits
by Vitaly V Ganusov & Afsal Kolloli & Selvakumar Subbian - 1-27 Co-contraction embodies uncertainty: An optimal feedforward strategy for robust motor control
by Bastien Berret & Dorian Verdel & Etienne Burdet & Frédéric Jean - 1-30 An inductive bias for slowly changing features in human reinforcement learning
by Noa L Hedrich & Eric Schulz & Sam Hall-McMaster & Nicolas W Schuck - 1-30 A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates
by Baike She & Rebecca Lee Smith & Ian Pytlarz & Shreyas Sundaram & Philip E Paré - 1-32 Teaching deep networks to see shape: Lessons from a simplified visual world
by Christian Jarvers & Heiko Neumann - 1-33 Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations
by Aylin Bircan & Nurdan Kuru & Onur Dereli & Berkay Selçuk & Ogün Adebali
October 2024, Volume 20, Issue 10
- 1-10 Gene signatures for cancer research: A 25-year retrospective and future avenues
by Wei Liu & Huaqin He & Davide Chicco - 1-17 EEG microstate transition cost correlates with task demands
by Giacomo Barzon & Ettore Ambrosini & Antonino Vallesi & Samir Suweis - 1-17 Integrating information from historical data into mechanistic models for influenza forecasting
by Alessio Andronico & Juliette Paireau & Simon Cauchemez - 1-19 Enhancing insights in sexually transmitted infection mapping: Syphilis in Forsyth County, North Carolina, a case study
by Lani Fox & William C Miller & Dionne Gesink & Irene Doherty & Marc Serre - 1-20 IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation
by Haolin Jiang & Yulian Xu & Yunguang Tong & Dong Zhang & Ruhong Zhou - 1-20 Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals
by Michele Gentili & Kimberly Glass & Enrico Maiorino & Brian D Hobbs & Zhonghui Xu & Peter J Castaldi & Michael H Cho & Craig P Hersh & Dandi Qiao & Jarrett D Morrow & Vincent J Carey & John Platig & Edwin K Silverman - 1-21 Best practices for estimating and reporting epidemiological delay distributions of infectious diseases
by Kelly Charniga & Sang Woo Park & Andrei R Akhmetzhanov & Anne Cori & Jonathan Dushoff & Sebastian Funk & Katelyn M Gostic & Natalie M Linton & Adrian Lison & Christopher E Overton & Juliet R C Pulliam & Thomas Ward & Simon Cauchemez & Sam Abbott - 1-21 PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites
by Yun Zuo & Xingze Fang & Jiayong Wan & Wenying He & Xiangrong Liu & Xiangxiang Zeng & Zhaohong Deng - 1-24 Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data
by Safiye Celik & Jan-Christian Hütter & Sandra Melo Carlos & Nathan H Lazar & Rahul Mohan & Conor Tillinghast & Tommaso Biancalani & Marta M Fay & Berton A Earnshaw & Imran S Haque - 1-24 Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer
by Lianghong Chen & Zi Huai Huang & Yan Sun & Mike Domaratzki & Qian Liu & Pingzhao Hu - 1-25 A Computational Framework for Understanding the Impact of Prior Experiences on Pain Perception and Neuropathic Pain
by Malin Ramne & Jon Sensinger - 1-25 Regularizing hyperparameters of interacting neural signals in the mouse cortex reflect states of arousal
by Dmitry R Lyamzin & Andrea Alamia & Mohammad Abdolrahmani & Ryo Aoki & Andrea Benucci - 1-27 Computational joint action: Dynamical models to understand the development of joint coordination
by Cecilia De Vicariis & Vinil T Chackochan & Laura Bandini & Eleonora Ravaschio & Vittorio Sanguineti - 1-27 Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history
by Gabriel A A Silva & Avril M Harder & Kenneth B Kirksey & Samarth Mathur & Janna R Willoughby - 1-28 The optimal spatially-dependent control measures to effectively and economically eliminate emerging infectious diseases
by Fan Xia & Yanni Xiao & Junling Ma - 1-29 Compression-based inference of network motif sets
by Alexis Bénichou & Jean-Baptiste Masson & Christian L Vestergaard - 1-29 Why aphid virus retention needs more attention: Modelling aphid behaviour and virus manipulation in non-persistent plant virus transmission
by Elin K Falla & Nik J Cunniffe - 1-32 Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson’s disease
by Adam M Roth & John H Buggeln & Joanna E Hoh & Jonathan M Wood & Seth R Sullivan & Truc T Ngo & Jan A Calalo & Rakshith Lokesh & Susanne M Morton & Stephen Grill & John J Jeka & Michael J Carter & Joshua G A Cashaback - 1-34 Learning probability distributions of sensory inputs with Monte Carlo predictive coding
by Gaspard Oliviers & Rafal Bogacz & Alexander Meulemans - 1-38 Bayesian polynomial neural networks and polynomial neural ordinary differential equations
by Colby Fronk & Jaewoong Yun & Prashant Singh & Linda Petzold - 1-39 Mcadet: A feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection
by Saishi Cui & Sina Nassiri & Issa Zakeri - 1-45 A flexible generative algorithm for growing in silico placentas
by Diana C de Oliveira & Hani Cheikh Sleiman & Kelly Payette & Jana Hutter & Lisa Story & Joseph V Hajnal & Daniel C Alexander & Rebecca J Shipley & Paddy J Slator
September 2024, Volume 20, Issue 9
- 1-9 Ten simple rules for successfully carrying out funded research projects
by Diego A Forero & Walter H Curioso & Wei Wang - 1-11 Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting
by Anis Ur Rahman & Gleb Tikhonov & Jari Oksanen & Tuomas Rossi & Otso Ovaskainen - 1-12 Ten quick tips for ensuring machine learning model validity
by Wilson Wen Bin Goh & Mohammad Neamul Kabir & Sehwan Yoo & Limsoon Wong - 1-17 Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies
by Adrian J Green & Lisa Truong & Preethi Thunga & Connor Leong & Melody Hancock & Robyn L Tanguay & David M Reif - 1-17 Bayesian clustering with uncertain data
by Kath Nicholls & Paul D W Kirk & Chris Wallace - 1-18 Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases
by Joseph Shingleton & David Mustard & Steven Dyke & Hannah Williams & Emma Bennett & Thomas Finnie - 1-19 Calibrating dimension reduction hyperparameters in the presence of noise
by Justin Lin & Julia Fukuyama - 1-20 Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency
by Eslam Abousamra & Marlin Figgins & Trevor Bedford - 1-20 Construct prognostic models of multiple myeloma with pathway information incorporated
by Shuo Wang & ShanJin Wang & Wei Pan & YuYang Yi & Junyan Lu - 1-21 A hierarchy of metabolite exchanges in metabolic models of microbial species and communities
by Ylva Katarina Wedmark & Jon Olav Vik & Ove Øyås - 1-22 HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures
by Olav N L Aga & Morten Brun & Kazeem A Dauda & Ramon Diaz-Uriarte & Konstantinos Giannakis & Iain G Johnston - 1-23 Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter
by Jolanda Malamud & Sinan Guloksuz & Ruud van Winkel & Philippe Delespaul & Marc A F De Hert & Catherine Derom & Evert Thiery & Nele Jacobs & Bart P F Rutten & Quentin J M Huys - 1-23 Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data
by Michiel Stock & Wim Van Criekinge & Dimitri Boeckaerts & Steff Taelman & Maxime Van Haeverbeke & Pieter Dewulf & Bernard De Baets - 1-23 HELP: A computational framework for labelling and predicting human common and context-specific essential genes
by Ilaria Granata & Lucia Maddalena & Mario Manzo & Mario Rosario Guarracino & Maurizio Giordano - 1-23 The primacy model and the structure of olfactory space
by Hamza Giaffar & Sergey Shuvaev & Dmitry Rinberg & Alexei A Koulakov - 1-24 Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model
by Yanpeng Yang & Yanyi Zheng & Quan Zou & Jian Li & Hailin Feng - 1-24 SEMbap: Bow-free covariance search and data de-correlation
by Mario Grassi & Barbara Tarantino - 1-24 Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments
by Janice Yang & Neil J Daily & Taylor K Pullinger & Tetsuro Wakatsuki & Eric A Sobie - 1-25 Impact of phylogeny on the inference of functional sectors from protein sequence data
by Nicola Dietler & Alia Abbara & Subham Choudhury & Anne-Florence Bitbol - 1-25 Learning to integrate parts for whole through correlated neural variability
by Zhichao Zhu & Yang Qi & Wenlian Lu & Jianfeng Feng - 1-28 GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments
by Cecile Le Sueur & Magnus Rattray & Mikhail Savitski - 1-29 A Physics-Informed Neural Network approach for compartmental epidemiological models
by Caterina Millevoi & Damiano Pasetto & Massimiliano Ferronato - 1-31 Finding the rhythm: Humans exploit nonlinear intrinsic dynamics of compliant systems in periodic interaction tasks
by Annika Schmidt & Marion Forano & Arne Sachtler & Davide Calzolari & Bernhard M Weber & David W Franklin & Alin Albu-Schäffer - 1-31 Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing
by Breanne Sparta & Timothy Hamilton & Gunalan Natesan & Samuel D Aragones & Eric J Deeds - 1-32 Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803
by Tobias Pfennig & Elena Kullmann & Tomáš Zavřel & Andreas Nakielski & Oliver Ebenhöh & Jan Červený & Gábor Bernát & Anna Barbara Matuszyńska - 1-43 The role of training variability for model-based and model-free learning of an arbitrary visuomotor mapping
by Carlos A Velázquez-Vargas & Nathaniel D Daw & Jordan A Taylor
August 2024, Volume 20, Issue 8
- 1-11 Ten simple rules for successfully managing EU research grants
by David G Pina - 1-16 Rhythmidia: A modern tool for circadian period analysis of filamentous fungi
by Alex T Keeley & Jeffrey M Lotthammer & Jacqueline F Pelham - 1-21 Bird song comparison using deep learning trained from avian perceptual judgments
by Lies Zandberg & Veronica Morfi & Julia M George & David F Clayton & Dan Stowell & Robert F Lachlan - 1-21 Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands
by Catherine M Byrne & Ana Citlali Márquez & Bing Cai & Daniel Coombs & Soren Gantt - 1-21 Upper bounds for integrated information
by Alireza Zaeemzadeh & Giulio Tononi - 1-22 Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention
by Keyvan Mahjoory & Andreas Bahmer & Molly J Henry - 1-22 Diffusion model predicts the geometry of actin cytoskeleton from cell morphology
by Honghan Li & Shiyou Liu & Shinji Deguchi & Daiki Matsunaga - 1-22 The rules of multiplayer cooperation in networks of communities
by Diogo L Pires & Mark Broom - 1-22 scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization
by Yuqing Qian & Quan Zou & Mengyuan Zhao & Yi Liu & Fei Guo & Yijie Ding - 1-23 iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites
by Lin Yuan & Ling Zhao & Jinling Lai & Yufeng Jiang & Qinhu Zhang & Zhen Shen & Chun-Hou Zheng & De-Shuang Huang - 1-23 Attentional selection and communication through coherence: Scope and limitations
by Priscilla E Greenwood & Lawrence M Ward - 1-23 COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms
by Teemu J Rintala & Vittorio Fortino - 1-25 Influence of surprise on reinforcement learning in younger and older adults
by Christoph Koch & Ondrej Zika & Rasmus Bruckner & Nicolas W Schuck - 1-25 Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions
by Efrat Cohen-Davidi & Isana Veksler-Lublinsky - 1-25 Reliable estimation of tree branch lengths using deep neural networks
by Anton Suvorov & Daniel R Schrider - 1-26 Understanding patient-derived tumor organoid growth through an integrated imaging and mathematical modeling framework
by Einar Bjarki Gunnarsson & Seungil Kim & Brandon Choi & J Karl Schmid & Karn Kaura & Heinz-Josef Lenz & Shannon M Mumenthaler & Jasmine Foo - 1-28 scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data
by Fengdi Zhao & Xin Ma & Bing Yao & Qing Lu & Li Chen - 1-31 Signatures of hierarchical temporal processing in the mouse visual system
by Lucas Rudelt & Daniel González Marx & F Paul Spitzner & Benjamin Cramer & Johannes Zierenberg & Viola Priesemann - 1-32 A general model unifying the adaptive, transient and sustained properties of ON and OFF auditory neural responses
by Ulysse Rançon & Timothée Masquelier & Benoit R Cottereau - 1-32 Interacting particle models on the impact of spatially heterogeneous human behavioral factors on dynamics of infectious diseases
by Yunfeng Xiong & Chuntian Wang & Yuan Zhang
July 2024, Volume 20, Issue 7
- 1-12 BCI Toolbox: An open-source python package for the Bayesian causal inference model
by Haocheng Zhu & Ulrik Beierholm & Ladan Shams - 1-12 Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
by Patrick Bryant & Frank Noé - 1-14 Nine quick tips for open meta-analyses
by David Moreau & Kristina Wiebels - 1-15 Fixation times on directed graphs
by David A Brewster & Martin A Nowak & Josef Tkadlec - 1-17 Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong
by Yiu-Chung Lau & Songwei Shan & Dong Wang & Dongxuan Chen & Zhanwei Du & Eric H Y Lau & Daihai He & Linwei Tian & Peng Wu & Benjamin J Cowling & Sheikh Taslim Ali - 1-17 Detection of disease-specific signatures in B cell repertoires of lymphomas using machine learning
by Paul Schmidt-Barbo & Gabriel Kalweit & Mehdi Naouar & Lisa Paschold & Edith Willscher & Christoph Schultheiß & Bruno Märkl & Stefan Dirnhofer & Alexandar Tzankov & Mascha Binder & Maria Kalweit - 1-17 Competitive advantages of T-even phage lysis inhibition in response to secondary infection
by Ulrik Hvid & Namiko Mitarai - 1-19 When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty
by Nathan J Doyle & Fergus Cumming & Robin N Thompson & Michael J Tildesley - 1-20 Nonlinear fusion is optimal for a wide class of multisensory tasks
by Marcus Ghosh & Gabriel Béna & Volker Bormuth & Dan F M Goodman - 1-21 Identifying cell states in single-cell RNA-seq data at statistically maximal resolution
by Pascal Grobecker & Thomas Sakoparnig & Erik van Nimwegen - 1-21 Probabilistic neural transfer function estimation with Bayesian system identification
by Nan Wu & Isabel Valera & Fabian Sinz & Alexander Ecker & Thomas Euler & Yongrong Qiu - 1-22 Generating information-dense promoter sequences with optimal string packing
by Virgile Andreani & Eric J South & Mary J Dunlop - 1-23 Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations
by Yingjun Ma & Yuanyuan Ma - 1-23 Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers
by David R Penas & Meysam Hashemi & Viktor K Jirsa & Julio R Banga - 1-23 Identifying topologically associating domains using differential kernels
by Luka Maisuradze & Megan C King & Ivan V Surovtsev & Simon G J Mochrie & Mark D Shattuck & Corey S O’Hern - 1-23 Quantifying massively parallel microbial growth with spatially mediated interactions
by Florian Borse & Dovydas Kičiatovas & Teemu Kuosmanen & Mabel Vidal & Guillermo Cabrera-Vives & Johannes Cairns & Jonas Warringer & Ville Mustonen - 1-24 Estimating error rates for single molecule protein sequencing experiments
by Matthew Beauregard Smith & Kent VanderVelden & Thomas Blom & Heather D Stout & James H Mapes & Tucker M Folsom & Christopher Martin & Angela M Bardo & Edward M Marcotte - 1-24 Detecting and quantifying heterogeneity in susceptibility using contact tracing data
by Beth M Tuschhoff & David A Kennedy - 1-25 scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics
by Gustavo Magaña-López & Laurence Calzone & Andrei Zinovyev & Loïc Paulevé - 1-26 Modeling soybean growth: A mixed model approach
by Maud Delattre & Yusuke Toda & Jessica Tressou & Hiroyoshi Iwata - 1-27 A low-dimensional approximation of optimal confidence
by Pierre Le Denmat & Tom Verguts & Kobe Desender - 1-27 Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission
by Elias Rosenblatt & Jonathan D Cook & Graziella V DiRenzo & Evan H Campbell Grant & Fernando Arce & Kim M Pepin & F Javiera Rudolph & Michael C Runge & Susan Shriner & Daniel P Walsh & Brittany A Mosher - 1-28 FedGMMAT: Federated generalized linear mixed model association tests
by Wentao Li & Han Chen & Xiaoqian Jiang & Arif Harmanci - 1-32 Jointly efficient encoding and decoding in neural populations
by Simone Blanco Malerba & Aurora Micheli & Michael Woodford & Rava Azeredo da Silveira - 1-36 NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies
by Thomas Couppey & Louis Regnacq & Roland Giraud & Olivier Romain & Yannick Bornat & Florian Kolbl - 1-37 An integrative approach to protein sequence design through multiobjective optimization
by Lu Hong & Tanja Kortemme - 1-37 Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis
by Harry Saxton & Xu Xu & Torsten Schenkel & Richard H Clayton & Ian Halliday
June 2024, Volume 20, Issue 6
- 1-9 Ten simple rules for implementing electronic lab notebooks (ELNs)
by Justine Vandendorpe & Beatrix Adam & Jeanne Wilbrandt & Birte Lindstädt & Konrad U Förstner - 1-9 Ten simple rules for computational biologists collaborating with wet lab researchers
by Mark D Robinson & Peiying Cai & Martin Emons & Reto Gerber & Pierre-Luc Germain & Samuel Gunz & Siyuan Luo & Giulia Moro & Emanuel Sonder & Anthony Sonrel & Jiayi Wang & David Wissel & Izaskun Mallona - 1-10 Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club
by Roberto Efraín Díaz & Stephanie A Wankowicz - 1-16 Knotted artifacts in predicted 3D RNA structures
by Bartosz A Gren & Maciej Antczak & Tomasz Zok & Joanna I Sulkowska & Marta Szachniuk - 1-16 ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning
by Youcheng Li & Leann Lac & Qian Liu & Pingzhao Hu - 1-16 Older adults select different but not simpler strategies than younger adults in risky choice
by Florian Bolenz & Thorsten Pachur - 1-17 Missing data in amortized simulation-based neural posterior estimation
by Zijian Wang & Jan Hasenauer & Yannik Schälte - 1-19 mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics
by Kris Sankaran & Pratheepa Jeganathan - 1-20 Infection patterns in simple and complex contagion processes on networks
by Diego Andrés Contreras & Giulia Cencetti & Alain Barrat - 1-20 Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways
by Leopold Zehetner & Diana Széliová & Barbara Kraus & Juan A Hernandez Bort & Jürgen Zanghellini - 1-21 Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data
by Tina Yao & Endrit Pajaziti & Michael Quail & Silvia Schievano & Jennifer Steeden & Vivek Muthurangu - 1-21 GEM-based computational modeling for exploring metabolic interactions in a microbial community
by Soraya Mirzaei & Mojtaba Tefagh - 1-22 Beyond homogeneity: Assessing the validity of the Michaelis–Menten rate law in spatially heterogeneous environments
by Seolah Shin & Seok Joo Chae & Seunggyu Lee & Jae Kyoung Kim - 1-22 Zero-shot denoising of microscopy images recorded at high-resolution limits
by Sebastian Salwig & Jakob Drefs & Jörg Lücke - 1-23 An algorithm to build synthetic temporal contact networks based on close-proximity interactions data
by Audrey Duval & Quentin J Leclerc & Didier Guillemot & Laura Temime & Lulla Opatowski - 1-23 Machine learning prediction of malaria vaccine efficacy based on antibody profiles
by Jacqueline Wistuba-Hamprecht & Bernhard Reuter & Rolf Fendel & Stephen L Hoffman & Joseph J Campo & Philip L Felgner & Peter G Kremsner & Benjamin Mordmüller & Nico Pfeifer - 1-24 Strong association between genomic 3D structure and CRISPR cleavage efficiency
by Shaked Bergman & Tamir Tuller - 1-26 Threshold-awareness in adaptive cancer therapy
by MingYi Wang & Jacob G Scott & Alexander Vladimirsky