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Nature Computational Science, Volume 2
Volume 2, Number 1, 2022
- A look back at 2021. 1
- Fernando Chirigati:
Machine learning to guide mathematicians. 2 - Jie Pan:
Mining literature for perovskite solar cells. 3 - Kaitlin McCardle:
Predicting oxidation states iteratively. 4 - Ananya Rastogi:
Effect of spatial sampling on phylogeography. 5 - Mark E. Tuckerman
:
The curse of dimensionality loses its power. 6-7 - Daniel Osório
Interpretable multi-modal data integration. 8-9 - Catherine D. Schuman
Opportunities for neuromorphic computing algorithms and applications. 10-19 - Dongdong Wang, Yanze Wang
Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics. 20-29 - Nikita Gourianov
A quantum-inspired approach to exploit turbulence structures. 30-37 - Nam D. Nguyen
A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data. 38-46 - Lukas P. A. Arts
The fast continuous wavelet transformation (fCWT) for real-time, high-quality, noise-resistant time-frequency analysis. 47-58 - Phillip J. Brown, J. Edward F. Green
Publisher Correction: A rigid body framework for multicellular modeling. 59
Volume 2, Number 2, 2022
- Cover runners-up of 2021. 61
- Fernando Chirigati:
Crypto and technology for the people. 62-63 - Jie Pan:
Reinstating functionality of complex systems. 64 - Ananya Rastogi:
Modeling the building blocks of life. 65 - Kaitlin McCardle
Theory and experimentation to assess reactivity. 66 - Fernando Chirigati:
Co-occurrence and similarity revisited. 67 - Koji Fukagata
Towards quantum computing of turbulence. 68-69 - Madhur Srivastava
Revisiting signal analysis in the big data era. 70-71 - Ata Kalirad, Ralf J. Sommer
The art of mechanistic modeling in biology. 72-73 - Jean-Baptiste Masson
Counting biomolecules with Bayesian inference. 74-75 - Cartographs enable interpretation of complex network visualizations. 76-77
- Saurabh Kalikar, Chirag Jain, Md. Vasimuddin, Sanchit Misra
Accelerating minimap2 for long-read sequencing applications on modern CPUs. 78-83 - Christiane V. R. Hütter
Network cartographs for interpretable visualizations. 84-89 - Andrea Scharf
A laboratory and simulation platform to integrate individual life history traits and population dynamics. 90-101 - J. Shepard Bryan IV, Ioannis Sgouralis
Diffraction-limited molecular cluster quantification with Bayesian nonparametrics. 102-111 - Rasha Atwi
An automated framework for high-throughput predictions of NMR chemical shifts within liquid solutions. 112-122 - Pranesh Padmanabhan
Modeling how antibody responses may determine the efficacy of COVID-19 vaccines. 123-131 - Hao Hou, Brent S. Pedersen, Aaron R. Quinlan
Author Correction: Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools. 132
Volume 2, Number 3, 2022
- Acing the peer review process. 133
- Kaitlin McCardle
Computational chemistry for all. 134-136 - Fernando Chirigati:
Cultural diversity through the lenses of ecology. 137 - Kaitlin McCardle
Theoretical insights into single-atom catalysts. 138 - Jie Pan:
Machine learning for spectral properties. 139 - Joshua T. Schiffer
Correlates of protection via modeling. 140-141 - Guillermo E. Parada, Martin Hemberg
Bridge over troubled transcripts. 142-143 - Vibhuti Gupta
Post-transplant dynamic risk prediction. 144-145 - Towards accurate predictions of NMR chemical shifts in liquid solutions. 146-147
- Qimin Zhang
Accurate assembly of multi-end RNA-seq data with Scallop2. 148-152 - Xueou Liu
Dynamic forecasting of severe acute graft-versus-host disease after transplantation. 153-159 - Ting-Ting Gao
Autonomous inference of complex network dynamics from incomplete and noisy data. 160-168 - Yingheng Tang, Jichao Fan, Xinwei Li, Jianzhu Ma
Physics-informed recurrent neural network for time dynamics in optical resonances. 169-178 - Ian T. Hoffecker
Stochastic modeling of antibody binding predicts programmable migration on antigen patterns. 179-192 - Roxana Zeraati
A flexible Bayesian framework for unbiased estimation of timescales. 193-204 - Catherine D. Schuman
Publisher Correction: Opportunities for neuromorphic computing algorithms and applications. 205
Volume 2, Number 4, 2022
- And the Turing Award goes to... 207
- Theresa Stadler, Carmela Troncoso:
Why the search for a privacy-preserving data sharing mechanism is failing. 208-210 - Fernando Chirigati:
A key player in high-performance computing. 211-212 - Jie Pan:
Quantum Monte Carlo guided by quantum computing. 213 - Kaitlin McCardle
Making light work of hydride transfer. 214 - Ananya Rastogi:
Modeling plant circadian clocks. 215 - Fernando Chirigati:
Gauging urban development with neural networks. 216 - Aditya Goenka, Lin Liu
Smart lockdowns to control COVID-19. 217-218 - Manish K. Gupta
The yin-yang codec for archival DNA storage. 219-220 - Antibodies as programmable, bipedal walkers. 221-222
- David J. Haw
Optimizing social and economic activity while containing SARS-CoV-2 transmission using DAEDALUS. 223-233 - Zhi Ping
Towards practical and robust DNA-based data archiving using the yin-yang codec system. 234-242 - Minjeong Cha
Unifying structural descriptors for biological and bioinspired nanoscale complexes. 243-252 - Igor Muniz Soares
Improving lab-of-origin prediction of genetically engineered plasmids via deep metric learning. 253-264 - Xiaogen Zhou
Progressive assembly of multi-domain protein structures from cryo-EM density maps. 265-275
Volume 2, Number 5, 2022
- Cracking the code review process. 277
- Thilo Rieg
From mechanistic insight towards clinical implementation using normative modeling. 278-280 - Fernando Chirigati:
Fighting hate speech and misinformation online. 281-283 - Kaitlin McCardle
Neural-network wavefunctions. 284 - Jie Pan:
Expanding the capability of autonomous microscopy. 285 - Ananya Rastogi:
Impact of aspirin on cancer incidence. 286 - Fernando Chirigati:
AI for resource-constrained medical fields. 287 - Xi-Nian Zuo
Efficiently pruning brain connectomes. 288-289 - Leo Lahti
Enhancing biomarkers with co-abundance. 290-291 - Huan Tran
Accelerating quantum molecular simulations. 292-293 - Universal descriptors to predict interactions of inorganic nanoparticles with proteins. 294-295
- Using metric learning to identify the lab-of-origin of engineered DNA. 296-297
- Varsha Sreenivasan
GPU-accelerated connectome discovery at scale. 298-306 - Liwen Xiao
Large-scale microbiome data integration enables robust biomarker identification. 307-316 - Jia Zhao, Gefei Wang, Jingsi Ming, Zhixiang Lin, Yang Wang, Snigdha Agarwal, Aditi Agrawal, Ahmad Al-Moujahed, Alina Alam, Megan A. Albertelli, Paul Allegakoen, Thomas Ambrosi, Jane Antony, Steven Artandi, Fabienne Aujard, Kyle Awayan, Ankit Baghel, Isaac Bakerman, Trygve E. Bakken, Jalal Baruni, Philip Beachy, Biter Bilen, Olga B. Botvinnik, Scott D. Boyd, Deviana Burhan, Kerriann M. Casey, Charles Chan, Charles A. Chang, Stephen Chang, Ming Chen, Michael F. Clarke, Sheela Crasta, Rebecca Culver, Jessica D'Addabbo, Spyros Darmanis, Roozbeh Dehghannasiri, Song-Lin Ding, Connor V. Duffy, Jacques Epelbaum, F. Hernán Espinoza, Camille Ezran, Jean Farup, James E. Ferrell Jr, Hannah K. Frank, Margaret Fuller, Astrid Gillich, Elias Godoy, Dita Gratzinger, Lisbeth A. Guethlein, Yan Hang, Kazuteru Hasegawa, Rebecca D. Hodge, Malachia Hoover, Franklin W. Huang, Kerwyn Casey Huang, Shelly Huynh, Taichi Isobe, Carly Israel, Sori Jang, Qiuyu Jing, Robert C. Jones, Jengmin Kang, Caitlin J. Karanewsky, Jim Karkanias, Justus Kebschull, Aaron Kershner, Lily Kim, Seung K. Kim, E. Christopher Kirk, Winston Koh, Silvana Konermann, William Kong, Mark A. Krasnow, Christin Kuo, Corinne Lautier, Song Eun Lee, Ed S. Lein, Rebecca Lewis, Peng Li, Shengda Lin, Shixuan Liu, Yin Liu, Gabriel Loeb, Jonathan Z. Long, Wan-Jin Lu, Katherine Lucot, Liqun Luo, Aaron McGeever, Ross Metzger, Jingsi Ming, Thomas J. Montine, Antoine de Morree, Maurizio Morri, Karim Mrouj, Shravani Mukherjee, Ahmad Nabhan, Saba Nafees, Norma Neff, Patrick Neuhöfer, Patricia Nguyen, Jennifer Okamoto, Julia Eve Olivieri, Youcef Ouadah, Honor Paine, Peter Parham, Jozeph L. Pendleton, Lolita Penland, Martine Perret, Angela Oliveira Pisco, Zhen Qi, Stephen R. Quake, Ute Radespiel, Thomas A. Rando, Hajanirina Noëline Ravelonjanahary, Andriamahery Razafindrakoto, Julia Salzman, Nicholas Schaum, Robert Schopler, Bronwyn Scott, Liza Shapiro, Hosu Sin, Rahul Sinha, Rene Sit, Geoff Stanley, Lubert Stryer, Varun Ramanan Subramaniam, Aditi Swarup, Weilun Tan, Alexander Tarashansky, Aris Taychameekiatchai, Jérémy Terrien, Kyle J. Travaglini, Andoni Urtasun, Sivakamasundari, Avin Veerakumar, Venkata Naga Pranathi Vemuri, Jean-Michel Verdier, Iwijn De Vlaminck, Douglas Vollrath, Bo Wang, Bruce Wang, Gefei Wang, Michael F. Z. Wang, Sheng Wang, James Webber, Hannah Weinstein, Irving L. Weissman, Amanda L. Wiggenhorn, Cathy V. Williams, Patricia Wright, Albert Y. Wu, Angela Ruohao Wu, Tony Wyss-Coray, Bao Xiang, Jia Yan, Can Yang, Jinxurong Yang, Anne D. Yoder, Brian Yu, Andrea R. Yung, Yue Zhang, Jia Zhao, Zicheng Zhao:
Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets. 317-330 - Michael Scherbela
Solving the electronic Schrödinger equation for multiple nuclear geometries with weight-sharing deep neural networks. 331-341 - Xueou Liu
Author Correction: Dynamic forecasting of severe acute graft-versus- host disease after transplantation. 342 - Ting-Ting Gao
Publisher Correction: Autonomous inference of complex network dynamics from incomplete and noisy data. 343
Volume 2, Number 6, 2022
- Enough is enough. 345
- Anirudh S. Chellappa, Madhulika Sahoo
Gender inequality infiltrates the in silico modeling world. 346-347 - Ananya Rastogi:
Digging deeper into the gut microbiome. 348-349 - Kaitlin McCardle
Theoretical progress toward sustainable batteries. 350 - Jie Pan:
Stabilizing quantum GANs. 351 - Ananya Rastogi:
Cellular scale modeling of cytoskeletal assemblies. 352 - Ananya Rastogi:
Neuromechanical modeling of adult fly. 353 - Xin Zhou
Graphing cell relations in spatial transcriptomics. 354-355 - Majid Khabbazian, Hosna Jabbari
AI-powered aptamer generation. 356-357 - Ricardo Vinuesa, Steven L. Brunton
Enhancing computational fluid dynamics with machine learning. 358-366 - He Li
Deep-learning density functional theory Hamiltonian for efficient ab initio electronic-structure calculation. 367-377 - Natsuki Iwano, Tatsuo Adachi, Kazuteru Aoki, Yoshikazu Nakamura, Michiaki Hamada
Generative aptamer discovery using RaptGen. 378-386 - Xiaoqiao Chen
Minimal gene set discovery in single-cell mRNA-seq datasets with ActiveSVM. 387-398 - Jiachen Li
Cell clustering for spatial transcriptomics data with graph neural networks. 399-408
Volume 2, Number 7, 2022
- Mathematics, the queen of sciences. 409
- Jie Pan:
Quantum experiment design via interpretable DL. 410 - Kaitlin McCardle
A move in the light direction. 411 - Fernando Chirigati:
Effects of mutations on SARS-CoV-2 fitness. 412 - Ananya Rastogi:
Modeling and combating misinformation spread. 413 - Boris Kramer
Learning state variables for physical systems. 414-415 - Jue Wang
Protein sequence design by deep learning. 416-417 - Improving the efficiency of ab initio electronic-structure calculations by deep learning. 418-419
- ActiveSVM selects minimal gene sets from gene expression data. 420-421
- Graph embedding enables cell identification from spatial transcripts. 422-423
- Christian Vorwerk
Quantum embedding theories to simulate condensed systems on quantum computers. 424-432 - Boyuan Chen
Automated discovery of fundamental variables hidden in experimental data. 433-442 - Wenbin Xu
Predicting binding motifs of complex adsorbates using machine learning with a physics-inspired graph representation. 443-450 - Yufeng Liu
Rotamer-free protein sequence design based on deep learning and self-consistency. 451-462
Volume 2, Number 8, 2022
- Turing patterns, 70 years later. 463-464
- Raymond R. Tan
Computing optimal carbon dioxide removal portfolios. 465-466 - Fernando Chirigati:
Bringing the pulsatile release system to light. 467 - Jie Pan:
Improving segregation prediction. 468 - Kaitlin McCardle
The value of quantum effects in reaction rates. 469 - Ananya Rastogi:
Network science to study the origins of life. 470 - John Meluso
Model supports storied social network theory. 471-472 - Stefano Di Talia
Geometry and symmetry-breaking in cell polarity. 473-474 - Stefano Recanatesi
Untangling network information flow. 475-476 - Machine learning reveals how complex molecules bind to catalyst surfaces. 477-478
- Elena Cuoco
Computational challenges for multimodal astrophysics. 479-485 - Shanshan Wang, Menglin Huang
Effective lifetime of non-equilibrium carriers in semiconductors from non-adiabatic molecular dynamics simulations. 486-493 - Daniel Carmody
The effect of co-location on human communication networks. 494-503 - Pearson W. Miller
Forced and spontaneous symmetry breaking in cell polarization. 504-511 - Evren Gokcen
Disentangling the flow of signals between populations of neurons. 512-525 - Yufeng Liu
Publisher Correction: Rotamer-free protein sequence design based on deep learning and self-consistency. 526
Volume 2, Number 9, 2022
- A computational perspective on the Nobel Prize. 527-528
- Alex Zunger:
Bridging the gap between density functional theory and quantum materials. 529-532 - Stephen Shang, Xiangmeng S. Cai
Computation empowers CRISPR discovery and technology. 533-535 - Mojib Latif:
The roadmap of climate models. 536-538 - Kaitlin McCardle
A collective effort for building DFT. 539-541 - Kaitlin McCardle
Curiosity-driven method development. 542-544 - Fernando Chirigati:
The Universe's expansion in the eyes of computers. 545-547 - Kaitlin McCardle
Quantum mechanics guided by simplicity. 548-549 - Jie Pan:
Making complex systems computable. 550-552 - Fernando Chirigati:
How to change harmful beliefs. 553 - Jie Pan:
Mathematically probing membrane fluctuations. 554 - Iryna Omelchenko:
Controlling patterns of synchrony. 555 - Kaitlin McCardle
Accelerated mass spectra analysis. 556 - Christian Kuttner
Escaping the local catalytic activity space. 557 - Ananya Rastogi:
DNA clustering made more efficient. 558 - Lauren McGough
Getting the most out of noisy surveillance data. 559-560 - Kathy Leung
Mixing patterns and the spread of pandemics. 561-562 - Calculating effective carrier lifetimes in semiconductor crystals under realistic conditions. 563-564
- Machine learning approach finds nonlinear patterns of neurodegenerative disease progression. 565-566
- Marco Cerezo
Challenges and opportunities in quantum machine learning. 567-576 - Can Kizilkale, Farid Rashidi Mehrabadi
Fast intratumor heterogeneity inference from single-cell sequencing data. 577-583 - Kris V. Parag
Quantifying the information in noisy epidemic curves. 584-594 - Qingtao Cao, Babak Heydari
Micro-level social structures and the success of COVID-19 national policies. 595-604 - Divya Ramamoorthy
Identifying patterns in amyotrophic lateral sclerosis progression from sparse longitudinal data. 605-616
Volume 2, Number 10, 2022
- Dos and don'ts in a cover letter. 617
- Harry Geddes:
Rational design of mechanical metamaterials. 618 - Jie Pan:
Machine learning proved efficient. 619 - Kaitlin McCardle
Classical-quantum advantage boundary for enzymes. 620 - Iryna Omelchenko:
Keeping the power grid stable. 621 - Fernando Chirigati:
Nowcasting food security. 622 - Ananya Rastogi:
Making sense of bacterial toxin evolution. 623 - Francesco Dal Corso
Bio-inspired adaptive grasper by chiral wrinkling. 624-625 - Paul Romatschke
Simulating fluids, gases and everything in between. 626-627 - Maurice J. Chacron
The role of ADM in brain function. 628-629 - Designing efficient urban bike path networks that meet the needs of cyclists. 630-631
- Fan Xu
Chiral topographic instability in shrinking spheres. 632-640 - Victor E. Ambrus
Fast kinetic simulator for relativistic matter. 641-654 - Christoph Steinacker
Demand-driven design of bicycle infrastructure networks for improved urban bikeability. 655-664 - Afroditi Talidou
Homeostatic coordination and up-regulation of neural activity by activity-dependent myelination. 665-676 - Juan Li
Evolution of cooperation through cumulative reciprocity. 677-686
Volume 2, Number 11, 2022
- Pioneering quantum information science. 687-688
- Tammie R. Nelson, Sebastian Fernandez Alberti
Modeling excited-state molecular dynamics beyond the Born-Oppenheimer regime. 689-692 - Jie Pan:
Active learning for alloy design. 693 - Sumin Jin:
Making heat capacity prediction more reliable. 694 - Kaitlin McCardle
On the cost-accuracy trade-off in electrolytes. 695 - Iryna Omelchenko:
Reducing the network dimensionality. 696 - Fernando Chirigati:
Computational models of social learning. 697 - Ananya Rastogi:
Learning about few-shot concept learning. 698 - Leonardo Banchi
Robust quantum classifiers via NISQ adversarial learning. 699-700 - Katrin Erk
Understanding the combined meaning of words. 701-702 - Expanding materials science with universal many-body graph neural networks. 703-704
- Predicting the shape of crystals with 'unknowable' surface energies. 705-706
- Single-cell-specific drug activities are revealed by a tensor imputation algorithm. 707-708
- Cumulative reciprocity can sustain cooperation in repeated social interactions. 709-710
- Wenhui Ren, Weikang Li
Experimental quantum adversarial learning with programmable superconducting qubits. 711-717 - Chi Chen
A universal graph deep learning interatomic potential for the periodic table. 718-728 - Luqing Wang, Sharmila N. Shirodkar, Zhuhua Zhang
Defining shapes of two-dimensional crystals with undefinable edge energies. 729-735 - Siyuan Chen
A structural optimization algorithm with stochastic forces and stresses. 736-744 - Mariya Toneva
Combining computational controls with natural text reveals aspects of meaning composition. 745-757 - Michio Iwata
Pathway trajectory analysis with tensor imputation reveals drug-induced single-cell transcriptomic landscape. 758-770 - Pearson W. Miller
Author Correction: Forced and spontaneous symmetry breaking in cell polarization. 771 - Yuan Ping
Author Correction: Computational design of quantum defects in two-dimensional materials. 772
Volume 2, Number 12, 2022
- Seamless sharing and peer review of code. 773
- Iryna Omelchenko:
Artificial agents that negotiate and reach agreements. 774 - Yang Shen
Predicting protein structure from single sequences. 775-776 - Haitao Liu
Efficient simulators for multi-source nanophotonics. 777-778 - Zachary del Rosario
Synthesizing domain science with machine learning. 779-780 - Pieter Meysman
Simulations that capture antigen-antibody complexity. 781-782 - The meaning emerging from combining words can be detected in space but not time. 783-784
- Joseph D. Butner
Mathematical modeling of cancer immunotherapy for personalized clinical translation. 785-796 - Zhenxian Zheng
Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. 797-803 - Wenkai Wang
Single-sequence protein structure prediction using supervised transformer protein language models. 804-814 - Ho-Chun Lin
Fast multi-source nanophotonic simulations using augmented partial factorization. 815-822 - Ethan Pickering
Discovering and forecasting extreme events via active learning in neural operators. 823-833 - Joseph Bakarji, Jared Callaham, Steven L. Brunton, J. Nathan Kutz:
Dimensionally consistent learning with Buckingham Pi. 834-844 - Philippe A. Robert
Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction. 845-865 - Luqing Wang, Sharmila N. Shirodkar, Zhuhua Zhang
Publisher Correction: Defining shapes of two-dimensional crystals with undefinable edge energies. 866
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