Article
Biochemistry & Molecular Biology
Vildan Bozok Cetintas, Zekeriya Duzgun, Taner Akalin, Erkin Ozgiray, Eda Dogan, Zafer Yildirim, Nevhis Akinturk, Huseyin Biceroglu, Yesim Ertan, Buket Kosova
Summary: This study investigated the stability, structural and functional effects, and pathogenicity of 12 missense PTEN mutations in glioblastoma patients. Computational tools and molecular dynamic simulation revealed deleterious effects, with some mutations showing significant protein stability decrease.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Education, Scientific Disciplines
Tingzhe Sun, Zhengjun Zhao
Summary: Teaching the contents of signaling in molecular biology is challenging due to the lack of mechanistic details in textbooks. This study introduces MATLAB simulations to interpret the dynamic mechanisms of key signaling pathways, improving students' learning experience. The use of MATLAB simulations engages students and reinforces their understanding of signaling pathways.
EDUCATION FOR CHEMICAL ENGINEERS
(2023)
Article
Biochemical Research Methods
Nafiseh Sedaghat, Tamon Stephen, Leonid Chindelevitch
Summary: This article addresses the problem of computing EFMs and MCSs in metabolic networks. It proposes a method based on monotone Boolean functions and presents six techniques to optimize the computation process. The proposed improvements significantly reduce the running time, as demonstrated by applying them to various models.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Automation & Control Systems
Denis Lebedev, Kostas Margellos, Paul Goulart
Summary: This study addresses the revenue management problem of finding profit-maximizing prices for delivery time slots in attended home delivery. By analyzing three approximate DP algorithms, it is found that the gradient-bounded DP algorithm outperforms others in terms of computation time and profit-generation capabilities. Real-world data is used for analysis and stress-testing the robustness of pricing policies to errors in model parameter estimates.
IEEE TRANSACTIONS ON CONTROL SYSTEMS TECHNOLOGY
(2022)
Article
Engineering, Civil
Mehrzad Mehrabipour, Ali Hajbabaie
Summary: This study proposes a distributed gradient-based approach to solve system optimal dynamic traffic assignment. The algorithm decomposes the problem into local sub-problems and achieves consensus on the values of common decision variables through communication. It finds high quality solutions with a finite number of iterations.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2022)
Article
Computer Science, Artificial Intelligence
Xuanming Liu, Tingjian Ge, Yinghui Wu
Summary: This paper addresses the problem of finding densest lasting subgraphs in large dynamic graphs, considering the time duration of the subgraph pattern. A framework called EMU is proposed, which extends the conventional EM approach by optimizing user-defined utility functions. The validation and comparison of EMU algorithms for densest lasting subgraph problem using real-world data show the effectiveness and efficiency of the proposed techniques.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2022)
Article
Immunology
David Brown, Michael Altermatt, Tatyana Dobreva, Sisi Chen, Alexander Wang, Matt Thomson, Viviana Gradinaru
Summary: Engineered variants of recombinant adeno-associated viruses are rapidly being developed to meet the demand for gene therapy delivery vehicles with specific cell-type and tissue tropisms. An experimental and computational single-cell RNA sequencing pipeline has been developed to characterize barcoded rAAV pools at high resolution, revealing both confirmed and unidentified AAV capsid targeting biases.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Automation & Control Systems
Benjamin Flamm, Annika Eichler, Joseph Warrington, John Lygeros
Summary: The proposed method presents an approximate solution for solving nonlinear control problems by preserving part of the nonlinear model and using a linear relaxation model. A Benders decomposition-based solution algorithm is used to iterate between solving the nonlinear and linear parts, showing practicality and convergence after a finite number of iterations. The approach is more practical than conventional dynamic programming and a multi-cell McCormick envelope approximation, demonstrating near-optimal solutions in a shrinking horizon setting.
IEEE TRANSACTIONS ON CONTROL SYSTEMS TECHNOLOGY
(2021)
Article
Automation & Control Systems
Guido Carnevale, Andrea Camisa, Giuseppe Notarstefano
Summary: This article focuses on studying an online version of the emerging distributed constrained aggregative optimization framework for applications in cooperative robotics. Inspired by an existing scheme, a distributed algorithm named projected aggregative tracking is proposed to solve the online optimization problem. The article proves the bounded dynamic regret and linear convergence rate in the static case. Numerical examples also demonstrate the effectiveness of the approach in a robotic surveillance scenario.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2023)
Article
Biochemistry & Molecular Biology
Shahzaib Ahamad, Kanipakam Hema, Vijay Kumar, Dinesh Gupta
Summary: The study revealed that the R142Q mutation on TTBK1 leads to structural instability, disrupting its biological functions, and could be used as future diagnostic markers in treating Alzheimer's disease.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2021)
Article
Management
Qingyin Ma, John Stachurski
Summary: This paper systematically investigates the idea of transforming the Bellman equation to address challenging dynamic programming problems, with a focus on improving computational efficiency. It provides a characterization of valid transformations of the Bellman equation and examines solutions of the transformed equations and corresponding algorithms. The research demonstrates new approaches to various dynamic programming problems and shows increased computational efficiency through time complexity arguments and numerical experiments.
OPERATIONS RESEARCH
(2021)
Article
Economics
Christopher Ferrall
Summary: This paper discusses the methods of designing, solving, and estimating dynamic programming models using the open source package niqlow. It explains why such a package has not appeared earlier and the importance of the object-oriented approach followed by niqlow. An example is provided to illustrate the process of expanding models and applying different solution methods. The niqlow approach offers a new way to organize empirical DP literature, making it more accessible to new researchers. Features for efficiency and customization are also highlighted.
COMPUTATIONAL ECONOMICS
(2023)
Article
Biochemistry & Molecular Biology
Tzahi Gabzi, Yitzhak Pilpel, Tamar Friedlander
Summary: This article investigates the fitness landscape of a yeast tRNA gene and finds that the wild type allele is sub-optimal. It also rules out the possibility that the wild type is the fittest on average or located on a local fitness maximum under four different conditions. The study further reveals that the wild type is mutationally robust, while more fit variants are typically mutationally fragile. Similar observations have been made in viral genomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Automation & Control Systems
Mohamad Amin Sharifi Kolarijani, Peyman Mohajerin Esfahani
Summary: The study proposes two novel numerical schemes for the approximate implementation of dynamic programming operation by discretizing state and input spaces, solving the dual problem corresponding to the DP operation. The proposed approach can significantly reduce the time complexity of the DP operation for specific problems with separable data in state and input variables, leading to an algorithmic transformation of minimization in DP operation to addition via discrete conjugation.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2023)
Article
Automation & Control Systems
Paul Nathaniel Beuchat, Joseph Warrington, John Lygeros
Summary: The article introduces an approximate dynamic programming approach to compute lower bounds on the optimal value function in a discrete time, continuous space, infinite horizon setting. By using Bellman inequality, the approach iteratively constructs a family of lower bounding approximate value functions and proposes a gradient ascent algorithm to find stationary points. Numerical examples demonstrate that the algorithm computes tighter suboptimality bounds with comparable computation time compared to existing approaches.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2022)
Article
Multidisciplinary Sciences
Shin-ya Takemura, C. Shan Xu, Zhiyuan Lu, Patricia K. Rivlin, Toufiq Parag, Donald J. Olbris, Stephen Plaza, Ting Zhao, William T. Katz, Lowell Umayam, Charlotte Weaver, Harald F. Hess, Jane Anne Horne, Juan Nunez-Iglesias, Roxanne Aniceto, Lei-Ann Chang, Shirley Lauchie, Ashley Nasca, Omotara Ogundeyi, Christopher Sigmund, Satoko Takemura, Julie Tran, Carlie Langille, Kelsey Le Lacheur, Sari McLin, Aya Shinomiya, Dmitri B. Chklovskii, Ian A. Meinertzhagen, Louis K. Scheffer
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Biochemistry & Molecular Biology
Foong Lyn Chan, Benjamin Vinod, Karel Novy, Ralf B. Schittenhelm, Cheng Huang, Maheshi Udugama, Juan Nunez-Iglesias, Jane I. Lin, Linda Hii, Julie Chan, Hilda A. Pickett, Roger J. Daly, Lee H. Wong
NUCLEIC ACIDS RESEARCH
(2017)
Article
Multidisciplinary Sciences
Juan Nunez-Iglesias, Adam J. Blanch, Oliver Looker, Matthew W. Dixon, Leann Tilley
Article
Computer Science, Artificial Intelligence
Alexander Herzog, Peter Pastor, Mrinal Kalakrishnan, Ludovic Righetti, Jeannette Bohg, Tamim Asfour, Stefan Schaal
Article
Computer Science, Artificial Intelligence
Ludovic Righetti, Mrinal Kalakrishnan, Peter Pastor, Jonathan Binney, Jonathan Kelly, Randolph C. Voorhies, Gaurav S. Sukhatme, Stefan Schaal
Article
Mathematical & Computational Biology
Juan Nunez-Iglesias, Ryan Kennedy, Stephen M. Plaza, Anirban Chakraborty, William T. Katz
FRONTIERS IN NEUROINFORMATICS
(2014)
Article
Multidisciplinary Sciences
Stefan van der Walt, Johannes L. Schonberger, Juan Nunez-Iglesias, Francois Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu
Article
Microbiology
Oliver Looker, Adam J. Blanch, Boyin Liu, Juan Nunez-Iglesias, Paul J. McMillan, Leann Tilley, Matthew W. A. Dixon
Article
Biochemical Research Methods
Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, Stefan J. van der Walt, Matthew Brett, Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson, Eric Jones, Robert Kern, Eric Larson, C. J. Carey, Ilhan Polat, Yu Feng, Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman, Ian Henriksen, E. A. Quintero, Charles R. Harris, Anne M. Archibald, Antonio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt
Article
Robotics
Julian Ibarz, Jie Tan, Chelsea Finn, Mrinal Kalakrishnan, Peter Pastor, Sergey Levine
Summary: Deep reinforcement learning has shown promise in enabling physical robots to learn complex skills in the real world, which presents numerous challenges in perception and movement. Real-world robotics provides a unique domain for evaluating deep RL algorithms, addressing challenges that are often overlooked in mainstream RL research.
INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH
(2021)
Article
Materials Science, Multidisciplinary
Mia Maric, Rhys Thomas, Juan Nunez-Iglesias, Michael Atkinson, Johannes Bertsch, Philipp Frankel, Christopher Race, Pierre Barberis, Florent Bourlier, Michael Preuss, Pratheek Shanthraj
Summary: In this study, an open-source software package called HAPPy is introduced for the analysis of hydride networks in zirconium alloys. It can calculate the radial hydride fraction and mean hydride length, and characterize the connectivity of the microstructure. The proposed methodology is validated and shown to be robust, highlighting the importance of standardized image analysis workflows.
JOURNAL OF NUCLEAR MATERIALS
(2022)
Article
Biology
Alex Reichenbach, Rachel E. Clarke, Romana Stark, Sarah Haas Lockie, Mathieu Mequinion, Harry Dempsey, Sasha Rawlinson, Felicia Reed, Tara Sepehrizadeh, Michael DeVeer, Astrid C. Munder, Juan Nunez-Iglesias, David C. Spanswick, Randall Mynatt, Alexxai Kravitz, Christopher Dayas, Robyn Brown, Zane B. Andrews
Summary: This study found that metabolic sensing in AgRP neurons is crucial for regulating motivation for food reward by modulating dopamine release in the striatum.
Article
Biochemistry & Molecular Biology
Adam J. Blanch, Juan Nunez-Iglesias, Arman Namvar, Sebastien Menant, Oliver Looker, Vijay Rajagopal, Wai-Hong Tham, Leann Tilley, Matthew W. A. Dixon
Summary: The study demonstrates that as reticulocytes mature into RBCs, there is a decrease in cell surface area and an increase in the density of the spectrin-actin network, along with slight increases in inter-junctional distance and junctional density. Additionally, the edge region of mature RBCs contains more junctional complexes compared to the dimple region, supported by a 2% increase in band 4.1 density.
JOURNAL OF STRUCTURAL BIOLOGY-X
(2022)
Proceedings Paper
Computer Science, Theory & Methods
Larissa Heinrich, Jan Funke, Constantin Pape, Juan Nunez-Iglesias, Stephan Saalfeld
MEDICAL IMAGE COMPUTING AND COMPUTER ASSISTED INTERVENTION - MICCAI 2018, PT II
(2018)
Article
Microscopy
Emmanuelle Gouillart, Juan Nunez-Iglesias, Stefan van der Walt
ADVANCED STRUCTURAL AND CHEMICAL IMAGING
(2016)