Article
Computer Science, Interdisciplinary Applications
Changjie Chen, Jasmeet Judge, David Hulse
Summary: This paper introduces an open-source tool called PyLUSAT for conducting land use suitability analysis. The tool was evaluated against ArcMap and showed higher efficiency in terms of speed and accuracy. Additionally, PyLUSAT is compatible with multiple platforms, highly extensible, and supports parallel computing, automation, and customization.
ENVIRONMENTAL MODELLING & SOFTWARE
(2022)
Article
Meteorology & Atmospheric Sciences
Louis W. Uccellini, Richard W. Spinrad, Dorothy M. Koch, Craig N. McLean, William M. Lapenta
Summary: NOAA has partnered with the Weather Enterprise to launch the Earth Prediction Innovation Center (EPIC) in order to accelerate improvements to the nation's forecast system. EPIC utilizes a community-driven framework to transform the U.S. national forecast systems into a more powerful and effective Earth prediction system.
BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY
(2022)
Article
Chemistry, Physical
Anupam Anand Ojha, Saumya Thakur, Surl-Hee Ahn, Rommie E. Amaro
Summary: Recent advances in computational power and algorithms have extended the time scales of molecular dynamics (MD) simulations. However, MD simulations still face limitations in observing conformational transitions associated with biomolecular processes. To address this challenge, enhanced sampling techniques such as the weighted ensemble (WE) method have been developed to estimate kinetic rate constants by sampling transitions between metastable states using weighted trajectories. In this study, deep-learned kinetic modeling approaches are introduced to extract statistically relevant information from short MD trajectories and provide a well-sampled initial state distribution for WE simulations. This hybrid approach overcomes statistical bias and produces a refined free energy landscape closer to the steady state, enabling efficient sampling of kinetic properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemical Research Methods
Eli J. Larson, Melissa R. Pergande, Michelle E. Moss, Kalina J. Rossler, R. Kent Wenger, Boris Krichel, Harini Josyer, Jake A. Melby, David S. Roberts, Kyndalanne Pike, Zhuoxin Shi, Hsin-Ju Chan, Bridget Knight, Holden T. Rogers, Kyle A. Brown, Irene M. Ong, Kyowon Jeong, Michael T. Marty, Sean J. McIlwain, Ying Ge
Summary: MASH Native is a software package that integrates native mass spectrometry (nMS) with top-down proteomics (TDP), providing comprehensive analysis of protein complexes and proteoform identification and characterization. It supports various data formats and offers multiple options for deconvolution, database searching, and spectral summing, serving as a one-stop shop for characterizing both native protein complexes and proteoforms.
Article
Chemistry, Inorganic & Nuclear
Benny Danilo Belviso, Francesco Marin, Sara Fuertes, Violeta Sicilia, Rosanna Rizzi, Fulvio Ciriaco, Chiara Cappuccino, Eric Dooryhee, Aurelia Falcicchio, Lucia Maini, Angela Altomare, Rocco Caliandro
Summary: Anionic complexes with vapochromic behavior were investigated in this study, showing color changes upon heating and subsequent reversion upon water absorption. The structural changes were found to depend on the transition metal ion, while the ligand influenced critical temperature and molecular plane inclination with respect to the unit cell planes.
INORGANIC CHEMISTRY
(2021)
Article
Computer Science, Information Systems
Ignacio Perez-Hurtado, David Orellana-Martin, Miguel A. Martinez-del-Amor, Luis Valencia-Cabrera, Agustin Riscos-Nunez
Summary: This paper presents the challenges of validating and testing P system models in membrane computing and proposes a new design of the P-Lingua language that allows users to define custom variants and derivation modes, among other improvements. It also includes a set of command-line tools for parsing and simulating P-Lingua 5 files.
INFORMATION SCIENCES
(2022)
Article
Ecology
Subhasis Ray, Mark A. Stopfer
Summary: Automatic tracking of multiple animals is important for studying behaviors, but it is challenging due to issues like discontinuities in animal motion. The software toolkit Argos addresses these challenges by providing tools for compressing videos, generating training sets for a neural network, tracking animals in videos, and facilitating manual review and correction of tracks. Argos can help reduce the data storage and analysis workload, speed up the analysis process, and enable tracking of markerless animals in complex environments for extended periods.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Rhys A. Farrer
Summary: HaplotypeTools is a powerful resource for analyzing hybrid or recombinant diploid or polyploid genomes and determining parental ancestry for sub-genomic regions. The toolset utilizes a method of identifying overlapping sites and extending them to phase variant sites, while also providing utility scripts for downstream analysis, achieving high accuracy in various tests.
BMC BIOINFORMATICS
(2021)
Article
Computer Science, Information Systems
Malik Muhammad Ali Shahid, Shahida Sulaiman, Mohammed Al-Sarem, Aqeel Ur Rahman, Salman Iqbal, Rab Nawaz Bashir, Arfat Ahmad Khan, Momen M. Alrawi, Rashiq R. Marie, Settawit Poochaya
Summary: Conventionally, web portal reliability is validated using conventional methods, but these methods are not effective. This paper proposes the inclusion of quality factors like usability in addition to conventional testing to improve reliability. Testing profiles, including software operational profile, input space profile, and usability profile, are employed to measure reliability. The proposed scheme is compared with the conventional method and the results show its effectiveness, providing recommendations for testing and measuring reliability in web-based software or applications.
CMC-COMPUTERS MATERIALS & CONTINUA
(2023)
Article
Ecology
Daniel Edler, Johannes Klein, Alexandre Antonelli, Daniele Silvestro
Summary: raxmlGUI 2.0 is a redesigned graphical interface that seamlessly integrates with RAxML binaries, providing automated workflows for phylogenetic analysis, supporting multiple calls to RAxML, automatically specifying partition settings, and model testing to select the best substitution models.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Computer Science, Theory & Methods
Jude Haris, Perry Gibson, Jose Cano, Nicolas Bohm Agostini, David Kaeli
Summary: In this paper, we introduce SECDA-TFLite, an open source toolkit for developing DNN hardware accelerators within the TFLite framework. The toolkit uses the SECDA methodology to reduce the design time for optimized DNN inference accelerators on edge devices with FPGAs. SECDA-TFLite includes modules for cost-effective simulation, profiling, and data communication. A case study demonstrates significant performance improvements compared to a CPU-only baseline. The code is available at https://github.com/gicLAB/SECDA-TFLite.
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING
(2023)
Article
Biochemical Research Methods
Jacob L. Steenwyk, Thomas J. Buida, Abigail L. Labella, Yuanning Li, Xing-Xing Shen, Antonis Rokas
Summary: PhyKIT is a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, aiding in handling, examining, and extracting biological meaning from increasingly large phylogenomic datasets.
Article
Chemistry, Multidisciplinary
Amit Kumar Halder, M. Natalia Dias Soeiro Cordeiro
Summary: QSAR modelling is a commonly used computational tool, but traditional approaches have limitations due to being based on a limited number of conditions. To overcome this drawback, multitasking or multitarget QSAR (mt-QSAR) methods have emerged to integrate diverse chemical and biological data, enhancing the reliability of modelling.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Chemistry, Analytical
Johan Lillja, Kyle D. Duncan, Ingela Lanekoff
Summary: Mass spectrometry imaging (MSI) techniques provide high sensitivity and selectivity in revealing the spatial distributions of molecules on a surface. However, processing the large volumes of data generated by MSI into useful ion images can be challenging. In addition, the data handling strategies for continuous ionization sources differ from those used for pulsed ionization sources. Currently, there is a lack of data-handling software specifically designed for MSI data generated with continuous ionization sources and automatic gain control (AGC).
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Daniel Stribling, Lauren A. Gay, Rolf Renne
Summary: This study introduces a Python3 API and command-line toolkit called Hybkit for analyzing hybrid sequence data in the hyb file format, allowing customizable evaluation and annotation of hybrid characteristics. The Hybkit API includes various Python objects for developing custom analyses, miRNA-specific analysis methods, built-in plotting of analysis results, and incorporation of predicted miRNA/target interactions.
Article
Genetics & Heredity
Chen Xu, Bing Wang, Lin Yang, Lucas Zhongming Hu, Lanxing Yi, Yaxuan Wang, Shenglan Chen, Andrew Emili, Cuihong Wan
Summary: In this study, using co-fractionation coupled with LC-MS/MS, the researchers identified 291 multi-protein complexes and 24,092 protein-protein interactions in Synechocystis sp. PCC 6803. These interactions reveal the roles of photosynthesis in various physiological processes and highlight the differences in protein functions between bacteria and higher plants.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Dan Yu, Nan Dai, Eric J. Wolf, Ivan R. Correa, Jujun Zhou, Tao Wu, Robert M. Blumenthal, Xing Zhang, Xiaodong Cheng
Summary: PCIF1 is a methyltransferase that can methylate RNA, with a preference for 20-O-methylated nucleotides. It can also methylate uncapped nucleotides, although with lower activity. PCIF1 has opposing activities to the RNA demethylase FTO.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Sebastian Gruenberg, Eric J. Wolf, Jingming Jin, Mehul B. Ganatra, Kelly Becker, Cristian Ruse, Christopher H. Taron, Ivan R. Correa, Erbay Yigit
Summary: Combination of ribonucleases (RNases) is commonly used to digest RNA into oligoribonucleotide fragments for liquid chromatography-mass spectrometry (LC-MS) analysis. Cusativin and MC1, nucleotide-specific endoribonucleases, are ideal tools for RNA modification mapping due to their high specificity for cytidine and uridine. New efficient and time-saving protocols have been developed to enhance the expression and purification of these RNases, resulting in highly active recombinant enzymes.
PROTEIN EXPRESSION AND PURIFICATION
(2022)
Article
Biochemical Research Methods
Zhiwei Wang, Ni Pan, Jiahao Yan, Jian Wan, Cuihong Wan
Summary: This study identified and characterized short open reading frame-encoded microproteins in Drosophila melanogaster, revealing their critical roles in fly development. A significant number of these microproteins were previously unrecognized and were validated through de novo sequencing. These findings provide valuable data resources for growth and development research.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Bing Li, Zheng Zhang, Cuihong Wan
Summary: Microproteins play various vital biological functions and their specific roles in cell cycle regulation have been explored in this study using a combination of bottom-up and top-down proteomics. The analysis identified a total of 657 microproteins at different cell cycle stages, showing cell cycle-specific functions and the potential involvement of nonannotated novel microproteins encoded by ncRNA.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Biochemical Research Methods
Zheng Zhang, Yujie Li, Wenqian Yuan, Zhiwei Wang, Cuihong Wan
Summary: Short open reading frames (sORFs) have the potential to encode proteins, leading to a new research focus in proteomics. Mass spectrometry (MS) is a significant tool for directly detecting the sequence of sORF encoded peptides (SEPs), but the low abundance and short sequences of SEPs present challenges in detection.
Article
Biochemistry & Molecular Biology
Eliza S. Lee, Harrison W. Smith, Eric J. Wolf, Aysegul Guvenek, Yifan E. Wang, Andrew Emili, Bin Tian, Alexander F. Palazzo
Summary: This study reveals a quality control mechanism for nuclear retention and degradation of misprocessed mRNA. The researchers find that specific sequences associated with misprocessed mRNA require zinc finger protein ZFC3H1 and a component of spliceosomal U1 snRNP, U1-70K, for nuclear retention. They also demonstrate that disassembling nuclear speckles impairs the nuclear retention of these RNAs.
Article
Biochemical Research Methods
Yan Sun, Jiangmei Huang, Zhiwei Wang, Ni Pan, Cuihong Wan
Summary: This study identified stress-responsive microproteins in Saccharomyces cerevisiae using mass spectrometry-based proteomics, revealing their involvement in stress-related processes such as cell redox reactions, protein folding and degradation. It provides valuable information for understanding the functions of these microproteins and improving the stress tolerance of S. cerevisiae.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Eric J. Wolf, Sebastian Grunberg, Nan Dai, Tien-Hao Chen, Bijoyita Roy, Erbay Yigit, Ivan R. Correa
Summary: This study demonstrates the advantages of uridine-specific human endoribonuclease hRNase 4 over the benchmark enzyme RNase T1 in mRNA analysis, and evaluates the sequence, identity, and modifications of mRNA using liquid chromatography-mass spectrometry (LC-MS/MS) technology.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Zhao Peng, Jiaqiang Li, Xingpeng Jiang, Cuihong Wan
Summary: As a vital life form in the biosphere, cyanobacteria have been the subject of significant research growth. Protein-protein interactions (PPIs) play a crucial role in biological functions, regulating proteins and forming functional complexes. However, PPI studies in cyanobacteria lag behind those in mammals and lack integration. To address this, we developed CyanoMapDB, a database that provides experimental evidence of cyanobacterial PPIs. It includes 52,304 PPIs among 6,789 proteins from 23 cyanobacterial species, collected from UniProt, STRING, IntAct, and co-fractionation MS data. CyanoMapDB allows users to easily query proteins, explore interacting proteins from various sources, and visualize protein networks. It is expected to advance research in cyanobacteria and plants.
Article
Biochemical Research Methods
Zheng Zhang, Tao Tian, Ni Pan, Yi Wang, Mingbo Peng, Xinbo Zhao, Zhenwei Pan, Cuihong Wan
Summary: The incidence rate of atrial fibrillation (AF) has remained high in recent years, and the molecular mechanism of disease development remains unclear. Microproteins, which are ribosomally translated gene products, have been found to play important biological roles but have received little attention in AF research. In this study, we analyzed the microproteomic profiles of 65 AF patients and 65 healthy subjects. We identified 4 microproteins that were significantly different, including 3 annotated ones and 1 novel one. By using machine learning methods, we developed a diagnostic model with microproteins that had comparable and excellent performance to a model with global proteins. Our findings confirm the abnormal expression of microproteins in AF and provide new insights into the mechanism study of AF.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Zhao Peng, Aishuake Huwanixi, Cuihong Wan
Summary: In this study, a smORF database in N. flagelliforme was constructed, and 18 novel microproteins were identified using LS-MS/MS analysis. These microproteins include five ribosomal proteins, one RNA polymerase subunit, and one acetohydroxy acid isomeroreductase. The findings expand our understanding of smORFs-encoded microproteins and their relationship with the stress response of extremophilic microorganisms.
Article
Multidisciplinary Sciences
Shengjie Li, Die Peng, Ni Pan, Shaohui Wang, Zheng Zhang, Cuihong Wan
Summary: Short open reading frame-encoded peptides (SEPs), ranging from 2 to 100 amino acids, play important roles in various biological processes. In this study, we analyzed SEPs in five different brain regions of mice using mass spectrometry-based proteomics. We identified 373 SEPs, with approximately 83% of them being novel. Half of the identified SEPs were encoded by non-coding RNA, and about one-third showed orthology across species. Each brain region had specific SEPs, such as IP_1018875 in the frontal cortex, which may be related to autophagy and neuronal signaling. These findings expand our understanding of the mouse brain proteome and provide valuable insights for future studies on the function of SEPs.
Article
Biochemical Research Methods
Jiahao Yan, Yuhe Ding, Zhao Peng, Lu Qin, Jingyu Gu, Cuihong Wan
Summary: In this study, label-free quantitative proteomics was used to explore the protein profiling during zebrafish's embryogenesis. A total of 5961 proteins were identified and divided into 11 modules based on weighted gene coexpression network analysis. Some proteins potentially involved in activating zygotic genes were discovered, and 137 novel proteins were identified.
JOURNAL OF PROTEOME RESEARCH
(2023)
