Article
Biochemical Research Methods
Milot Mirdita, Konstantin Schutze, Yoshitaka Moriwaki, Lim Heo, Sergey Ovchinnikov, Martin Steinegger
Summary: ColabFold combines fast homology search and optimized model utilization to offer accelerated prediction of protein structures and complexes, with a processing speed that is 40-60 times faster. It serves as a free and accessible platform for protein folding, capable of predicting close to 1,000 structures per day.
Article
Biochemical Research Methods
Zhiqiang Pang, Guangyan Zhou, Jessica Ewald, Le Chang, Orcun Hacariz, Niladri Basu, Jianguo Xia
Summary: Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) is widely used in global metabolomics studies, but there are still challenges in data processing, statistical analysis, and functional interpretation. To overcome these barriers, the MetaboAnalyst platform has been updated to provide step-by-step instructions.
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Biochemical Research Methods
Givanna H. Putri, Simon Anders, Paul Theodor Pyl, John E. Pimanda, Fabio Zanini
Summary: HTSeq 2.0 provides an expanded application programming interface, including a new representation for sparse genomic data, enhancements for htseq-count to accommodate single-cell omics, a new script for data using cell and molecular barcodes, improved documentation, testing and deployment, bug fixes, and Python 3 support.
Review
Biochemical Research Methods
Lambda Moses, Lior Pachter
Summary: This article reviews spatial transcriptomics research since 1987 and provides a detailed analysis of trends and applications of related technologies and methods. The study offers historical context and guidance for current research.
Article
Biochemical Research Methods
Dmitry Ershov, Minh-Son Phan, Joanna W. Pylvanainen, Stephane U. Rigaud, Laure Le Blanc, Arthur Charles-Orszag, James R. W. Conway, Romain F. Laine, Nathan H. Roy, Daria Bonazzi, Guillaume Dumenil, Guillaume Jacquemet, Jean-Yves Tinevez
Summary: TrackMate is an automated tracking software that is used for analyzing bioimages. The new version, TrackMate 7, addresses modern research challenges by integrating advanced segmentation algorithms into tracking pipelines. This new version demonstrates its effectiveness across a wide range of bio-imaging experiments, combining machine and deep learning-based image segmentation with accurate object tracking for improved 2D and 3D tracking in biological research.
Article
Biochemical Research Methods
Jianbo Fu, Ying Zhang, Yunxia Wang, Hongning Zhang, Jin Liu, Jing Tang, Qingxia Yang, Huaicheng Sun, Wenqi Qiu, Yinghui Ma, Zhaorong Li, Mingyue Zheng, Feng Zhu
Summary: A peak table is a typical output of metabolomic experiments, and its processing is crucial in metabolomics research. The NOREVA protocol, a newly developed software tool, evaluates and optimizes data processing through various workflows, making data processing more efficient.
Article
Biochemical Research Methods
Giovanni Palla, Hannah Spitzer, Michal Klein, David Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle, Sergei Rybakov, Ignacio L. Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, Fabian J. Theis
Summary: Squidpy is a Python framework that combines tools from omics and image analysis to efficiently store, manipulate, and visualize spatial omics data. It is extensible and can be interfaced with other libraries for scalable analysis of spatial omics data.
Article
Biochemical Research Methods
Ryan R. Wick, Kathryn E. Holt
Summary: Polypolish is a new short-read polisher that uses all-per-read alignments to fix errors in repeat sequences that other polishers cannot. It performed well in benchmarking tests and introduced minimal errors during the polishing process.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Marius Lange, Volker Bergen, Michal Klein, Manu Setty, Bernhard Reuter, Mostafa Bakhti, Heiko Lickert, Meshal Ansari, Janine Schniering, Herbert B. Schiller, Dana Pe'er, Fabian J. Theis
Summary: Computational trajectory inference is a method to reconstruct cell state dynamics from single-cell RNA sequencing experiments, but it requires prior knowledge of the direction of biological processes. CellRank is a new approach that allows single-cell fate mapping in scenarios where the direction is unknown, such as regeneration, reprogramming, and disease.
Article
Biochemical Research Methods
Chaoran Chen, Sarah Nadeau, Michael Yared, Philippe Voinov, Ning Xie, Cornelius Roemer, Tanja Stadler
Summary: The CoV-Spectrum website provides support for identifying and tracking new SARS-CoV-2 variants, with flexible mutation search capabilities and analysis on various data sources to understand characteristics and transmission of different variants.
Article
Biochemical Research Methods
Haoyu Zhang, Quan Zou, Ying Ju, Chenggang Song, Dong Chen
Summary: This study presents a novel model based on sequence distance matrix and support vector machine (SVM) for predicting DNA 6mA modification. The model achieved high accuracy rates and correlation coefficients on rice and mouse data, showing significant advantages over traditional machine learning methods.
CURRENT BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Bin Li, Wen Zhang, Chuang Guo, Hao Xu, Longfei Li, Minghao Fang, Yinlei Hu, Xinye Zhang, Xinfeng Yao, Meifang Tang, Ke Liu, Xuetong Zhao, Jun Lin, Linzhao Cheng, Falai Chen, Tian Xue, Kun Qu
Summary: This study compares 16 integration methods using 45 paired datasets and 32 simulated datasets, finding that Tangram, gimVI, and SpaGE perform best in predicting RNA transcript distribution, while Cell2location, SpatialDWLS, and RCTD are top-performing methods for cell type deconvolution. The benchmark pipeline provided in the study helps researchers in selecting optimal integration methods for their datasets. The comprehensive benchmarking analysis presented in this work evaluates computational methods integrating spatial and single-cell transcriptomics data for transcript distribution prediction and cell type deconvolution.
Article
Biochemical Research Methods
Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten, Anastassis Perrakis
Summary: Artificial intelligence-based protein structure prediction has greatly impacted biomolecular sciences. However, the predicted protein models in the AlphaFold database lack coordinates for small molecules and ions necessary for structure and function. The AlphaFill algorithm addresses this issue by transplanting missing small molecules and ions from experimentally determined structures to predicted protein models.
Article
Biochemical Research Methods
Sarah Battat, David A. Weitz, George M. Whitesides
Summary: This article discusses how the field of microfluidics can increase its impact by improving technologies and enabling new functionalities, focusing on applications in diagnostics, food safety, and materials production. The article identifies technical challenges, including simplifying sample preparation procedures, finding materials for microfluidic device production, and automating the operation of microfluidic devices.
Article
Biochemical Research Methods
Nadav Brandes, Dan Ofer, Yam Peleg, Nadav Rappoport, Michal Linial
Summary: Self-supervised deep language modeling has achieved unprecedented success with natural language tasks, and the authors introduce a new deep language model called ProteinBERT specifically designed for proteins, which efficiently handles long sequences and achieves near or even better performance than other methods, providing an effective framework for rapid training of protein predictors.
Editorial Material
Biochemical Research Methods
John Jumper, Demis Hassabis
Article
Biochemical Research Methods
Jessy Lauer, Mu Zhou, Shaokai Ye, William Menegas, Steffen Schneider, Tanmay Nath, Mohammed Mostafizur Rahman, Valentina Di Santo, Daniel Soberanes, Guoping Feng, Venkatesh N. Murthy, George Lauder, Catherine Dulac, Mackenzie Weygandt Mathis, Alexander Mathis
Summary: This research extends the DeepLabCut toolbox to enable multi-animal pose estimation, animal identification, and tracking. It is of great significance for solving computer vision problems in multi-animal scenarios and provides a benchmark dataset for algorithm development.
Article
Biochemical Research Methods
John W. Hickey, Elizabeth K. Neumann, Andrea J. Radtke, Jeannie M. Camarillo, Rebecca T. Beuschel, Alexandre Albanese, Elizabeth McDonough, Julia Hatler, Anne E. Wiblin, Jeremy Fisher, Josh Croteau, Eliza C. Small, Anup Sood, Richard M. Caprioli, R. Michael Angelo, Garry P. Nolan, Kwanghun Chung, Stephen M. Hewitt, Ronald N. Germain, Jeffrey M. Spraggins, Emma Lundberg, Michael P. Snyder, Neil L. Kelleher, Sinem K. Saka
Summary: Recent developments in multiplexed protein imaging methods have provided detailed spatial and functional maps of complex tissues, utilizing antibodies against protein biomarkers. Key considerations for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets are essential as these approaches become more widely adopted. This Perspective offers guidance for robust and reproducible antibody-based highly multiplexed tissue imaging.
Review
Biochemical Research Methods
Maria Gavrilescu
Summary: Environmental pollution with heavy metals adversely affects soil quality and crop yields. Phytoremediation, using plants as hyperaccumulators, provides an environmentally friendly solution, but it is not without its drawbacks. Plant toxicity and low bioavailability of heavy metals in soil are major challenges. Various techniques have been proposed to enhance and expedite phytoremediation by increasing plant tolerance to heavy metal toxicity and promoting heavy metal extraction and transport.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
