Article
Multidisciplinary Sciences
Ashadun Nobi, Kamrul Hasan Tuhin, Jae Woo Lee
Summary: The study applied principal component analysis to the evolution of COVID-19 pandemic, identifying different dynamics of the pandemic in different countries. The first principal component played a crucial role in detecting different phases of the pandemic, with strong clusters observed for American and European countries.
Article
Biochemical Research Methods
Kuangnan Fang, Rui Ren, Qingzhao Zhang, Shuangge Ma
Summary: Dimension reduction techniques like PCA, PLS, and CCA are extensively used in the analysis of high-dimensional omics data. Integrative analysis, which outperforms meta-analysis and individual-data analysis, has been developed for multiple datasets with compatible designs. We developed the R package iSFun to facilitate integrative dimension reduction analysis, offering comprehensive analysis options under different models and penalties.
Article
Computer Science, Artificial Intelligence
Pei Li, Wenlin Zhang, Chengjun Lu, Rui Zhang, Xuelong Li
Summary: A novel robust kernel principal component analysis method with optimal mean (RKPCA-OM) is proposed to enhance the robustness of KPCA by automatically eliminating the optimal mean. The theoretical proof guarantees the convergence of the algorithm and the obtained optimal subspaces and means. Exhaustive experimental results validate the superiority of the proposed method.
Review
Genetics & Heredity
Matineh Rahmatbakhsh, Alla Gagarinova, Mohan Babu
Summary: Microbial pathogens have evolved diverse strategies to manipulate host systems, causing diseases through changes in the host-pathogen proteome. Mass spectrometry-based proteomics approaches are utilized to study disease progression but present challenges in data analysis. The study reviews steps in temporal and spatial analysis, offering best practices for data preprocessing, statistical analysis, and biological information extraction. Guidance is provided for novices and established users, with future directions and data analysis codes available for testing.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Asha M. Miles, Christian J. Posbergh, Heather J. Huson
Summary: New genetic markers associated with udder and teat conformation in cows were identified, and a composite risk index was proposed to determine potential genes related to mastitis. Integrating genetic information into breeding programs can efficiently reduce economic losses caused by mastitis.
Article
Engineering, Chemical
Abdalhamid Rahoma, Syed Imtiaz, Salim Ahmed
Summary: Sparse principal component analysis (SPCA) provides a sparse description of the loading matrix. This article proposes two methods to calculate confidence intervals of the loading values, which outperform traditional PCA and benchmark SPCA methods in fault detection and diagnosis.
CHEMICAL ENGINEERING SCIENCE
(2021)
Article
Multidisciplinary Sciences
Makoto Mizuno, Hideaki Aoyama, Yoshi Fujiwara
Summary: This study introduces a novel method called complex Hilbert principal component analysis (CHPCA) and constructs a synchronization network using Hodge decomposition, which enables the extraction of significant comovements with a time lead/delay in high-dimensional data and identification of the time-structure of correlations. Applied to Japanese beer market data, this method reveals co-movements across multiple products in the consumer choice process and uncovers remarkable customer heterogeneity.
Article
Biochemical Research Methods
Charles C. David, Chris S. Avery, Donald J. Jacobs
Summary: JEDi software is an upgraded tool that employs multithreading and user-friendly interface for rapid investigation of conformational motions of biopolymers, including multiple chain proteins. It offers options for Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) to construct covariance, correlation, and partial correlation matrices.
BMC BIOINFORMATICS
(2021)
Article
Cardiac & Cardiovascular Systems
Paul Pettersson-Pablo, Torbjoern K. Nilsson, Lars H. Breimer, Anita Hurtig-Wennlof
Summary: In healthy young adults, certain cardiovascular disease related proteins are correlated with Pulse-wave velocity (PWV), but not with augmentation index (AIX) or carotid-intima media thickness (cIMT). Age is a significant factor associated with vascular measurements.
BMC CARDIOVASCULAR DISORDERS
(2021)
Article
Biochemical Research Methods
Rola Houhou, Petra Rosch, Jurgen Popp, Thomas Bocklitz
Summary: In this study, Raman spectral data were analyzed using B-spline basis functions for approximation, followed by functional principal component analysis and linear discriminant analysis (FPCA-LDA) compared to classical PCA-LDA. Results showed that FPCA-LDA had higher mean sensitivities than PCA-LDA, especially with low signal-to-noise ratio and small peak shifts. However, both methods performed equally with higher signal-to-noise ratio, and a slight improvement was observed when FPCA-LDA was applied to experimental Raman data.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Materials Science, Characterization & Testing
Nitin Nagesh Kulkarni, Shweta Dabetwar, Jason Benoit, Tzuyang Yu, Alessandro Sabato
Summary: This study improves the accuracy of infrared thermography (IRT) in detecting voids underneath roadways by comparing and validating three advanced image-processing techniques. Among them, sparse principal component thermography (S-PCT) allows determining the physical size of voids with an accuracy above 95%. This research provides a foundation for advancing the use of IRT as a more accurate and cost-effective method for road condition monitoring.
NDT & E INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Yuanlin Wang, Yan Fan, Yi Jiang, Enquan Wang, Yu Song, Hongguang Chen, Feier Xu, Keliang Xie, Yonghao Yu
Summary: Through quantitative proteomics and bioinformatics analysis, Apoa2 protein and mRNA were identified as potential biomarkers for H-2 with a protective, causal relationship with sepsis. Additionally, causal relationships between HDL and type 2 diabetes with sepsis were also confirmed. These findings have significant implications for the treatment of H-2.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Leonardo C. J. Corvalan, Mariane B. Sobreiro, Larissa R. Carvalho, Renata O. Dias, Ramilla S. Braga-Ferreira, Cintia P. Targueta, Carlos M. e Silva-Neto, Bianca W. Berton, Ana Maria S. Pereira, Jose A. F. Diniz-filho, Mariana P. C. Telles, Rhewter Nunes
Summary: Serjania erecta is an important genetic resource with medicinal properties. We sequenced and analyzed its chloroplast genome, identifying differences between species and potential molecular markers.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Jeannette Jansen, Patricia Vieten, Francesca Pagliari, Rachel Hanley, Maria Grazia Marafioti, Luca Tirinato, Joao Seco
Summary: This study explored the interaction between hypoxia and ionizing radiation on gene expression, revealing 37 genes consistently regulated across all cell lines studied. DNA-repair related genes were down-regulated post-irradiation, while cell cycle-dependent genes showed consistent up-regulation. The results emphasize the importance of considering both oxygen and radiation effects in analyzing gene response to cancer radiation treatment.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Hemavathi Krishnan, Subash C. B. Gopinath, H. Zulhaimi, M. K. Md Arshad, Sreeramanan Subramaniam
Summary: The stable truncated 2' fluoro-RNA aptamer selectively binds with factor IX protein, contributing to the upstream interruption of the blood coagulation pathway. Rational analysis was conducted to evaluate the structural orientation and binding interactions between the aptamer and FIX. Molecular docking identified key interactions between the aptamer and FIX, while molecular dynamic simulation revealed the strength and stability of the aptamer-FIX complex.
PROCESS BIOCHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Buettner, Marco Wagenstetter, Ziga Avsec, Adam Gayoso, Nir Yosef, Marta Interlandi, Sergei Rybakov, Alexander Misharin, Fabian J. Theis
Summary: scArches is a deep learning strategy for mapping query datasets on top of a reference, allowing efficient and decentralized reference construction while preserving biological state information and removing batch effects. It generalizes to multimodal reference mapping and can impute missing modalities.
NATURE BIOTECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Giovanni Palla, David S. Fischer, Aviv Regev, Fabian J. Theis
Summary: Methods for profiling RNA and protein expression in a spatially resolved manner have rapidly advanced, but clear articulation of key biological questions and development of computational tools are crucial. Decisions on molecular features and inclusion of cell shape in analysis need to be made by developers. Optimal ways to compare tissue samples at different length scales are still being sought.
NATURE BIOTECHNOLOGY
(2022)
Review
Endocrinology & Metabolism
Karin Hrovatin, David S. Fischer, Fabian J. Theis
Summary: Single-cell metabolic modeling provides a new perspective for understanding cellular functions. The presented modeling approaches vary in terms of input requirements, assumptions, scalability, modeled metabolic layers, and newly gained insights. We believe that the use of prior metabolic knowledge will lead to more robust predictions and will pave the way for mechanistic and interpretable machine-learning models.
MOLECULAR METABOLISM
(2022)
Article
Genetics & Heredity
Bo Hu, Sara Lelek, Bastiaan Spanjaard, Hadil El-Sammak, Mariana Guedes Simoes, Janita Mintcheva, Hananeh Aliee, Ronny Schaefer, Alexander M. Meyer, Fabian Theis, Didier Y. R. Stainier, Daniela Panakova, Jan Philipp Junker
Summary: This study identifies specialized activated fibroblast cell states in the regenerating zebrafish heart using single-cell transcriptomics and spatiotemporal analysis, and reveals the origin of these cell states and the regulatory mechanism of endocardial fibroblast response.
Article
Biochemistry & Molecular Biology
Bob A. Hersbach, David S. Fischer, Giacomo Masserdotti, Deeksha, Karolina Mojzisova, Thomas Waltzhoeni, Diego Rodriguez-Terrones, Matthias Heinig, Fabian J. Theis, Magdalena Goetz, Stefan H. Stricker
Summary: Collide-seq, a single-cell protocol, has shed light on the basic principles of fate erasure and cell identity conflict resolution in direct reprogramming. It revealed the lack of a common mechanism for the loss of fibroblast-specific gene expression and showed that the abrupt transcriptional changes in converting cells occur when critical levels of reprogramming factors are reached. The study also demonstrated that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
David S. Fischer, Anna C. Schaar, Fabian J. Theis
Summary: A graph neural network is used to model how cells communicate in tissues. Existing models of intercellular communication only consider receptor-ligand signaling and ignore spatial proximity. This study presents a node-centric expression modeling method that estimates the impact of niche composition on gene expression from spatial molecular profiling data. The method successfully recovers signatures of molecular processes involved in cell communication.
NATURE BIOTECHNOLOGY
(2023)
Article
Cell Biology
Mohammad Lotfollahi, Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-zadeh, Carlos Talavera-Lopez, Alexander V. Misharin, Fabian J. Theis
Summary: Lotfollahi et al. propose ExpiMap, a biologically informed deep-learning model for interpretable reference mapping of RNA sequencing data. ExpiMap maps cells into biologically understandable components representing known 'gene programs', allowing for detailed analysis and interpretation of single-cell data.
NATURE CELL BIOLOGY
(2023)
Article
Neurosciences
Alessandro Zambusi, Klara Tereza Novoselc, Saskia Hutten, Sofia Kalpazidou, Christina Koupourtidou, Rico Schieweck, Sven Aschenbroich, Lara Silva, Ayse Seda Yazgili, Frauke van Bebber, Bettina Schmid, Gabriel Moeller, Clara Tritscher, Christian Stigloher, Claire Delbridge, Swetlana Sirko, Zeynep Irem Gunes, Sabine Liebscher, Jurgen Schlegel, Hananeh Aliee, Fabian Theis, Silke Meiners, Michael Kiebler, Dorothee Dormann, Jovica Ninkovic
Summary: The study reveals that clearing lipid droplets and TDP-43(+) condensates is crucial for restoring microglial cells to their nonactivated state and achieving scarless regeneration in zebrafish. The accumulation of these cellular components is also observed in postmortem brain tissues of patients with traumatic brain injury.
NATURE NEUROSCIENCE
(2022)
Article
Endocrinology & Metabolism
Sophie Tritschler, Moritz Thomas, Anika Boettcher, Barbara Ludwig, Janine Schmid, Undine Schubert, Elisabeth Kemter, Eckhard Wolf, Heiko Lickert, Fabian J. Theis
Summary: This study provides a high-resolution transcriptional map of healthy human islet cells and their murine and porcine counterparts. The findings suggest both commonalities and differences in transcriptional profiles across different species, with important identity and functional markers shared between species. The pig data better recapitulated the heterogeneity and functional gene expression of human islet cells compared to the mouse data.
MOLECULAR METABOLISM
(2022)
Article
Biochemical Research Methods
Hannah Spitzer, Scott Berry, Mark Donoghoe, Lucas Pelkmans, Fabian J. Theis
Summary: CAMPA is a deep learning framework that learns representations of molecular pixel profiles from multiplexed images. It clusters these representations to quantify subcellular landmarks and captures interpretable cellular phenotypes. Using this framework, the study reveals the changes in subcellular organization upon perturbation of RNA synthesis, RNA processing, or cell size, and uncovers the links between the molecular composition of membraneless organelles and cell-to-cell variability in bulk RNA synthesis rates.
Review
Oncology
Stefanie Baerthel, Chiara Falcomata, Roland Rad, Fabian J. Theis, Dieter Saur
Summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer with a heterogeneous genetic landscape and an immunosuppressive tumor microenvironment. Recent advances in single-cell sequencing and spatial transcriptomics have provided insights into the diversity and plasticity of PDAC, both in its malignant cells and the surrounding tissue. This review highlights the importance of single-cell analysis in understanding PDAC and discusses the potential of multimodal approaches to study its biology and response to therapy.
Article
Genetics & Heredity
Lieke Michielsen, Mohammad Lotfollahi, Daniel Strobl, Lisa Sikkema, Marcel J. T. Reinders, Fabian J. Theis, Ahmed Mahfouz
Summary: Single-cell genomics is generating a large amount of data, which can be integrated to create comprehensive reference atlases of tissue. However, there is a lack of systematic approach to harmonize cell type annotation terminology and depth across different datasets.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Meeting Abstract
Respiratory System
L. Yang, I. Angelidis, L. Heumos, M. Ansari, S. Zhou, C. Mayr, L. Simon, M. Strunz, F. Theis, H. Adler, H. Schiller
EUROPEAN RESPIRATORY JOURNAL
(2022)
Meeting Abstract
Respiratory System
N. J. Lang, M. Ansari, L. Yang, S. Zhou, D. Porras-Gonzalez, A. Agami, C. H. Mayr, B. Hooshiar Kashani, L. Heumos, M. Gerckens, Y. Chen, J. Schniering, M. Stoleriu, R. Hatz, J. Behr, F. J. Theis, G. Burgstaller, H. B. Schiller
EUROPEAN RESPIRATORY JOURNAL
(2022)
Meeting Abstract
Immunology
N. Reusch, S. Mueller, K. Bassler, L. Bonaguro, J. Schulte-Schrepping, L. Balsevicius, K. Dahm, V Isakzai, T. Kapellos, S. Warnat-Herresthal, C. Kroeger, S. Agrawal, N. Balzer, T. Pecht, M. Becker, P. Guenther, C. Osei-Sarpong, W. Fujii, A. Horne, M. Lotfollahi, Y. Ji, E. Dudkin, H. J. C. Ferreira, E. Hinkley, M. Beyer, K. Haendler, J. Hasenauer, R. J. Argueello, F. Theis, M. Schmolz, A. Aschenbrenner, T. Ulas, J. L. Schultze
EUROPEAN JOURNAL OF IMMUNOLOGY
(2022)