Editorial Material
Biochemical Research Methods
Lin Tang
Summary: The iNMF algorithm efficiently integrates large-scale, continually arriving single-cell multi-omic datasets.
Article
Chemistry, Analytical
Anastasia Sarycheva, Anton Grigoryev, Dmitry Sidorchuk, Gleb Vladimirov, Philipp Khaitovich, Olga Efimova, Olga Gavrilenko, Elena Stekolshchikova, Evgeny N. Nikolaev, Yury Kostyukevich
Summary: Mass spectrometry imaging (MSI) is a vital tool for visualizing compound distributions in biological tissues, allowing for the investigation of molecular organization and detection of abnormal regions. However, the complexity of spectral data presents challenges in analyzing large datasets and conducting exploratory visualization. Techniques such as principal component analysis and non-negative matrix factorization are used to address these challenges in MSI data analysis.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
George C. Linderman, Jun Zhao, Manolis Roulis, Piotr Bielecki, Richard A. Flavell, Boaz Nadler, Yuval Kluger
Summary: A key challenge in analyzing single cell RNA-sequencing data is the presence of a large number of false zeros. The authors propose a method based on low-rank matrix approximation to impute these false zeros while preserving true zeros. The advantages of this method are demonstrated on simulated and biological datasets.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Yang Liu, Tao Wang, Bin Zhou, Deyou Zheng
Summary: Integration of multiple single-cell RNA sequencing datasets is improved by creating a common reference space using a new algorithm.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shichao Ma, Xiunan Fang, Yu Yao, Jianfu Li, Daniel C. Morgan, Yongyan Xia, Crystal S. M. Kwok, Michelle C. K. Lo, Dickson M. D. Siu, Kevin K. Tsia, Andrian Yang, Joshua W. K. Ho
Summary: StarmapVis is a convenient web application that provides an interactive downstream analysis of single-cell expression or spatial transcriptomic data. It offers visualization tools from multiple angles to display clustering information and connectivity networks among coordinates. The tool also has a unique feature of automated animation of camera view and provides a useful animated transition between two-dimensional spatial omic data and three-dimensional single cell coordinates.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemical Research Methods
Wang Ruohan, Zhang Yuwei, Wang Mengbo, Feng Xikang, Wang Jianping, Li Shuai Cheng
Summary: The advances in single-cell DNA sequencing have allowed us to understand the genetic heterogeneity of cancer cells. However, existing methods face challenges in accurately estimating copy number variations due to high noise and low coverage. In this study, we propose an efficient method called SeCNV that uses structural entropy to profile copy numbers. SeCNV outperforms other tools in terms of accuracy and is capable of handling large datasets.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemical Research Methods
Erik Christensen, Ping Luo, Andrei Turinsky, Mia Husic, Alaina Mahalanabis, Alaine Naidas, Juan Javier Diaz-Mejia, Michael Brudno, Trevor Pugh, Arun Ramani, Parisa Shooshtari
Summary: This study evaluates 17 cell-based and 9 cluster-based scRNA-seq labelling algorithms using 8 cancer datasets, providing a comprehensive assessment of these methods in a cancer-specific context. The results show that cell-based methods generally outperform cluster-based methods in terms of performance and speed. Additionally, larger cell numbers in training data have a positive impact on prediction scores for cell-based methods. The best performing algorithms are scPred and SVM, with suggestions for algorithm selection provided.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemical Research Methods
Erik Christensen, Ping Luo, Andrei Turinsky, Mia Husic, Alaina Mahalanabis, Alaine Naidas, Juan Javier Diaz-Mejia, Michael Brudno, Trevor Pugh, Arun Ramani, Parisa Shooshtari
Summary: Single-cell RNA sequencing (scRNA-seq) clustering and labelling methods are used to determine cellular composition. This study assesses different scRNA-seq labelling algorithms using cancer datasets. Results show that cell-based methods generally outperform cluster-based methods. The study also provides suggestions for algorithm selection.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Shilu Zhang, Saptarshi Pyne, Stefan Pietrzak, Spencer Halberg, Sunnie Grace McCalla, Alireza Fotuhi Siahpirani, Rupa Sridharan, Sushmita Roy
Summary: The authors developed a method called single-cell Multi-Task Network Inference (scMTNI) to accurately infer the dynamics of cell type-specific Gene Regulatory Networks (GRNs) from scRNA-seq and scATAC-seq datasets. This method can identify key regulators and accurately model network dynamics for diverse processes such as cellular reprogramming and differentiation.
NATURE COMMUNICATIONS
(2023)
Article
Computer Science, Software Engineering
Harish Doraiswamy, Julien Tierny, Paulo J. S. Silva, Luis Gustavo Nonato, Claudio Silva
Summary: Multidimensional Projection is a fundamental tool for analyzing and visualizing high-dimensional data, with most methods aiming to preserve dissimilarity measures such as Euclidean distance. In addition to geometric properties, topological invariants like connected components and loops are also important for reliable analysis of structures like clusters and outliers. TopoMap is a novel projection technique that provides topological guarantees during the mapping process, improving confidence in visual analytics and aiding in the assessment of other projection methods.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Biotechnology & Applied Microbiology
Ashwin Narayan, Bonnie Berger, Hyunghoon Cho
Summary: den-SNE and densMAP are density-preserving visualization tools based on t-SNE and UMAP, able to accurately incorporate transcriptomic variability information and reveal the transcriptomic variability of single-cell RNA sequencing data, with applications in various biological processes.
NATURE BIOTECHNOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Zsolt T. Kosztyan, Marcell T. Kurbucz, Attila I. Katona
Summary: This work introduces a novel network-based (nonparametric) dimensionality reduction analysis (NDA) method for addressing the high-dimensional, low-sample-size problem in data science. The NDA method constructs a correlation graph and detects modules using a modularity-based community detection method. It determines a linear combination of variables weighted by their eigenvector centralities (EVCs) and can effectively select important variables. The experimental results demonstrate that NDA outperforms existing methods in terms of interpretability and ease of use.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Immunology
Ke-Yue Ma, Alexandra A. Schonnesen, Chenfeng He, Amanda Y. Xia, Eric Sun, Eunise Chen, Katherine R. Sebastian, Yu-Wan Guo, Robert Balderas, Mrinalini Kulkarni-Date, Ning Jiang
Summary: The study introduces a new high-throughput method for simultaneous profiling of TCR sequences, cognate antigen specificities, gene expression, and surface-protein expression from tens of thousands of single cells, providing valuable insights into T cell responses.
Article
Chemistry, Analytical
Chuanlu Liu, Shuliang Wang, Hanning Yuan, Yingxu Dang, Xiaojia Liu
Summary: Detecting correlations in high-dimensional datasets is crucial for data mining and knowledge discovery. However, detecting multivariable correlations, especially trivariate associations, remains challenging. In this study, the authors propose a novel quadratic optimized trivariate information coefficient (QOTIC) algorithm to address this problem. QOTIC achieves high accuracy by employing a quadratic optimization procedure and demonstrates superior generality and equitability compared to existing methods. Furthermore, QOTIC outperforms previous methods in both accuracy and time-efficiency. Extensive experiments validate the excellent performance of QOTIC.
Review
Immunology
Grainne Jameson, Mark W. Robinson
Summary: This review explores the potential novel functions of human liver-resident NK cells identified in scRNA-seq studies and identifies up-regulated and down-regulated genes associated with these cell clusters.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Critical Care Medicine
Daniela Farkas, A. A. Roger Thompson, Aneel R. Bhagwani, Schuyler Hultman, Hyun Ji, Naveen Kotha, Grant Farr, Nadine D. Arnold, Adam Braithwaite, Helen Casbolt, Jennifer E. Cole, Ian Sabroe, Claudia Monaco, Carlyne D. Cool, Elena A. Goncharova, Allan Lawrie, Laszlo Farkas
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2019)
Review
Cardiac & Cardiovascular Systems
Jose Tunon, Lina Badimon, Marie-Luce Bochaton-Piallat, Bertrand Cariou, Mat J. Daemen, Jesus Egido, Paul C. Evans, Imo E. Hoefer, Daniel F. J. Ketelhuth, Esther Lutgens, Christian M. Matter, Claudia Monaco, Sabine Steffens, Erik Stroes, Cecile Vindis, Christian Weber, Magnus Back
CARDIOVASCULAR RESEARCH
(2019)
Article
Endocrinology & Metabolism
Somer Matar, Anna Malczewska, Kjell Oberg, Lisa Bodei, Harry Aslanian, Anna Lewczuk-Myslicka, Pier Luigi Filosso, Alejandro L. Suarez, Agnieszka Kolasinska-Cwikla, Matteo Roffinella, Beata Kos-Kudla, Jaroslaw B. Cwikla, Ignat A. Drozdov, Mark Kidd, Irvin M. Modlin
NEUROENDOCRINOLOGY
(2020)
Article
Multidisciplinary Sciences
Mark Kidd, Ignat A. Drozdov, Somer Matar, Nicole Gurunlian, Nicholas J. Ferranti, Anna Malczewska, Philip Bennett, Lisa Bodei, Irvin M. Modlin
Editorial Material
Endocrinology & Metabolism
Irvin M. Modlin, Mark Kidd, Ignat A. Drozdov, Lisa Bodei
NEUROENDOCRINOLOGY
(2020)
Article
Cell Biology
Christopher J. M. Piper, Elizabeth C. Rosser, Kristine Oleinika, Kiran Nistala, Thomas Krausgruber, Andre F. Rendeiro, Aggelos Banos, Ignat Drozdov, Matteo Villa, Scott Thomson, Georgina Xanthou, Christoph Bock, Brigitta Stockinger, Claudia Mauri
Review
Medicine, Research & Experimental
Anna Malczewska, Beata Kos-Kudla, Mark Kidd, Ignat Drozdov, Lisa Bodei, Somer Matar, Kjell Oberg, Irvin M. Modlin
ADVANCES IN MEDICAL SCIENCES
(2020)
Article
Radiology, Nuclear Medicine & Medical Imaging
Lisa Bodei, Mark S. Kidd, Aviral Singh, Wouter A. van der Zwan, Stefano Severi, Ignat A. Drozdov, Anna Malczewska, Richard P. Baum, Dik J. Kwekkeboom, Giovanni Paganelli, Eric P. Krenning, Irvin M. Modlin
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2020)
Article
Cell Biology
Elizabeth C. Rosser, Christopher J. M. Piper, Diana E. Matei, Paul A. Blair, Andre F. Rendeiro, Michael Orford, Dagmar G. Alber, Thomas Krausgruber, Diego Catalan, Nigel Klein, Jessica J. Manson, Ignat Drozdov, Christoph Bock, Lucy R. Wedderburn, Simon Eaton, Claudia Mauri
Article
Endocrinology & Metabolism
Mark Kidd, Alexandra Kitz, Ignat Drozdov, Irvin Modlin
Summary: The NETest is a multigene assay for neuroendocrine tumors, with high diagnostic accuracy. Integration of different gene components enhances prognostic accuracy of the NETest.
NEUROENDOCRINOLOGY
(2021)
Article
Multidisciplinary Sciences
Ignat Drozdov, Daniel Forbes, Benjamin Szubert, Mark Hall, Chris Carlin, David J. Lowe
Article
Oncology
Irvin M. Modlin, Mark Kidd, Kjell Oberg, Massimo Falconi, Pier Luigi Filosso, Andrea Frilling, Anna Malczewska, Ronald Salem, Christos Toumpanakis, Faidon-Marios Laskaratos, Stefano Partelli, Matteo Roffinella, Claudia von Arx, Beata Kos Kudla, Lisa Bodei, Ignat A. Drozdov, Alexandra Kitz
Summary: Surgery is crucial for treating neuroendocrine tumors, with R0 resection being essential. The blood biomarker NETest accurately identifies NETs and elevated scores post-surgery predict recurrence with high accuracy. Surgery decreases NETest levels, but elevated levels post-surgery can indicate residual disease and potential recurrence.
ANNALS OF SURGICAL ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Inhye Park, Michael E. Goddard, Jennifer E. Cole, Natacha Zanin, Leo-Pekka Lyytikainen, Terho Lehtimaki, Evangelos Andreakos, Marc Feldmann, Irina Udalova, Ignat Drozdov, Claudia Monaco
Summary: CLEC4A2 is a distinguishing feature of vascular resident macrophages that have athero-protective properties. It promotes monocyte-to-macrophage differentiation and is critical for maintaining vascular homeostasis. CLEC4A2 deficiency leads to dysfunctional cholesterol metabolism and worsens the development of atherosclerosis.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ignat Drozdov, Benjamin Szubert, Elaina Reda, Peter Makary, Daniel Forbes, Sau Lee Chang, Abinaya Ezhil, Srikanth Puttagunta, Mark Hall, Chris Carlin, David J. Lowe
Summary: The developed AI algorithm CovIx can differentiate normal, abnormal, non-COVID-19 pneumonia, and COVID-19 CXRs effectively, achieving an area under the receiver operating characteristic curve for COVID-19 of 0.86. It performs on-par with four board-certified radiologists and is able to triage CXRs rapidly for further patient testing and/or isolation in emergency departments.
SCIENTIFIC REPORTS
(2021)