Article
Biochemical Research Methods
Rui Ren, Kuangnan Fang, Qingzhao Zhang, Shuangge Ma
Summary: Densely measured SNP data pose challenges in analysis due to high dimensionality, but a functional analysis strategy can overcome this issue. However, the lack of portable and user-friendly software hampers practical use of these methods. This study fills the gap by developing the comprehensive package FunctanSNP, which provides convenient and reliable tools for analyzing SNP and other densely measured data.
Article
Environmental Sciences
Aude Ratier, Virgile Baudrot, Milena Kaag, Aurelie Siberchicot, Christelle Lopes, Sandrine Charles
Summary: This paper introduces the functions and applications of the R-package rbioacc, which can be used to analyze data from bioaccumulation tests. The package provides TK parameter estimates, bioaccumulation metrics, and supports environmental risk assessment, in compliance with regulatory requirements.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Biochemical Research Methods
Ryan M. Riley, Sandra E. Spencer Miko, Ryan D. Morin, Gregg B. Morin, Gian Luca Negri
Summary: Targeted and semitargeted mass spectrometry-based approaches are reliable methods to consistently detect and quantify low abundance proteins of clinical significance. However, their development is time-consuming and often requires costly libraries of synthetic peptides. To address this, we developed PeptideRanger, an R package that identifies peptides from proteins of interest with physiochemical properties suitable for mass spectrometry analysis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Brenda Pardo, Abby Spangler, Lukas M. Weber, Stephanie C. Page, Stephanie C. Hicks, Andrew E. Jaffe, Keri Martinowich, Kristen R. Maynard, Leonardo Collado-Torres
Summary: This study introduces a software package that enables interactive exploration of spatial transcriptomics data generated using the Visium platform. The package allows users to analyze and understand spatially-resolved data through interactive visualization tools.
Article
Biochemical Research Methods
Ann-Kristin Becker, Marcus Dorr, Stephan B. Felix, Fabian Frost, Hans J. Grabe, Markus M. Lerch, Matthias Nauck, Uwe Volker, Henry Volzke, Lars Kaderali
Summary: The study introduces an automated workflow combining network learning and clustering to reveal disease-associated biomarker networks from healthcare data. This approach automatically detects related feature groups and models their interactions, leading to easily analyzable network models.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Menno J. de Jong, Joost F. de Jong, A. Rus Hoelzel, Axel Janke
Summary: SambaR is an integrative and user-friendly R package designed to automate and simplify quality control and population-genetic analyses of biallelic SNP data sets. Users can perform mainstream population-genetic analyses with fewer than 10 commands and generate a wide variety of ready-to-publish graphs.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Environmental Sciences
Dan E. Kelley, Jaimie Harbin, Clark Richards
Summary: The R package argoFloats facilitates identification, downloading, caching, and analysis of oceanographic data collected by Argo profiling floats. The package has close connections with the oce package, making it familiar to R users analyzing oceanographic data of other kinds. Benefits of using argoFloats in everyday tasks specific to Argo data, such as downloading data, quality control, and producing diagnostic plots, are outlined in the paper.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemical Research Methods
Zuguang Gu, Daniel Huebschmann
Summary: Spiral layout has two major advantages in data visualization, improving visualization resolution and revealing periodic patterns. The R package spiralize provides a general solution with numerous graphics functions for users to easily implement self-defined high-level graphics.
Article
Biochemical Research Methods
Ramiro Magno, Isabel Duarte, Ana-Teresa Maia
Summary: The PGS Catalog is an open database that contains 721 polygenic scores from over 133 publications, with the REST API being the only method for programmatic access. The quincunx R package provides a client interface to the PGS Catalog REST API, allowing users to query, retrieve, filter, and integrate metadata associated with polygenic scores in tidy table format.
Article
Biochemical Research Methods
Antoine Bodein, Marie-Pier Scott-Boyer, Olivier Perin, Kim-Anh Le Cao, Arnaud Droit
Summary: This text introduces the R package timeOmics, a generic analytical framework for integrating longitudinal multi-omics data. The package includes functions for pre-processing, modeling, and clustering to help researchers identify molecular features strongly associated with time. It is demonstrated in a case study to detect seasonal patterns of various molecular and clinical variables in patients with diabetes mellitus.
Article
Biochemical Research Methods
Xiaoyu Liang, Ying Hu, Chunhua Yan, Ke Xu
Summary: The study introduces a novel R package, i2d, for simulating image data through digital convolution, enabling information extraction and analysis in biomedical and biological research. Additionally, the package includes efficient methods for graph clustering based on simulated data to dissect complex gene networks.
Article
Multidisciplinary Sciences
Wikum Dinalankara, Qian Ke, Donald Geman, Luigi Marchionni
Summary: Divergence analysis is a novel framework that transforms high-dimensional omics data into digitized codes, facilitating simple and effective analysis on different omics platforms.
Article
Mathematics
Mohsen Soltanifar, Chel Hee Lee
Summary: This paper presents a new statistical software package, SimSST, which allows researchers to simulate stop signal task (SST) data under generalized scenarios. The package is based on the non-independent horse race model, copulas in probability theory, and the ExGaussian or Shifted Wald distributional assumption for go and stop processes. It offers sixteen scenarios for simulating SST data. A working example is provided to evaluate the precision of parameter estimations, and limitations and future work directions for the package are discussed.
Article
Biochemical Research Methods
Zachary B. Abrams, Dwayne G. Tally, Lynne Abruzzo, Kevin R. Coombes
Summary: Cytogenetics data, stored as karyotypes, are now being analyzed on a large scale thanks to tools like CytoGPS. The development of RCytoGPS further facilitates the analysis and visualization of karyotype data, advancing the field of computational cytogenetic pathology.
Article
Biochemistry & Molecular Biology
Devon DeRaad
Summary: The SNPfiltR package in R provides functionalities for customizable and reproducible SNP filtering pipeline. It extends existing SNP filtering functionalities by automating the visualization of key parameters.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Oncology
Tenna Vesterman Henriksen, Noelia Tarazona, Amanda Frydendahl, Thomas Reinert, Francisco Gimeno-Valiente, Juan Antonio Carbonell-Asins, Shruti Sharma, Derrick Renner, Dina Hafez, Desamparados Roda, Marisol Huerta, Susana Rosello, Anders Husted Madsen, Uffe S. Love, Per Vadgaard Andersen, Ole Thorlacius-Ussing, Lene Hjerrild Iversen, Kare Andersson Gotschalck, Himanshu Sethi, Alexey Aleshin, Andres Cervantes, Claus Lindbjerg Andersen
Summary: The study demonstrates the strong prognostic value of serial postoperative ctDNA analysis in predicting recurrence and assessing tumor growth rate. The novel combination of ctDNA detection and growth rate assessment provides unique opportunities for guiding treatment decisions.
CLINICAL CANCER RESEARCH
(2022)
Article
Medical Laboratory Technology
Tenna Henriksen, Simon O. Drue, Amanda Frydendahl, Christina Demuth, Mads H. Rasmussen, Thomas Reinert, Jakob S. Pedersen, Claus L. Andersen
Summary: This study characterized noise in ddPCR assays and developed two novel ctDNA calling methods informed by assay-specific noise profiles. The results demonstrate that considering noise and DNA input amounts can improve the sensitivity and specificity of ctDNA detection.
CLINICAL CHEMISTRY
(2022)
Article
Oncology
Thomas Reinert, Lena Marie Skindhoj Petersen, Tenna Vesterman Henriksen, Marie Obo Larsen, Mads Heilskov Rasmussen, Amanda Frydendahl Boll Johansen, Nadia Ogaard, Michael Knudsen, Iver Nordentoft, Soren Vang, Soren Rasmus Palmelund Krag, Anders Riegels Knudsen, Frank Viborg Mortensen, Claus Lindbjerg Andersen
Summary: This study found that monitoring ctDNA status in plasma can detect the risk of recurrence in colorectal liver metastases patients earlier and can potentially assist in clinical decision-making in cases of indeterminate CT findings, reducing time-to-intervention.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Mathematics, Applied
Linard Hoessly, Carsten Wiuf, Panqiu Xia
Summary: This article introduces a mathematical operation for summing chemical reactions and studies its algebraic properties and applications in stochastic reaction networks.
EUROPEAN JOURNAL OF APPLIED MATHEMATICS
(2022)
Article
Biology
Gabriel Renaud, Maibritt Norgaard, Johan Lindberg, Henrik Gronberg, Bram De Laere, Jorgen Bjerggaard Jensen, Michael Borre, Claus Lindbjerg Andersen, Karina Dalsgaard Sorensen, Lasse Maretty, Soren Besenbacher
Summary: This study proposes a novel unsupervised method, non-negative matrix factorization (NMF), to accurately infer tumor fragment length distribution and detect cancer using cell-free DNA (cfDNA) sequencing. The study demonstrates that NMF can accurately infer tumor fragment length distribution and correlate with ctDNA levels. It also shows that using NMF on genomic regions can identify fragment length signatures associated with open chromatin.
Editorial Material
Oncology
Mikail Gogenur, Noor Al-Huda Hadi, Camilla Qvortrup, Claus Lindbjerg Andersen, Ismail Gogenur
ANNALS OF SURGICAL ONCOLOGY
(2022)
Editorial Material
Oncology
Claus L. Andersen, Ellen Heitzer
Article
Multidisciplinary Sciences
Laia Simo-Riudalbas, Sandra Offner, Evarist Planet, Julien Duc, Laurence Abrami, Sagane Dind, Alexandre Coudray, Mairene Coto-Llerena, Caner Ercan, Salvatore Piscuoglio, Claus Lindbjerg Andersen, Jesper Bertram Bramsen, Didier Trono
Summary: The early diagnosis of colorectal cancer (CRC) is an unmet medical need. In this study, the authors characterized cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) and identified the role of POU5F1B in CRC growth and metastasis. They found that the expression of POU5F1B, driven by a primate-specific endogenous retroviral promoter, is a strong negative prognostic biomarker in CRC. They also demonstrated that POU5F1B promotes CRC cell proliferation and metastatic potential by inducing intracellular signaling events and the release of trans-acting factors involved in cell growth and adhesion. These findings provide interesting leads for the development of cancer therapies.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Malthe Sebro Rasmussen, Genis Garcia-Erill, Thorfinn Sand Korneliussen, Carsten Wiuf, Anders Albrechtsen
Summary: This article presents a stochastic expectation-maximization algorithm for inferring the site frequency spectrum from NGS data, addressing the bias, high computational demands, and overfitting issues. The algorithm significantly reduces runtime and enables estimation with constant, trivial RAM usage, while improving downstream inference.
Article
Multidisciplinary Sciences
Martin Santamarina-Garcia, Jenifer Brea-Iglesias, Jesper Bertram Bramsen, Mar Fuentes-Losada, Francisco Javier Caneiro-Gomez, Jose Angel Vazquez-Bueno, Hector Lazare-Iglesias, Natalia Fernandez-Diaz, Laura Sanchez-Rivadulla, Yoel Z. Betancor, Miriam Ferreiro-Pantin, Pablo Conesa-Zamora, Jose Ramon Antunez-Lopez, Masahito Kawazu, Manel Esteller, Claus Lindbjerg Andersen, Jose M. C. Tubio, Rafael Lopez-Lopez, Juan Ruiz-Banobre
Summary: Deficient DNA MMR activity leads to tumors with hypermutator phenotype called microsatellite instability (MSI). MSI has become an important predictive biomarker for anti-PD-1 therapies in various tumor types. In this study, we developed and validated MSIMEP, a computational tool for predicting MSI status from microarray DNA methylation tumor profiles of colorectal cancer samples. We demonstrated the high performance of MSIMEP in predicting MSI in different colorectal cancer cohorts and tested its consistency in other tumor types. The MSIMEP models showed better performance compared to a MLH1 promoter methylation-based model in colorectal cancer.
Article
Public, Environmental & Occupational Health
Jesper Nors, Trine Block Mattesen, Deirdre Cronin -Fenton, Aurelie Mailhac, Jesper Bertram Bramsen, Kare Andersson Gotschalck, Rune Erichsen, Claus Lindbjerg Andersen
Summary: The purpose of this study is to revalidate a registry-based algorithm for identifying colorectal cancer recurrence in a contemporary cohort and to investigate the accuracy of estimating the time to recurrence. The algorithm detects recurrence based on diagnosis codes, receipt of chemotherapy, or pathological tissue assessment. In the validation cohort, the algorithm showed a sensitivity of 94% and a specificity of 98%. Restricting the algorithm to chemotherapy codes from oncology departments improved its positive predictive value. Overall, this algorithm is suitable for future observational studies.
CLINICAL EPIDEMIOLOGY
(2023)
Article
Oncology
Jonas Kabel, Tenna Vesterman Henriksen, Christina Demuth, Amanda Frydendahl, Mads Heilskov Rasmussen, Jesper Nors, Nicolai J. Birkbak, Anders Husted Madsen, Uffe S. Love, Per Vadgaard Andersen, Thomas Kolbro, Alessio Monti, Ole Thorlacius-Ussing, Mikail Gogenur, Jeppe Kildsig, Nis Hallundbaek Schlesinger, Peter Bondeven, Lene Hjerrild Iversen, Kare Andersson Gotschalck, Claus Lindbjerg Andersen
Summary: Investigating the impact of tumor cell whole-genome doubling (WGD) on the detection of circulating tumor DNA (ctDNA), it was found that tumors with WGD have a higher likelihood of ctDNA detection. This is particularly significant for early-stage cancer. The study suggests that ctDNA is a promising biomarker for the early detection of cancer and residual disease.
Review
Oncology
Jamie E. Medina, Nicholas C. Dracopoli, Peter B. Bach, Anna Lau, Robert B. Scharpf, Gerrit A. Meijer, Claus Lindbjerg Andersen, Victor E. Velculescu
Summary: This study evaluates progress in early cancer detection tests and discusses the challenges in demonstrating their clinical utility before implementing them into routine clinical care.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Multidisciplinary Sciences
Carsten Wiuf, Abhishek Behera, Abhinav Singh, Manoj Gopalkrishnan
Summary: In this study, we propose a novel reaction network scheme called the Baum-Welch (BW) reaction network for learning parameters of hidden Markov models (HMMs). The scheme encodes all variables using separate species and each reaction in the scheme changes only one molecule from one species to another. We show that the BW algorithm and the reaction network scheme have the same fixed points and that the expectation step and the maximization step of the reaction network converge fast and compute the same values as the E-step and M-step of the BW algorithm. Simulation results demonstrate that our reaction network learns the same parameters as the BW algorithm and the log-likelihood increases continuously.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Biotechnology & Applied Microbiology
Mikkel H. Christensen, Simon O. Drue, Mads H. Rasmussen, Amanda Frydendahl, Iben Lyskjaer, Christina Demuth, Jesper Nors, Kare A. Gotschalck, Lene H. Iversen, Claus L. Andersen, Jakob Skou Pedersen
Summary: Circulating tumor DNA detection using NGS data shows potential for cancer identification and characterization. However, distinguishing tumor signal from errors in blood is challenging. We propose DREAMS, a method for estimating error rates and develop statistical methods for variant calling and cancer detection. Evaluation on colorectal cancer patients demonstrates that DREAMS outperforms current methods.
