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Biochemical Research Methods
Milena A. Cardoso, Luis E. A. Rizzardi, Leonardo W. Kume, Clarice Groeneveld, Sheyla Trefflich, Diego A. A. Morais, Rodrigo J. S. Dalmolin, Bruce A. J. Ponder, Kerstin B. Meyer, Mauro A. A. Castro
Summary: This study presents TreeAndLeaf, an R/Bioconductor package that implements a hybrid layout strategy for representing tree diagrams with a focus on the leaves. The package allows projection of multiple layers of information onto a graph-tree diagram.
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Biochemical Research Methods
Pedro Manuel Martinez-Garcia, Miguel Garcia-Torres, Federico Divina, Jose Terron-Bautista, Irene Delgado-Sainz, Francisco Gomez-Vela, Felipe Cortes-Ledesma
Summary: TOP2B is a crucial enzyme for resolving topological problems related to DNA metabolism and chromatin structure, but its catalytic mechanism may lead to unintended DNA double-strand breaks. By using machine learning, we have developed a predictive model for TOP2B binding based on accessible chromatin and architectural factors. This model accurately reflects experimental data, demonstrating the importance of TOP2B for chromatin accessibility and organization.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Zuguang Gu, Daniel Huebschmann
Summary: rGREAT is a new R/Bioconductor package that implements the GREAT algorithm locally, providing updated annotation data, support for numerous organisms and gene set collections, and extensibility for user customization.
Article
Multidisciplinary Sciences
Haixia Li, Jianjun Wang, Juchuanli Tu
Summary: RNA editing is a process that alters RNA sequence, with nonsynonymous editing significantly enriched in ubiquitination sites. Previous research found that lysine codons are enriched in the preferred deamination sites for RNA editing. Our study found that mRNA with edited ubiquitination sites can be translated into protein, and these editing sites showed differential editing in tumor samples and were correlated with clinical outcomes. Additionally, these genes were specifically enriched in the immune response pathway.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Michael A. Skinnider, Charley Cai, R. Greg Stacey, Leonard J. Foster
Summary: PrInCE is an R/Bioconductor package that uses machine-learning to infer protein-protein interaction networks from CF-MS data, with improvements in runtime and memory requirements and new features such as tests for co-eluting protein complexes and differential network analysis. Extensively documented and fully compatible with Bioconductor classes, PrInCE can seamlessly fit into existing proteomics workflows.
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Biochemical Research Methods
Mercedeh Movassagh, Steven J. Schiff, Joseph N. Paulson
Summary: Recent advancements in genomics have allowed researchers to explore the interplay between genetic mutations and microbiome data, providing insights into disease progression and individual responses to treatment interventions.
Article
Biochemical Research Methods
Pooja Gangras, Aditi Merchant
Summary: Cell surface proteins play a crucial role in tissue-specific delivery of therapeutics and are regulated by alternative splicing. The development of bioinformatic approaches for benchmarking and predicting protein isoform topologies is important. In this study, we introduce surfaltr, an R package that allows rapid evaluation and prediction of isoform topologies, and demonstrate its utility in analyzing novel surface protein isoforms.
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Biochemical Research Methods
Dolors Pelegi-Siso, Paula de Prado, Justiina Ronkainen, Mariona Bustamante, Juan R. Gonzalez
Summary: This study developed a software package that can compute several existing DNAm adult/childhood and gestational age clocks, while also providing visualization functions and other features necessary for DNAm age clocks, such as missing data imputation of cell types estimates.
Article
Biology
Daniel Castillo-Secilla, Juan Manuel G. Galvez, Francisco Carrillo-Perez, Marta Verona-Almeida, Daniel Redondo-Sanchez, Francisco Manuel Ortuno, Luis Javier Herrera, Ignacio Rojas
Summary: KnowSeq is a powerful software designed to automate and integrate bioinformatic tools for complex gene expression analysis and disease gene signature identification. It provides a unified environment, advanced algorithms, automatic HTML report generation, and biological knowledge extraction to assist decision-making processes.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
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Genetics & Heredity
Zuguang Gu, Daniel Hubschmann Bschmann
Summary: Functional enrichment analysis is an important bioinformatics method for evaluating the biological importance of gene lists. The researchers proposed a new method called binary cut for clustering functional terms, which showed consistent similarities within clusters and exclusivity between clusters. They demonstrated the effectiveness of binary cut through comprehensive benchmarks on simulated and real-world datasets.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Plant Sciences
Zachary James Winn, Emily Hudson-Arns, Mikayla Hammers, Noah DeWitt, Jeanette Lyerly, Guihua Bai, Paul St. Amand, Punya Nachappa, Scott Haley, Richard Esten Mason
Summary: The HaploCatcher R package was developed to predict specific haplotypes in genome-wide genotyped wheat lines. Training set and marker-derived haplotypes demonstrated good predictive performance. The package can be used by breeding programs to predict haplotypes for early generation material.
Article
Biochemical Research Methods
Carsten Henneges, Joseph N. Paulson
Summary: This study presents a novel and quick feature selection algorithm called GameRank, which builds calibrated and discriminating predictive models by directly optimizing model performance metrics. In clinical settings, this algorithm can be used to identify high and low-risk patients with high efficiency.
Article
Multidisciplinary Sciences
Peijian Shi, Johan Gielis, Brady K. Quinn, Karl J. Niklas, David A. Ratkowsky, Julian Schrader, Honghua Ruan, Lin Wang, Ulo Niinennets
Summary: This article introduces an R package called 'biogeom' that can simulate and fit various shapes found in nature. It includes multiple parametric and growth-rate equations, which can generate the profiles of different natural objects and provide quantitative information about shape and ontogenetic modification of shape.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2022)
Article
Biochemical Research Methods
Zuguang Gu, Daniel Hubschmann
Summary: In this work, a new strategy of hierarchical consensus partitioning is proposed to effectively solve the issues faced by standard methods in identifying large numbers of stable subgroups. The results demonstrate that hierarchical consensus partitioning can reveal more meaningful subgroups.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Kuan-Hao Chao, Yi-Wen Hsiao, Yi-Fang Lee, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang
Summary: RNA-Seq analysis has fundamentally changed researchers' understanding of the transcriptome in biological research, allowing exploration of transcription's biological impact. The RNASeqR package offers an automated six-step RNA-Seq analysis in a pure R environment, providing essential tabular and graphical results for further biological interpretation.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
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Biochemical Research Methods
Federico Comoglio, Cem Sievers, Renato Paro
BMC BIOINFORMATICS
(2015)
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Multidisciplinary Sciences
Tomonori Katsuyama, Federico Comoglio, Makiko Seimiya, Erik Cabuy, Renato Paro
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Cell Biology
Federico Comoglio, Tommy Schlumpf, Virginia Schmid, Remo Rohs, Christian Beisel, Renato Paro
Article
Hematology
Roland Walter, Kuan-Ting Pan, Carmen Doebele, Federico Comoglio, Katarzyna Tomska, Hanibal Bohnenberger, Ryan M. Young, Laura Jacobs, Ulrich Keller, Halvard Boenig, Michael Engelke, Andreas Rosenwald, Henning Urlaub, Louis M. Staudt, Hubert Serve, Thorsten Zenz, Thomas Oellerich
Article
Biochemistry & Molecular Biology
Constanze Schneider, Thomas Oellerich, Hanna-Mari Baldauf, Sarah-Marie Schwarz, Dominique Thomas, Robert Flick, Hanibal Bohnenberger, Lars Kaderali, Lena Stegmann, Anjali Cremer, Margarethe Martin, Julian Lohmeyer, Martin Michaelis, Veit Hornung, Christoph Schliemann, Wolfgang E. Berdel, Wolfgang Hartmann, Eva Wardelmann, Federico Comoglio, Martin-Leo Hansmann, Alexander F. Yakunin, Gerd Geisslinger, Philipp Stroebel, Nerea Ferreiros, Hubert Serve, Oliver T. Keppler, Jindrich Cinatl
Article
Multidisciplinary Sciences
Jasmin Corso, Kuan-Ting Pan, Roland Walter, Carmen Doebele, Sebastian Mohr, Hanibal Bohnenberger, Philipp Stroebel, Christof Lenz, Mikolaj Slabicki, Jennifer Huellein, Federico Comoglio, Michael A. Rieger, Thorsten Zenz, Juergen Wienands, Michael Engelke, Hubert Serve, Henning Urlaub, Thomas Oellerich
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Cell Biology
Simon Hauri, Federico Comoglio, Makiko Seimiya, Moritz Gerstung, Timo Glatter, Klaus Hansen, Ruedi Aebersold, Renato Paro, Matthias Gstaiger, Christian Beisel
Article
Immunology
Stephen J. Loughran, Federico Comoglio, Fiona K. Hamey, Alice Giustacchini, Youssef Errami, Eleanor Earp, Berthold Gottgens, Sten Eirik W. Jacobsen, Adam J. Mead, Brian Hendrich, Anthony R. Green
JOURNAL OF EXPERIMENTAL MEDICINE
(2017)
Article
Genetics & Heredity
Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, Quentin Szabo, Anne Xuereb, Christophe Klopp, Alexei Aravin, Renato Paro, Frederic Bantignies, Giacomo Cavalli
Article
Biochemistry & Molecular Biology
Federico Comoglio, Hyun Jung Park, Stefan Schoenfelder, Iros Barozzi, Daniel Bode, Peter Fraser, Anthony R. Green
Article
Multidisciplinary Sciences
Cem Sievers, Federico Comoglio, Makiko Seimiya, Gunter Merdes, Renato Paro
Article
Cell Biology
Federico Comoglio, Marta Simonatto, Sara Polletti, Xin Liu, Stephen T. Smale, Iros Barozzi, Gioacchino Natoli
GENES & DEVELOPMENT
(2019)
Article
Hematology
Anne C. Wilke, Carmen Doebele, Alena Zindel, Kwang Seok Lee, Sara A. Rieke, Michele Ceribelli, Federico Comoglio, James D. Phelan, James Q. Wang, Yana Pikman, Dominique Jahn, Bjoern Haeupl, Constanze Schneider, Sebastian Scheich, Frances A. Tosto, Hanibal Bohnenberger, Philipp Stauder, Frank Schnuetgen, Mikolaj Slabicki, Zana A. Coulibaly, Sebastian Wolf, Kamil Bojarczuk, Bjoern Chapuy, Christian H. Brandts, Philipp Stroebel, Caroline A. Lewis, Michael Engelke, Xincheng Xu, Hahn Kim, Thanh Hung Dang, Roland Schmitz, Daniel J. Hodson, Kimberly Stegmaier, Henning Urlaub, Hubert Serve, Clemens A. Schmitt, Fernando Kreuz, Gero Knittel, Joshua D. Rabinowitz, Hans Christian Reinhardt, Matthew G. Vander Heiden, Craig Thomas, Louis M. Staudt, Thorsten Zenz, Thomas Oellerich
Summary: This study identified vulnerabilities in Burkitt lymphoma (BL) through genome-scale CRISPR-Cas9 screens and validated serine hydroxymethyltransferase 2 (SHMT2) as a potential drug target. Mechanistically, SHMT2 inhibition disrupted the oncogenic transcription factor TCF3 and collapsed tonic BCR signaling, providing new perspectives for innovative therapies.
Article
Oncology
Sebastian Mohr, Carmen Doebele, Federico Comoglio, Tobias Berg, Julia Beck, Hanibal Bohnenberger, Gabriela Alexe, Jasmin Corso, Philipp Stroebel, Astrid Wachter, Tim Beissbarth, Frank Schnuetgen, Anjali Cremer, Nadine Haetscher, Stefanie Goellner, Arefeh Rouhi, Lars Palmqvist, Michael A. Rieger, Timm Schroeder, Halvard Boenig, Carsten Meuller-Tidow, Florian Kuchenbauer, Ekkehard Schuetz, Anthony R. Green, Henning Urlaub, Kimberly Stegmaier, R. Keith Humphries, Hubert Serve, Thomas Oellerich
