He, Dongze Patro, Rob
Published in
Bioinformatics (Oxford, England)
The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the comp...
Han, Xu Wang, Wanli Ma, Li-Hua Ai-Ramahi, Ismael Botas, Juan MacKenzie, Kevin Allen, Genevera I Young, Damian W Liu, Zhandong Maletic-Savatic, Mirjana
...
Published in
Bioinformatics (Oxford, England)
Nuclear magnetic resonance spectroscopy (NMR) is widely used to analyze metabolites in biological samples, but the analysis requires specific expertise, it is time-consuming, and can be inaccurate. Here, we present a powerful automate tool, SPatial clustering Algorithm-Statistical TOtal Correlation SpectroscopY (SPA-STOCSY), which overcomes challen...
Sahay, Shabnam Adhikari, Shishir Hormoz, Sahand Chakrabarti, Shaon
Published in
Bioinformatics (Oxford, England)
Detecting oscillations in time series remains a challenging problem even after decades of research. In chronobiology, rhythms (for instance in gene expression, eclosion, egg-laying, and feeding) tend to be low amplitude, display large variations amongst replicates, and often exhibit varying peak-to-peak distances (non-stationarity). Most currently ...
Del Core, Luca Pellin, Danilo Wit, Ernst C Grzegorczyk, Marco A
Published in
Bioinformatics (Oxford, England)
Investigating cell differentiation under a genetic disorder offers the potential for improving current gene therapy strategies. Clonal tracking provides a basis for mathematical modelling of population stem cell dynamics that sustain the blood cell formation, a process known as haematopoiesis. However, many clonal tracking protocols rely on a subse...
Theiss, Maria Hériché, Jean-Karim Russell, Craig Helekal, David Soppitt, Alisdair Ries, Jonas Ellenberg, Jan Brazma, Alvis Uhlmann, Virginie
Published in
Bioinformatics (Oxford, England)
The nuclear pore complex (NPC) is the only passageway for macromolecules between nucleus and cytoplasm, and an important reference standard in microscopy: it is massive and stereotypically arranged. The average architecture of NPC proteins has been resolved with pseudoatomic precision, however observed NPC heterogeneities evidence a high degree of ...
Choi, Hyunjun Moran, Jay Matsumoto, Nicholas Hernandez, Miguel E Moore, Jason H
Published in
Bioinformatics (Oxford, England)
Biomedical and healthcare domains generate vast amounts of complex data that can be challenging to analyze using machine learning tools, especially for researchers without computer science training. Aliro is an open-source software package designed to automate machine learning analysis through a clean web interface. By infusing the power of large l...
Fernández-Torras, Adrià Locatelli, Martina Bertoni, Martino Aloy, Patrick
Published in
Bioinformatics (Oxford, England)
Living a Big Data era in Biomedicine, there is an unmet need to systematically assess experimental observations in the context of available information. This assessment would offer a means for a comprehensive and robust validation of biomedical data results and provide an initial estimate of the potential novelty of the findings. Here we present BQ...
Batisti Biffignandi, Gherard Bellinzona, Greta Petazzoni, Greta Sassera, Davide Zuccotti, Gian Vincenzo Bandi, Claudio Baldanti, Fausto Comandatore, Francesco Gaiarsa, Stefano
Published in
Bioinformatics (Oxford, England)
Bacterial Healthcare-Associated Infections (HAIs) are a major threat worldwide, which can be counteracted by establishing effective infection control measures, guided by constant surveillance and timely epidemiological investigations. Genomics is crucial in modern epidemiology but lacks standard methods and user-friendly software, accessible to use...
Johnson, Brian Shuai, Yubo Schweinsberg, Jason Curtius, Kit
Published in
Bioinformatics (Oxford, England)
While evolutionary approaches to medicine show promise, measuring evolution itself is difficult due to experimental constraints and the dynamic nature of body systems. In cancer evolution, continuous observation of clonal architecture is impossible, and longitudinal samples from multiple timepoints are rare. Increasingly available DNA sequencing da...
Shi, Yang Wang, Mengqiao Shi, Weiping Lee, Ji-Hyun Kang, Huining Jiang, Hui
Published in
Bioinformatics (Oxford, England)
Small P-values are often required to be accurately estimated in large-scale genomic studies for the adjustment of multiple hypothesis tests and the ranking of genomic features based on their statistical significance. For those complicated test statistics whose cumulative distribution functions are analytically intractable, existing methods usually ...
