4,872 results match your criteria computational pipeline


Mobile Computational Photography: A Tour.

Annu Rev Vis Sci 2021 Sep;7:571-604

Google Research, Mountain View, California 94043, USA; email:

The first mobile camera phone was sold only 20 years ago, when taking pictures with one's phone was an oddity, and sharing pictures online was unheard of. Today, the smartphone is more camera than phone. How did this happen? This transformation was enabled by advances in computational photography-the science and engineering of making great images from small-form-factor, mobile cameras. Read More

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September 2021

DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria.

Bioinformatics 2021 Sep 15. Epub 2021 Sep 15.

Department of Molecular Biophysics and Biochemistry.

Summary: Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification. Read More

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September 2021

Mapping the landscape of synthetic lethal interactions in liver cancer.

Theranostics 2021 26;11(18):9038-9053. Epub 2021 Aug 26.

Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China.

Almost all the current therapies against liver cancer are based on the "one size fits all" principle and offer only limited survival benefit. Fortunately, synthetic lethality (SL) may provide an alternate route towards individualized therapy in liver cancer. The concept that simultaneous losses of two genes are lethal to a cell while a single loss is non-lethal can be utilized to selectively eliminate tumors with genetic aberrations. Read More

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A data-driven architecture using natural language processing to improve phenotyping efficiency and accelerate genetic diagnoses of rare disorders.

HGG Adv 2021 Jul 11;2(3). Epub 2021 May 11.

The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.

Effective genetic diagnosis requires the correlation of genetic variant data with detailed phenotypic information. However, manual encoding of clinical data into machine-readable forms is laborious and subject to observer bias. Natural language processing (NLP) of electronic health records has great potential to enhance reproducibility at scale but suffers from idiosyncrasies in physician notes and other medical records. Read More

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Classification of Complex Emotions Using EEG and Virtual Environment: Proof of Concept and Therapeutic Implication.

Front Hum Neurosci 2021 26;15:711279. Epub 2021 Aug 26.

Cognitive Neuroscience and Neuroinformatics Unit, D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil.

During the last decades, neurofeedback training for emotional self-regulation has received significant attention from scientific and clinical communities. Most studies have investigated emotions using functional magnetic resonance imaging (fMRI), including the real-time application in neurofeedback training. However, the electroencephalogram (EEG) is a more suitable tool for therapeutic application. Read More

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Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline.

Nat Protoc 2021 Sep 10. Epub 2021 Sep 10.

Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA.

The continued improvement of combinatorial CRISPR screening platforms necessitates the development of new computational pipelines for scoring combinatorial screening data. Unlike for single-guide RNA (sgRNA) pooled screening platforms, combinatorial scoring for multiplexed systems is confounded by guide design parameters such as the number of gRNAs per construct, the position of gRNAs along constructs, and additional features that may impact gRNA expression, processing or capture. In this protocol we describe Orthrus, an R package for processing, scoring and analyzing combinatorial CRISPR screening data that addresses these challenges. Read More

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September 2021

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

Nat Biotechnol 2021 09 9;39(9):1151-1160. Epub 2021 Sep 9.

CCR Collaborative Bioinformatics Resource (CCBR), Office of Science and Technology Resources, Center for Cancer Research, Bethesda, MD, USA.

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Read More

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September 2021

Accelerating antibiotic discovery through artificial intelligence.

Commun Biol 2021 Sep 9;4(1):1050. Epub 2021 Sep 9.

Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

By targeting invasive organisms, antibiotics insert themselves into the ancient struggle of the host-pathogen evolutionary arms race. As pathogens evolve tactics for evading antibiotics, therapies decline in efficacy and must be replaced, distinguishing antibiotics from most other forms of drug development. Together with a slow and expensive antibiotic development pipeline, the proliferation of drug-resistant pathogens drives urgent interest in computational methods that promise to expedite candidate discovery. Read More

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September 2021

Whole-Genome Analysis of De Novo Somatic Point Mutations Reveals Novel Mutational Biomarkers in Pancreatic Cancer.

Cancers (Basel) 2021 Aug 30;13(17). Epub 2021 Aug 30.

BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia.

It is now known that at least 10% of samples with pancreatic cancers (PC) contain a causative mutation in the known susceptibility genes, suggesting the importance of identifying cancer-associated genes that carry the causative mutations in high-risk individuals for early detection of PC. In this study, we develop a statistical pipeline using a new concept, called gene-motif, that utilizes both mutated genes and mutational processes to identify 4211 3-nucleotide PC-associated gene-motifs within 203 significantly mutated genes in PC. Using these gene-motifs as distinguishable features for pancreatic cancer subtyping results in identifying five PC subtypes with distinguishable phenotypes and genotypes. Read More

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A rigged model of the breast for preoperative surgical planning.

J Biomech 2021 Aug 4;128:110645. Epub 2021 Aug 4.

Department of Computational Science, Université du Luxembourg, Esch-sur-Alzette, Luxembourg; China Medical University Hospital, China Medical University, Taichung, Taiwan. Electronic address:

In breast surgical practice, drawing is part of the preoperative planning procedure and is essential for a successful operation. In this study, we design a pipeline to assist surgeons with patient-specific breast surgical drawings. We use a deformable torso model containing the surgical patterns to match any breast surface scan. Read More

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The classification of skateboarding tricks transfer learning pipelines.

PeerJ Comput Sci 2021 18;7:e680. Epub 2021 Aug 18.

Innovative Manufacturing, Mechatronics and Sports Laboratory, Faculty of Manufacturing and Mechatronics Engineering Technology, Universiti Malaysia Pahang, Pekan, Pahang, Malaysia.

This study aims at classifying flat ground tricks, namely Ollie, Kickflip, Shove-it, Nollie and Frontside 180, through the identification of significant input image transformation on different transfer learning models with optimized Support Vector Machine (SVM) classifier. A total of six amateur skateboarders (20 ± 7 years of age with at least 5.0 years of experience) executed five tricks for each type of trick repeatedly on a customized ORY skateboard (IMU sensor fused) on a cemented ground. Read More

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A multi-model ensemble digital twin solution for real-time unsteady flow state estimation of a pumping station.

ISA Trans 2021 Aug 24. Epub 2021 Aug 24.

China University of Petroleum-Beijing, Beijing Key Laboratory of Urban Oil and Gas Distribution Technology, Beijing, 102249, China.

This paper proposes a digital twin solution for unsteady flow state estimation in a pumping station. Digital twin is expected to accurately estimate the real-time hydraulic parameters of blind spots of the pumping station system even under some adverse conditions including the interference of observation noise and model parameters drift. To solve these challenges, a digital twin framework integrating the model-driven method, control theory and data-driven method is presented. Read More

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ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves.

PLoS Comput Biol 2021 Sep 7;17(9):e1009285. Epub 2021 Sep 7.

Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America.

Electrical stimulation and block of peripheral nerves hold great promise for treatment of a range of disease and disorders, but promising results from preclinical studies often fail to translate to successful clinical therapies. Differences in neural anatomy across species require different electrodes and stimulation parameters to achieve equivalent nerve responses, and accounting for the consequences of these factors is difficult. We describe the implementation, validation, and application of a standardized, modular, and scalable computational modeling pipeline for biophysical simulations of electrical activation and block of nerve fibers within peripheral nerves. Read More

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September 2021

Automated Registration-Based Temporal Bone Computed Tomography Segmentation for Applications in Neurotologic Surgery.

Otolaryngol Head Neck Surg 2021 Sep 7:1945998211044982. Epub 2021 Sep 7.

Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.

Objective: This study investigates the accuracy of an automated method to rapidly segment relevant temporal bone anatomy from cone beam computed tomography (CT) images. Implementation of this segmentation pipeline has potential to improve surgical safety and decrease operative time by augmenting preoperative planning and interfacing with image-guided robotic surgical systems.

Study Design: Descriptive study of predicted segmentations. Read More

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September 2021

GALAXY Workflow for Bacterial Next-Generation Sequencing De Novo Assembly and Annotation.

Curr Protoc 2021 Sep;1(9):e242

Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.

Whole-genome sequencing of prokaryotes is now readily available and affordable on next-generation sequencing platforms. However, the process of de novo assembly can be complicated and tedious for those without a background in computational biology, bioinformatics, or UNIX. Licenses for commercial bioinformatics software may be costly and limited in flexibility. Read More

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September 2021

Potential colchicine binding site inhibitors unraveled by virtual screening, molecular dynamics and MM/PBSA.

Comput Biol Med 2021 Aug 28;137:104817. Epub 2021 Aug 28.

Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/n, Ribeirão Preto, SP, 14040-903, Brazil; Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, SP, Brazil.

Microtubules have been widely studied in recent decades as an important pharmacological target for the treatment of cancer especially due to its key role in the mitosis process. Among the constituents of the microtubules, αβ-tubulin dimers stand out in view of their four distinct interaction sites, including the so-called colchicine binding site (CBS) - a promising target for the development of new tubulin modulators. When compared to other tubulin sites, targeting the CBS is advantageous because this site is able to host ligands with lower molecular volume and lipophilicity, thus reducing the chances of entailing the phenomenon of multiple drug resistance (MDR) - one of the main reasons of failure in chemotherapy. Read More

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Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks.

Front Mol Biosci 2021 18;8:715972. Epub 2021 Aug 18.

Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.

Modern proteins have been shown to share evolutionary relationships subdomain-sized fragments. The assembly of such fragments through duplication and recombination events led to the complex structures and functions we observe today. We previously implemented a pipeline that identified more than 1,000 of these fragments that are shared by different protein folds and developed a web interface to analyze and search for them. Read More

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Simulating the time evolving geometry, mechanical properties, and fibrous structure of bioprosthetic heart valve leaflets under cyclic loading.

J Mech Behav Biomed Mater 2021 Nov 19;123:104745. Epub 2021 Aug 19.

James T. Willerson Center for Cardiovascular Modeling and Simulation, Oden Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712-0027, USA. Electronic address:

Currently, the most common replacement heart valve design is the 'bioprosthetic' heart valve (BHV), which has important advantages in that it does not require permanent anti-coagulation therapy, operates noiselessly, and has blood flow characteristics similar to the native valve. BHVs are typically fabricated from glutaraldehyde-crosslinked pericardial xenograft tissue biomaterials (XTBs) attached to a rigid, semi-flexible, or fully collapsible stent in the case of the increasingly popular transcutaneous aortic valve replacement (TAVR). While current TAVR assessments are positive, clinical results to date are generally limited to <2 years. Read More

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November 2021

Covalent flexible peptide docking in Rosetta.

Chem Sci 2021 Aug 12;12(32):10836-10847. Epub 2021 Jul 12.

Department of Chemical and Structural Biology, The Weizmann Institute of Science Rehovot 7610001 Israel

Electrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains a challenge. Here, we present Rosetta CovPepDock, a computational pipeline for peptide docking that incorporates covalent binding between the peptide and a receptor cysteine. Read More

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Improving reproducibility in synchrotron tomography using implementation-adapted filters.

J Synchrotron Radiat 2021 Sep 12;28(Pt 5):1583-1597. Epub 2021 Aug 12.

Computational Imaging, Centrum Wiskunde and Informatica, Amsterdam, The Netherlands.

For reconstructing large tomographic datasets fast, filtered backprojection-type or Fourier-based algorithms are still the method of choice, as they have been for decades. These robust and computationally efficient algorithms have been integrated in a broad range of software packages. The continuous mathematical formulas used for image reconstruction in such algorithms are unambiguous. Read More

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September 2021

Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource.

Mol Biol Evol 2021 Sep 1. Epub 2021 Sep 1.

Department of General and Medical Genetics, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. Read More

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September 2021

Detecting copy number variation in next generation sequencing data from diagnostic gene panels.

BMC Med Genomics 2021 Aug 31;14(1):214. Epub 2021 Aug 31.

Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway.

Background: Detection of copy number variation (CNV) in genes associated with disease is important in genetic diagnostics, and next generation sequencing (NGS) technology provides data that can be used for CNV detection. However, CNV detection based on NGS data is in general not often used in diagnostic labs as the data analysis is challenging, especially with data from targeted gene panels. Wet lab methods like MLPA (MRC Holland) are widely used, but are expensive, time consuming and have gene-specific limitations. Read More

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Systematic identification of non-canonical transcription factor motifs.

BMC Mol Cell Biol 2021 Aug 31;22(1):44. Epub 2021 Aug 31.

Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.

Sequence-specific transcription factors (TFs) recognize motifs of related nucleotide sequences at their DNA binding sites. Upon binding at these sites, TFs regulate critical molecular processes such as gene expression. It is widely assumed that a TF recognizes a single "canonical" motif, although recent studies have identified additional "non-canonical" motifs for some TFs. Read More

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Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis.

mBio 2021 Aug 31;12(4):e0114321. Epub 2021 Aug 31.

Broad Institutegrid.66859.34 of MIT and Harvard, Cambridge, Massachusetts, USA.

Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known ( = 44) or suspected ( = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Read More

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A scanner-specific framework for simulating CT images with tube current modulation.

Phys Med Biol 2021 Sep 13;66(18). Epub 2021 Sep 13.

Center for Virtual Imaging Trials, Carl E. Ravin Advanced Imaging Laboratories, Department of Radiology, Duke University School of Medicine, NC, United States of America.

Although tube current modulation (TCM) is routinely implemented in modern computed tomography (CT) scans, no existing CT simulator is capable of generating realistic images with TCM. The goal of this study was to develop such a framework to (1) facilitate patient-specific optimization of TCM parameters and (2) enable future virtual imaging trials (VITs) with more clinically realistic image quality and x-ray flux distributions. The framework was created by developing a TCM module and integrating it with an existing CT simulator (DukeSim). Read More

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September 2021

Platelet-coated circulating tumor cells are a predictive biomarker in patients with metastatic castrate resistant prostate cancer.

Mol Cancer Res 2021 Aug 30. Epub 2021 Aug 30.

Michelson Center for Convergent Bioscience, University of Southern California.

Metastatic Castration-Resistant Prostate Cancer (mCRPC) includes a subset of patients with particularly unfavorable prognosis characterized by combined defects in at least two of three tumor suppressors PTEN, RB1, and TP53 as aggressive variant prostate cancer molecular signature (AVPC-MS). We aimed to identify CTC signatures that could inform treatment decisions of mCRPC patients with cabazitaxel-carboplatin combination therapy versus cabazitaxel alone. Liquid biopsy samples were collected prospectively from 79 patients for retrospective analysis. Read More

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A Machine Learning Pipeline for Measurement of Arterial Stiffness in A-Mode Ultrasound.

IEEE Trans Ultrason Ferroelectr Freq Control 2021 Aug 30;PP. Epub 2021 Aug 30.

Arterial stiffness (AS) of the carotid artery is an early marker of stratifying cardiovascular disease risk. This paper aims to improve performance of ARTSENS, a non-invasive A-mode ultrasound-based device for measuring AS. The primary objective of ARTSENS is to enable measurement of elastic modulus using A-Mode ultrasound and Blood pressure. Read More

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Combined computational and intracellular peptide library screening: towards a potent and selective Fra1 inhibitor.

RSC Chem Biol 2021 Apr 29;2(2):656-668. Epub 2021 Jan 29.

Department of Biology & Biochemistry, University of Bath Claverton Down Bath BA2 7AY UK +44 (0)1225386867.

To date, most research into the inhibition of oncogenic transcriptional regulator, Activator Protein 1 (AP-1), has focused on heterodimers of cJun and cFos. However, the Fra1 homologue remains an important cancer target. Here we describe library design coupled with computational and intracellular screening as an effective methodology to derive an antagonist that is selective for Fra1 relative to Jun counterparts. Read More

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A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors.

Proteins 2021 Aug 29. Epub 2021 Aug 29.

School of Chemistry, University of Bristol, Bristol, UK.

Antibiotic resistance is a major threat to global public health. β-lactamases, which catalyze breakdown of β-lactam antibiotics, are a principal cause. Metallo β-lactamases (MBLs) represent a particular challenge because they hydrolyze almost all β-lactams and to date no MBL inhibitor has been approved for clinical use. Read More

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Deep learning-based parameter estimation in fetal diffusion-weighted MRI.

Neuroimage 2021 Aug 26;243:118482. Epub 2021 Aug 26.

Computational Radiology Laboratory (CRL), Department of Radiology, Boston Children's Hospital, and Harvard Medical School, USA.

Diffusion-weighted magnetic resonance imaging (DW-MRI) of fetal brain is challenged by frequent fetal motion and signal to noise ratio that is much lower than non-fetal imaging. As a result, accurate and robust parameter estimation in fetal DW-MRI remains an open problem. Recently, deep learning techniques have been successfully used for DW-MRI parameter estimation in non-fetal subjects. Read More

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