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PubMed2026

A genome-wide coverage-based pipeline for the identification of host-derived candidate DNA biomarkers from cell-free blood.

We have created a new data-analysis pipeline for the discovery of host-specific candidate DNA biomarkers derived from sequencing data of cell-free blood. Unlike approaches that rely on specific molecular or genetic signatures, our method leverages the coverage distribution of cell-free DNA sequences mapped to a reference genome, applying statistical analyses to identify informative short genomic regions for biomarker discovery. The pipeline is applicable to diverse diseases and can be used to analyze cell-free DNA sequences from plasma or serum to identify candidate biomarkers that are characteristic of disease states in mammals. Core functionalities were developed in Java and integrated with open-source software tools for the preprocessing of raw sequencing data, complemented by Python scripts for the machine-learning analysis and statistical validation. The pipeline is designed for HPC use and users can access the pipeline through a Galaxy workflow, which offers a user-friendly web interface for input selection prior to execution and analysis progress monitoring. Performance tests, carried out using duplicate sets of COVID-19 samples and controls, showed linear scalability of execution time with an increasing dataset size, as well as a substantial reduction in execution time through parallelized computation, whereby each HPC node is used to process the data of one chromosome. Further statistical tests confirmed the quality of the pipeline's results by showing that the set of identified candidate biomarkers remained stable across varying dataset sizes.

Biomarkers↗

PubMed2026

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Advances in data acquisition, artificial intelligence, and integrative bioinformatics are driving the rapid evolution of computational mass spectrometry, and in turn, transforming modern proteomics, metabolomics, and lipidomics. These developments have greatly increased the scale and complexity of mass spectrometry data, underscoring the importance of evolving accurate, transparent, efficient and reproducible data processing workflows. Addressing these challenges requires collaborative innovation that brings together expertise in software engineering, statistics, and biology. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of the European Proteomics Association (EuPA), fosters a culture of open, community-driven development through its biennial Developers Meetings and Winter Schools. This commentary summarizes the scientific background and outcomes of the EuBIC-MS Developers Meeting 2025, which took place in Novacella, Italy. Three keynote presentations highlighted major frontiers in the field: deep proteome and phosphoproteome profiling, text mining for protein-protein interaction extraction, and scalable proteomics for AI-driven drug discovery. Seven community-selected hackathons addressed emerging challenges such as single-cell proteomics data analysis, FAIR metadata extraction, deep learning frameworks, R-Python interoperability, and DIA validation. Together, these efforts demonstrate the potential for scientific and technical innovation to arise from open collaboration, and highlight how community-driven initiatives can accelerate progress in computational mass spectrometry. SIGNIFICANCE: Modern proteomics increasingly depends on computational advances to translate complex, high-dimensional data into biological knowledge. The EuBIC-MS Developers Meeting 2025 exemplifies how community-driven collaboration can directly accelerate this process by bringing together experts from bioinformatics, statistics, and experimental proteomics to co-develop open, interoperable, and reproducible analytical tools. By fostering shared software frameworks, transparent benchmarking, and collaborative problem solving, the EuBIC-MS community helps ensure that technological innovation translates into reliable biological insights. This collaborative model strengthens the foundation for quantitative, system-level understanding of proteomes and establishes a sustainable path for integrating artificial intelligence and next-generation data acquisition into routine biological discovery. This commentary shows some current highlights in the field of computational mass spectrometry and community-based approaches undertaken during the most recent Developers Meeting to solve these challenges. The approaches discussed and initiated during the meeting - ranging from deep proteome profiling and phosphosite mapping to text mining, single-cell data analysis, and FAIR metadata extraction - address key bottlenecks that currently limit the biological interpretability and comparability of proteomics data.

Mass Spectrometry↗

PubMedDate not supplied

Iplt--image processing library and toolkit for the electron microscopy community.

We present the foundation for establishing a modular, collaborative, integrated, open-source architecture for image processing of electron microscopy images, named iplt. It is designed around object oriented paradigms and implemented using the programming languages C++ and Python. In many aspects it deviates from classical image processing approaches. This paper intends to motivate developers within the community to participate in this on-going project. The iplt homepage can be found at http://www.iplt.org.

Image Processing, Computer-Assisted↗

PubMed2005

Automated molecular microscopy: the new Leginon system.

We report here on the current state of our efforts in automated molecular microscopy. Our primary automated data acquisition software system, Leginon, has been completely redesigned over the past two years. The new distributed system has been developed using the Python programming language and is compatible with both Linux and Windows operating systems. The new flexible architecture was designed to allow for the development of customized data collection protocols, several of which are described here. The system has been used to acquire data for approximately 150 experiments and we have demonstrated the capacity for high throughput data acquisition by acquiring images of more than 100,000 particles in a single session at the microscope.

Microscopy, Electron↗

PubMed2006

EMAN2: an extensible image processing suite for electron microscopy.

EMAN is a scientific image processing package with a particular focus on single particle reconstruction from transmission electron microscopy (TEM) images. It was first released in 1999, and new versions have been released typically 2-3 times each year since that time. EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1. The user-level programs are better documented, more straightforward to use, and written in the Python scripting language, so advanced users can modify the programs' behavior without any recompilation. A completely rewritten 3D transformation class simplifies translation between Euler angle standards and symmetry conventions. The core C++ library has over 500 functions for image processing and associated tasks, and it is modular with introspection capabilities, so programmers can add new algorithms with minimal effort and programs can incorporate new capabilities automatically. Finally, a flexible new parallelism system has been designed to address the shortcomings in the rigid system in EMAN1.

Algorithms↗

PubMed2006

SPARX, a new environment for Cryo-EM image processing.

SPARX (single particle analysis for resolution extension) is a new image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment with a novel data/process-flow infrastructure, an extensive library of Python scripts that perform specific TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library and cctbx, the open-source computational crystallography library from PHENIX. The design of the system is such that future inclusion of other image processing libraries is a straightforward task. The SPARX infrastructure intelligently handles retention of intermediate values, even those inside programming structures such as loops and function calls. SPARX and all dependencies are free for academic use and available with complete source.

Computational Biology↗

PubMed2006

SPIRE: the SPIDER reconstruction engine.

SPIRE is a Python program written to modernize the user interaction with SPIDER, the image processing system for electron microscopical reconstruction projects. SPIRE provides a graphical user interface (GUI) to SPIDER for executing batch files of SPIDER commands. It also lets users quickly view the status of a project by showing the last batch files that were run, as well as the data files that were generated. SPIRE handles the flexibility of the SPIDER programming environment through configuration files: XML-tagged documents that describe the batch files, directory trees, and presentation of the GUI for a given type of reconstruction project. It also provides the capability to connect to a laboratory database, for downloading parameters required by batch files at the start of a project, and uploading reconstruction results at the end of a project.

Computational Biology↗

PubMed2026

pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.

The increasing scale and complexity of proteomics data demand robust, scalable, and interpretable quality control (QC) frameworks to ensure data reliability and reproducibility. Here, we present pmultiqc, an open-source Python package that standardizes and generates web-based QC reports across multiple proteomics data analysis platforms. Built on top of the widely adopted MultiQC framework, pmultiqc offers specialized modules tailored to mass spectrometry workflows, with full initial support for quantms, DIA-NN, MaxQuant/MaxDIA, FragPipe, and mzIdentML/mzML-based pipelines. The package computes a wide range of QC metrics, including raw intensity distributions, identification rates, retention time consistency, and missing value patterns, and presents them in interactive, publication-ready reports. By leveraging sample metadata in the Sample and Data Relationship Format format, pmultiqc enables metadata-aware QC and introduces, for the first time in proteomics, QC reports and metrics guided by standardized sample metadata. Its modular architecture allows easy extension to new workflows and formats. Alongside comprehensive documentation and examples for running pmultiqc locally or integrated into existing workflows, we offer a cloud-based service that enables users to generate QC reports from their own data or public PRIDE datasets.

Proteomics↗

PubMed2006

What's in a name? The vervet predator calls and the limits of the Washburnian synthesis.

After the Second World War, a renaissance in field primatology took place in the United States under the aegis of the 'new physical anthropology'. Its leader, Sherwood Washburn, envisioned a science uniting studies of hominid fossils with Darwinian population genetics, experimental functional anatomy, and field observation of non-human primates and human hunter-gatherers. Thanks to Washburn's stimulus, his colleague at Berkeley, the bird ethologist Peter Marler, took up the study of the natural communicative behaviour of apes and monkeys. When Marler's first primatological student, Thomas Struhsaker, reported in the mid-1960s that the vervet monkeys of Amboseli, Kenya, give acoustically distinct alarm calls to different predators, and respond to alarm calls as if to the sight of those predators, a debate broke out over whether the vervet calls thus function as names, translating as 'leopard', 'eagle' and 'python'. Washburn and his students argued that no matter what the behavioural evidence, vervet calls could not be predator names, since monkeys had been shown to lack the neuroanatomical basis of naming. This controversy thus reveals, first, the persistence of older patterns of disciplinary allegiance within the new, synthetic physical anthropology; and second, the impotence of adaptationist Darwinism--common to both sides of the debate--as a force for unity.

Animal Communication↗

PubMed2005

A component-based software environment for visualizing large macromolecular assemblies.

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

Capsid↗

PubMed2026

Protocol to predict gene expression from transcriptomic data using PREDICT.

Linking DNA sequence variation to context-specific transcriptional programs is a critical challenge in regulatory genomics, especially for non-model organisms. Here, we present PREDICT, a modular Python package for discovering cis-regulatory elements and transcription factor binding motifs. We describe steps to identify enriched k-mers from differentially expressed genes, map them to known motifs, quantify their impact on gene expression, and visualize motif co-occurrences. PREDICT provides a robust, k-mer-based approach to uncover regulatory logic in diverse genomic systems. For complete details on the use and execution of this protocol, please refer to Yen et al. and Liu et al.1,2.

Gene Expression Profiling↗

PubMed2004

Molecular characterization of the leopard gecko POMC gene and expressional change in the testis by acclimation to low temperature and with a short photoperiod.

The gene for proopiomelanocortin (POMC), a common precursor of malanotropins, corticotropin, and beta-endorphin, was isolated and analyzed in the squamata species, the leopard gecko, Eublepharis macularius. Leopard gecko POMC (lgPOMC) cDNA is composed of 1299bp, excluding the poly(A) tail, and encodes 270 amino acids. The deduced amino acid sequence showed the same structural organization as that of other species and displayed identity with those of other vertebrates: 68% with mud turtles, 57/57% with African clawed frog A/B, 53% with chickens, and 45% with mice. In a phylogenic tree, the lgPOMC clustered with the sequences of the mud turtle POMC and python POMC. The lgPOMC gene comprises three exons and two introns and this structure is consistent with humans, rats, mice, African clawed frog and zebrafish. RT-PCR analysis revealed that the lgPOMC mRNA was expressed only in the whole brain, pituitary, and gonads. To analyze in more detail, a competitive assay system to quantify the expression levels of POMC mRNA was established. We measured the POMC mRNA expression levels in the leopard gecko testes following transfer from a condition of 29 degrees C, 16L/8D to 18 degrees C, 10L/14D over 6 weeks. This 6-week acclimation increased the POMC mRNA expression levels significantly. This suggests that the leopard gecko POMC-derived peptides play a role in the mediation of the effect of environmental factors on reproduction.

Amino Acid Sequence↗

PubMed1999

Bradykinin and its receptors in non-mammalian vertebrates.

The generation of bradykinin (BK) in blood by the action of the kallikrein-kinin system has been studied intensively in mammals but the system has received relatively little attention in non-mammalian vertebrates. The plasma of crocodilians and Testudines (turtles and tortoises) contains all the components of the kallikrein-kinin system found in mammals (prekallikrein activator, prekallikrein, kininogen, and kininases) and activation results in generation of [Thr6]-BK. Plasma of birds and snakes probably lacks a prekallikrein activator analogous to mammalian Factor XII but treatment with exogenous proteases (pig pancreatic kallikrein and/or trypsin) generates [Thr6, Leu8]-BK (chicken), [Ala1, Thr6]-BK (python) and [Val1, Thr6]-BK (colubrid snakes). The skins of certain frogs, particularly of the genus Rana, contain very high concentrations of BK-related peptides but their pathway of biosynthesis involves the action of cellular endoproteinase(s) cleaving at the site of single arginyl residues rather than by the action of the kallikrein-kinin system. Evidence for a prekallikrein activator in fish plasma is lacking but treatment with exogenous proteases generates [Arg0, Trp5, Leu8]-BK (trout and cod), [Trp5]-BK (bowfin and gar), [Met1, Met5]-BK (sturgeon). The cardiovascular actions and effects upon gastrointestinal smooth muscle of these peptides in their species of origin differ markedly. For example, intra-arterial injections of the native BK peptides into unanesthetized fish produce transient hypertension in the cod, complex depressor and pressor responses in the trout and bowfin and hypotension in the sturgeon. Pharmacological studies in snakes and fish and with the recombinantally expressed chicken BK receptor have demonstrated that the BK receptors in the tissues of non-mammalian vertebrates have appreciably different ligand binding properties from the well-characterized mammalian B1 and B2 receptors.

Amphibians↗

PubMed1993

Nonvenomous snakebite in Massachusetts: prophylactic antibiotics are unnecessary.

STUDY OBJECTIVE: To investigate wound infection in nonvenomous snakebite. DESIGN: Prospective clinical series. SETTING: Massachusetts Poison Control System. PARTICIPANTS: Seventy-two consecutive children and adults with nonenvenomated snakebite wounds. INTERVENTIONS: Patients were examined and advised that there was no published clinical evidence that prophylactic antibiotics were beneficial for nonenvenomated snakebites. They were re-examined five to ten days after the bite. MAIN RESULTS: Four patients used prophylactic antibiotics; 68 did not. There were no wound infections. Plain radiographs revealed a snake tooth fragment in the persistently tender wound of one patient bitten by his pet python. CONCLUSION: Despite reports that pathogenic bacteria can be isolated from snakes' mouths, nonenvenomated snakebites in Massachusetts usually do not require prophylactic antibiotic therapy. Radiography is occasionally indicated for persistently tender wounds inflicted by large snakes.

Adolescent↗

PubMed1999

Neuroendocrine peptides (insulin, pancreatic polypeptide, neuropeptide Y, galanin, somatostatin, substance P, and neuropeptide gamma) from the desert tortoise, Gopherus agassizii.

The traditional view that Testudines (tortoises and turtles) should be regarded as the surviving clade of the anapsid reptiles rather than classified with the diapsid reptiles (snakes, lizards, and crocodiles) has recently been challenged. Neuropeptide Y, neuropeptide gamma, and somatostatin-14 were isolated from an extract of the brain, substance P and galanin from an extract of the intestine, and insulin and pancreatic polypeptide from an extract of the pancreas of the desert tortoise, Gopherus agassizii. Despite that crocodilians did not appear until the late Triassic, the amino acid sequences of the tortoise peptides resemble those of the American alligator quite closely. The primary structures of neuropeptide Y, somatostatin-14, and neuropeptide gamma are the same in tortoise and alligator. The primary structures of substance P, insulin, galanin, and pancreatic polypeptide in the two species differ by 1, 3, 5, and 8 amino acid residues, respectively. Although fewer neurohormonal peptides from squamates (lizards and snakes) have been characterized, the primary structures of neuropeptide gamma, insulin, and pancreatic polypeptide from the Burmese python and the desert tortoise differ by 3, 8, and 18 residues, respectively. The data suggest, therefore, a closer phylogenetic relationship between Testudines and Crocodilians than that derived from 'classical' analyses based on morphological criteria and the fossil record.

Amino Acid Sequence↗

PubMed2002

EMXtalOrg: an EM tilt data organization and processing system.

The EMXtalOrg software package organizes and processes electron microscope (EM) data from indexed images of tilted two-dimensional (2D) protein crystals. The package, which is freely available, was written to facilitate the processing of amplitude and phase (aph) data from 2D EM projections into three-dimensional (3D) reconstructions. The suite takes as input contrast transfer function corrected aph files and generates lattice line data to yield HKL files which can be output for viewing 3D structures with existing data visualization programs. Additionally, the package offers a number of other processing features, and provides a convenient graphical interface for several image processing programs devoted to the analysis of 2D crystals. The package is written in the Python scripting language using the Tcl/ Tk toolkit for the graphical user interface, making it portable and easy to modify by the user. The package provides an integrated environment to simplify the process of obtaining 3D structures from 2D crystals.

Crystallization↗

PubMed1997

Exotic reptile bites.

Reptiles are a growing part of the exotic pet trade, and reptile bites have been considered innocuous in the emergency medicine literature. Two cases are reported of reptile bites, one from a green iguana and the other from a reticulated python. The treatment concerns associated with reptile bites are discussed.

Adult↗

PubMed2002

Snake phylogeny: evidence from nuclear and mitochondrial genes.

We constructed phylogenies of snakes from the c-mos and cytochrome b genes using conventional phylogenetic methods as well as the relatively new method of Bayesian inference. For all methods, there was excellent congruence between the c-mos and cytochrome b genes, implying a high level of support for the shared clades. Our results agree with previous studies in two important respects: first, that the scolecophidians and alethinophidians are monophyletic sister clades; and second, that the Colubroidea is a monophyletic group with the Acrochordidae as its sister clade. However, our results differ from previous studies in the finding that Loxocemus and Xenopeltis cluster with pythons. An additional noteworthy result from our data is that the genera Exiliboa and Ungaliophis, often placed with Tropidophis (and Trachyboa, not included in the present study) in the Tropidophiidae, are in reality boids.

Animals↗