Related papers: MotifbreakR v2: extended capability and database i…
Protein structures and functions are determined by a contiguous arrangement of amino acid sequences. Designing novel protein sequences and structures with desired geometry and functions is a complex task with large state spaces. Here we…
Bacterial plant pathogens rely on a battalion of transcription factors to fine-tune their response to changing environmental conditions and marshal the genetic resources required for successful pathogenesis. Prediction of transcription…
We introduce Motif-2-12.7B-Reasoning, a 12.7B parameter language model designed to bridge the gap between open-weight systems and proprietary frontier models in complex reasoning and long-context understanding. Addressing the common…
Gene co-expression databases in model plants such as Arabidopsis and rice have been extensively developed and utilised for predicting gene function and identifying functional modules for underlying biological processes. However, such tools…
In software, a vulnerability is a defect in a program that attackers might utilize to acquire unauthorized access, alter system functions, and acquire information. These vulnerabilities arise from programming faults, design flaws, incorrect…
Human fashion understanding is one crucial computer vision task since it has comprehensive information for real-world applications. This focus on joint human fashion segmentation and attribute recognition. Contrary to the previous works…
Inferring the activities of transcription factors from high-throughput transcriptomic or open chromatin profiling, such as RNA-/CAGE-/ATAC-Seq, is a long-standing challenge in systems biology. Identification of highly active master…
Recent tool-use frameworks powered by vision-language models (VLMs) improve image understanding by grounding model predictions with specialized tools. Broadly, these frameworks leverage VLMs and a pre-specified toolbox to decompose the…
Molecular docking is a crucial step in drug development, which enables the virtual screening of compound libraries to identify potential ligands that target proteins of interest. However, the computational complexity of traditional docking…
Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, motif finding algorithms of increasingly high performance are required to process the big…
Mutational signatures are patterns of somatic mutations in tumor genomes that provide insights into underlying mutagenic processes and cancer origin. Developing reliable methods for their estimation is of growing importance in cancer…
The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena. By utilizing…
Binary-only fuzzing often struggles with achieving thorough code coverage and uncovering hidden vulnerabilities due to limited insight into a program's internal dataflows. Traditional grey-box fuzzers guide test case generation primarily…
DNA microarrays are devices that are able, in principle, to detect and quantify the presence of specific nucleic acid sequences in complex biological mixtures. The measurement consists in detecting fluorescence signals from several spots on…
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…
Statistical analysis of evolutionary-related protein sequences provides insights about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their…
Computational analyses of, e.g., genomic, proteomic, or metabolomic data, commonly result in one or more sets of candidate genes, proteins, or enzymes. These sets are often the outcome of clustering algorithms. Subsequently, it has to be…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
The innovation of next-generation sequencing (NGS) techniques has significantly reduced the price of genome sequencing, lowering barriers to future medical research; it is now feasible to apply genome sequencing to studies where it would…
Set queries are fundamental operations in computer systems and applications.This paper addresses the fundamental problem of designing a probabilistic data structure that can quickly process set queries using a small amount of memory. We…