Genomics

Transcriptional architecture and Pol II regulation at promoters, enhancers, and enhancer clusters in Canis lupus familiaris
Samu V Himanen, Adelina Rabenius, Serhat Aktay, Joel Tekoniemi, Anniina Vihervaara

bioRxiv 2025.03.20.644285; doi: https://doi.org/10.1101/2025.03.20.644285 New Results

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CarpeDeam: A De Novo Metagenome Assembler for Heavily Damaged Ancient Datasets
Louis Kraft, Johannes Soeding, Martin Steinegger, Annika Jochheim, Antonio Fernandez-Guerra, Gabriel Renaud

bioRxiv 2024.08.09.607291; doi: https://doi.org/10.1101/2024.08.09.607291 New Results

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Completed genomes from Variovorax provide insight into genome diversification through horizontal gene transfer
Christopher J NeVille, Paul Orwin

bioRxiv 2025.03.19.644167; doi: https://doi.org/10.1101/2025.03.19.644167 New Results

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PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases
Jorge Eduardo Avila Cartes, Simone Ciccolella, Luca Denti, Raghuram Raghuram Dandinasivara, Gianluca Della Vedova, Paola Bonizzoni, Alexander Schonhuth

bioRxiv 2025.03.19.644115; doi: https://doi.org/10.1101/2025.03.19.644115 New Results

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Disinfecting eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data
Nikolay Oskolkov, Chenyu Jin, Samantha Lopez Clinton, Benjamin Guinet, Flore Wijnands, Ernst Johnson, Verena E. Kutschera, Cormac M. Kinsella, Peter D. Heintzman, Tom van der Valk

bioRxiv 2025.03.19.644176; doi: https://doi.org/10.1101/2025.03.19.644176 New Results

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A simplified hybrid capture approach retains high specificity and enables PCR-free workflow
Adeline Mah, Xiaodong Qi, June Zhao, Kelly Wiseman, Laure Edoli, Kyle Metcalfe, Kyle Donohoe, Micah Ojeda, Sophie Billings, Juan Moreno, Marina McCowin, Ben Krajacich, Kevin Green, Ram Adhikary, Andrew Boddicker, Joshua Chan, Peter Mains, Bryan Lajoie, Sean Devitt, Semyon Kruglyak, Shawn Levy, Michael Previte

bioRxiv 2025.03.18.644033; doi: https://doi.org/10.1101/2025.03.18.644033 New Results

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Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity
Kenneth Pham, Thomas Malachowski, Linda Zhou, Ji Hun Kim, Chuanbin Su, Jennifer E. Phillips-Cremins

bioRxiv 2025.03.19.644148; doi: https://doi.org/10.1101/2025.03.19.644148 New Results

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cfMethDB: a comprehensive cfDNA methylation data resource for cancer biomarkers
Yuanhui Sun, Zhixian Zhu, Qiangwei Zhou, Zhe Wang, Yuying Hou, Xionghui Zhou, Guoliang Li

bioRxiv 2025.03.19.644046; doi: https://doi.org/10.1101/2025.03.19.644046 New Results

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FULL-LENGTH HYBRID TRANSCRIPTOME OF THE OLFACTORY ROSETTE IN SENEGALESE SOLE (Solea senegalensis): AN ESSENTIAL GENOMIC RESOURCE TO IMPROVE REPRODUCTION AT FARMS
Dorinda Torres Sabino, Andres Blnco Hortas, Paula Rodriguez Villamayor, Inmaculada Rasines, Ignacio Martin, Carmen Bouza, Diego Robledo, Paulino Martinez

bioRxiv 2025.03.19.644159; doi: https://doi.org/10.1101/2025.03.19.644159 New Results

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Host traits impact the outcome of metagenomic library preparation from dental calculus samples across diverse mammals
Markella Moraitou, Johnny Richards, Chanah Bolyos, Konstantina Saliari, Emmanuel Gilissen, Zena Timmons, Andrew C. Kitchener, Olivier S. G. Pauwels, Richard Sabin, Phaedra Kokkini, Roberto Portela Miguez, Katerina Guschanski

bioRxiv 2025.03.19.643754; doi: https://doi.org/10.1101/2025.03.19.643754 New Results

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Genomics

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