Author

Marcus H. Stoiber

Lawrence Berkeley National Laboratory

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

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Bioinformatics· 3 Developmental Biology· 1

Signature Assays, Organisms & Methods

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Assay:long-read sequencing· 3 Approach:statistical model· 3 Approach:deep learning· 2 Research Focus:software / tool· 2 Research Focus:variant calling· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Abdul Kadir MukarramiD· 1 shared Ada Jiménez-GonzáleziD· 1 shared Alison C. McGarveyiD· 1 shared Anne E. EagleiD· 1 shared Benjamín Hernández-RodrígueziD· 1 shared Bernard PeersiD· 1 shared Boris LenhardiD· 1 shared Carl KingsfordiD· 1 shared

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2017-2024 · peak 2/yr

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10 top collaborators · 36 mutual co-author links

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1 shared paperDevelopmental Biology

Abdul Kadir MukarramORCID

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4 papers

Recent·Most cited

Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework

Haotian Teng, Marcus H. Stoiber, Ziv Bar‐Joseph, Carl Kingsford

The paper introduces Xron, a semi-supervised basecaller for detecting m6A methylation from nanopore sequencing by combining synthetic and experimental data.

Genome Research · Nov 1, 2024Peer-reviewedBioinformatics

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish

Damir Baranas̆ić, Matthias Hörtenhuber, Piotr J. Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Várnai, Yavor Hadzhiev, Ada Jiménez-González, Nan Li, Joseph W. Wragg, Fabio M. D’Orazio, Đorđe Relić, Mikhail V. Pachkov, Noèlia Díaz, , Ferenc Müller

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

Nature Genetics · Jul 1, 2022Peer-reviewedDevelopmental Biology

BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal

Marcus H. Stoiber, James Brown

BasecRAWller enables real-time nanopore basecalling directly from raw signals, offering streaming capabilities, tunable error rates, and efficient computation.

bioRxiv · May 1, 2017 · PreprintBioinformatics

De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

Marcus H. Stoiber, Joshua Quick, Rob S Egan, Ji Eun Lee, S Celniker, Robert K. Neely, Nicholas James Loman, Len A. Pennacchio, James B. Brown

Base-by-base tests of raw nanopore current, native versus amplified DNA, detect 4mC, 5mC and 6mA without training data, recovering seven methylases' motifs (AUC 0.62–0.97).

bioRxiv · Apr 10, 2017 · PreprintBioinformatics✦ In-depth digest