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David Heller
Researcher at Max Planck Society
Publications - 20
Citations - 670
David Heller is an academic researcher from Max Planck Society. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 9, co-authored 17 publications receiving 317 citations. Previous affiliations of David Heller include Hasso Plattner Institute & University of California, Santa Cruz.
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Journal ArticleDOI
SVIM: structural variant identification using mapped long reads.
David Heller,Martin Vingron +1 more
TL;DR: SVIM is unique in its capability of extracting both the genomic origin and destination of duplications, and compares favorably with existing tools in evaluations on simulated data and real datasets from Pacific Biosciences and Nanopore sequencing machines.
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Genotyping structural variants in pangenome graphs using the vg toolkit.
Glenn Hickey,David Heller,David Heller,Jean Monlong,Jonas Andreas Sibbesen,Jouni Sirén,Jordan M. Eizenga,Eric T. Dawson,Erik Garrison,Adam M. Novak,Benedict Paten +10 more
TL;DR: It is shown that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments and is benchmarked against state-of-the-art SV genotypes using three sequence-resolved SV catalogS generated by recent long-read sequencing studies.
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Chromosome-scale, haplotype-resolved assembly of human genomes.
Shilpa Garg,Arkarachai Fungtammasan,Andrew Carroll,Mike Chou,Anthony D. Schmitt,Xiang Zhou,Stephen Mac,Paul Peluso,Emily Hatas,Jay Ghurye,Jared Maguire,Medhat Mahmoud,Haoyu Cheng,David Heller,Justin M. Zook,Tobias Moemke,Tobias Marschall,Tobias Marschall,Fritz J. Sedlazeck,John Aach,Chen-Shan Chin,George M. Church,Heng Li +22 more
TL;DR: A method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day, outperforming other approaches in terms of both contiguity and phasing completeness.
Journal ArticleDOI
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
David Heller,David Heller,Ralf Krestel,Uwe Ohler,Martin Vingron,Annalisa Marsico,Annalisa Marsico +6 more
TL;DR: SSHMM, an RNA motif finder based on a hidden Markov model (HMM) and Gibbs sampling which fully captures the relationship between RNA sequence and secondary structure preference of a given RBP, is developed.
Journal ArticleDOI
The mole genome reveals regulatory rearrangements associated with adaptive intersexuality
Francisca M. Real,Francisca M. Real,Stefan A. Haas,Paolo Franchini,Peiwen Xiong,Oleg Simakov,Heiner Kuhl,Robert Schöpflin,Robert Schöpflin,David Heller,Mohammad Hossein Moeinzadeh,Verena Heinrich,Thomas Krannich,Annkatrin Bressin,Michaela F. Hartmann,Stefan A. Wudy,Dina K. N. Dechmann,Dina K. N. Dechmann,Alicia Hurtado,Francisco J. Barrionuevo,Magdalena Schindler,Magdalena Schindler,Izabela Harabula,Marco Osterwalder,Marco Osterwalder,Michael Hiller,Lars Wittler,Axel Visel,Axel Visel,Axel Visel,Bernd Timmermann,Axel Meyer,Martin Vingron,Rafael Jiménez,Stefan Mundlos,Stefan Mundlos,Darío G. Lupiáñez +36 more
TL;DR: Phylogenomic analyses identify altered regulation at the CYP17A1 and FGF9 loci that contribute to ovotestis formation in moles and highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.