Florian P Breitwieser
Florian P Breitwieser
Principal Software Engineer at SOPHiA Genetics
Verified email at
Cited by
Cited by
Centrifuge: rapid and sensitive classification of metagenomic sequences
D Kim, L Song, FP Breitwieser, SL Salzberg
Genome research 26 (12), 1721-1729, 2016
Bracken: estimating species abundance in metagenomics data
J Lu, FP Breitwieser, P Thielen, SL Salzberg
PeerJ Computer Science 3, e104, 2017
A review of methods and databases for metagenomic classification and assembly
FP Breitwieser, J Lu, SL Salzberg
Briefings in bioinformatics 20 (4), 1125-1136, 2019
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
FP Breitwieser, SL Salzberg
Bioinformatics 36 (4), 1303-1304, 2020
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
FP Breitwieser, DN Baker, SL Salzberg
Genome biology 19, 1-10, 2018
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
M Pertea, A Shumate, G Pertea, A Varabyou, FP Breitwieser, YC Chang, ...
Genome biology 19, 1-14, 2018
Metagenome analysis using the Kraken software suite
J Lu, N Rincon, DE Wood, FP Breitwieser, C Pockrandt, B Langmead, ...
Nature protocols 17 (12), 2815-2839, 2022
Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system
SL Salzberg, FP Breitwieser, A Kumar, H Hao, P Burger, FJ Rodriguez, ...
Neurology: Neuroimmunology & Neuroinflammation 3 (4), e251, 2016
General statistical modeling of data from protein relative expression isobaric tags
FP Breitwieser, A M ller, L Dayon, T K cher, A Hainard, PM Pichler, ...
Journal of Proteome Research, 2011
Fast and sensitive taxonomic assignment to metagenomic contigs
M Mirdita, M Steinegger, F Breitwieser, J Söding, E Levy Karin
Bioinformatics 37 (18), 3029-3031, 2021
Human contamination in bacterial genomes has created thousands of spurious proteins
FP Breitwieser, M Pertea, AV Zimin, SL Salzberg
Genome research 29 (6), 954-960, 2019
Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML
GE Winter, U Rix, SM Carlson, KV Gleixner, F Grebien, M Gridling, ...
Nature chemical biology 8 (11), 905-912, 2012
Initial characterization of the human central proteome
TR Burkard, M Planyavsky, I Kaupe, FP Breitwieser, T Bürckstümmer, ...
BMC systems biology 5 (1), 17, 2011
Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci 3: e104
J Lu, FP Breitwieser, P Thielen, SL Salzberg
Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ®-labelled specimens
KL Bennett, M Funk, M Tschernutter, FP Breitwieser, M Planyavsky, ...
Journal of proteomics 74 (2), 151-166, 2011
The lipid-modifying enzyme SMPDL3B negatively regulates innate immunity
LX Heinz, CL Baumann, MS Köberlin, B Snijder, R Gawish, G Shui, ...
Cell Reports 11 (12), 1919-1928, 2015
A comprehensive target selectivity survey of the BCR-ABL kinase inhibitor INNO-406 by kinase profiling and chemical proteomics in chronic myeloid leukemia cells
U Rix, LLR Rix, AS Terker, NV Fernbach, O Hantschel, M Planyavsky, ...
Leukemia 24 (1), 44-50, 2009
CD4+ T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2
N Boucheron, R Tschismarov, L Goeschl, MA Moser, S Lagger, ...
Nature immunology 15 (5), 439-448, 2014
Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics
PJ Simner, HB Miller, FP Breitwieser, G Pinilla Monsalve, CA Pardo, ...
Journal of clinical microbiology 56 (9), 10.1128/jcm. 00472-18, 2018
A Comparative Proteomic Study of Human Skin Suction Blister Fluid from Healthy Individuals Using Immunodepletion and iTRAQ-Labelling
AC Müller, FP Breitwieser, H Fischer, C Schuster, O Brandt, J Colinge, ...
Journal of Proteome Research, 2012
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