| Bracken: estimating species abundance in metagenomics data J Lu, FP Breitwieser, P Thielen, SL Salzberg PeerJ Computer Science 3, e104, 2017 | 1303 | 2017 |
| Centrifuge: rapid and sensitive classification of metagenomic sequences D Kim, L Song, FP Breitwieser, SL Salzberg Genome research 26 (12), 1721-1729, 2016 | 1263 | 2016 |
| 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 | 584 | 2019 |
| KrakenUniq: confident and fast metagenomics classification using unique k-mer counts FP Breitwieser, DN Baker, SL Salzberg Genome biology 19, 1-10, 2018 | 364 | 2018 |
| Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification FP Breitwieser, SL Salzberg Bioinformatics 36 (4), 1303-1304, 2020 | 363 | 2020 |
| 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 | 309 | 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 | 252 | 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 | 179 | 2016 |
| 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 | 154 | 2021 |
| 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 | 146 | 2011 |
| 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 | 137 | 2019 |
| Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci 3: e104 J Lu, FP Breitwieser, P Thielen, SL Salzberg | 125 | 2017 |
| 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 | 121 | 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 | 106 | 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 | 103 | 2015 |
| 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 | 101 | 2011 |
| 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 | 94 | 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 | 90 | 2014 |
| 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 | 84 | 2012 |
| 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 | 82 | 2018 |
Steven SalzbergBloomberg Distinguished Professor, Johns Hopkins UniversityVerified email at jhu.edu
