A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups.
暂无分享,去创建一个
Magnus Palmblad | Brian C Searle | Pratik Jagtap | Kevin L Knudtson | Rebecca L Hegstad-Davies | Nancy C Fisher | Susan M Meyn | Sheenah M Mische | Frances Weis-Garcia | John M Ashton | Marie Adams | John M. Ashton | Christopher E Mason | Julie A Dragon | Susan M. Meyn | Katia Sol Church | Kym M Delventhal | Laura Holmes | Christoph W Turck | B. Searle | P. Jagtap | C. Turck | K. Knudtson | Magnus Palmblad | F. Weis-Garcia | J. Dragon | S. Mische | Nancy C. Fisher | Christopher E. Mason | Kym Delventhal | Marie Adams | Laura Holmes | C. Mason | Rebecca L. Hegstad-Davies
[1] Erik Schultes,et al. The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.
[2] Vincent L. Butty,et al. Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction , 2017, BMC Genomics.
[3] Shawn Levy,et al. International Standards for Genomes, Transcriptomes, and Metagenomes. , 2017, Journal of biomolecular techniques : JBT.
[4] Thomas A Neubert,et al. MIRG Survey 2011: snapshot of rapidly evolving label-free technologies used for characterizing molecular interactions. , 2012, Journal of biomolecular techniques : JBT.
[5] A. Yamniuk,et al. ABRF-MIRG benchmark study: molecular interactions in a three-component system. , 2012, Journal of biomolecular techniques : JBT.
[6] Julie Gould. Core facilities: Shared support. , 2015, Nature.
[7] R. Angeletti,et al. Six-year study of peptide synthesis. , 1997, Methods in enzymology.
[8] G A Buck,et al. Multi-facility survey of oligonucleotide synthesis and an examination of the performance of unpurified primers in automated DNA sequencing. , 1996, BioTechniques.
[9] David L. Tabb,et al. The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses* , 2015, Molecular & Cellular Proteomics.
[10] Wei Shi,et al. Detecting and correcting systematic variation in large-scale RNA sequencing data , 2014, Nature Biotechnology.
[11] K. Medzihradszky,et al. Strategies for the synthesis of labeled peptides. , 2000, Journal of Biomolecular Techniques.
[12] Thomas A Neubert,et al. ABRF-PRG04: differentiation of protein isoforms. , 2007, Journal of biomolecular techniques : JBT.
[13] Mercè Crosas,et al. Data Authorship as an Incentive to Data Sharing. , 2017, The New England journal of medicine.
[14] P. Andrews,et al. Assignment of cysteine and tryptophan residues during protein sequencing: Results of ABRF-94SEQ , 1995 .
[15] S. Cohen,et al. Synthesis of a fluorescent derivatizing reagent, 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate, and its application for the analysis of hydrolysate amino acids via high-performance liquid chromatography. , 1993, Analytical biochemistry.
[16] Andrew A. Ott,et al. Building a Sustainable Portfolio of Core Facilities: a Case Study. , 2018, Journal of biomolecular techniques : JBT.
[17] Y. Mechref,et al. Glycoproteomics: Identifying the Glycosylation of Prostate Specific Antigen at Normal and High Isoelectric Points by LC–MS/MS , 2014, Journal of proteome research.
[18] R. Cook,et al. EDMAN SEQUENCING RESEARCH GROUP 2004 STUDY: MODIFIED AMINO ACIDS IN EDMAN SEQUENCING , 2005 .
[19] D. J. Strydom,et al. Sensitive Analysis of Cystine/Cysteine using 6-Aminoquinolyl-N-Hydroxysuccinimidyl Carbamate (AQC) Derivatives , 1993 .
[20] R. Pepperkok,et al. Institutional core facilities: prerequisite for breakthroughs in the life sciences , 2016, EMBO reports.
[21] A. Sporbert,et al. Advanced light microscopy core facilities: Balancing service, science and career , 2016, Microscopy research and technique.
[22] Bruce A. Stanley,et al. Mass Spectrometry Data Collection in Parallel at Multiple Core Facilities Operating TripleTOF 5600 and Orbitrap Elite/Velos Pro/Q Exactive Mass Spectrometers. , 2013 .
[23] W. T. Moore,et al. Formation of a Disulfide Bond in an Octreotide-Like Peptide: A Multicenter Study , 1996 .
[24] M. Lauer,et al. Reproducibility 2020 : Progress and priorities , 2017 .
[25] Lennart Martens,et al. Predicting tryptic cleavage from proteomics data using decision tree ensembles. , 2013, Journal of proteome research.
[26] ABRF-PRG05: de novo peptide sequence determination. , 2008, Journal of biomolecular techniques : JBT.
[27] G A Buck,et al. Accuracy of automated DNA sequencing: a multi-laboratory comparison of sequencing results. , 1995, BioTechniques.
[28] K. Williams,et al. 10 – A SYNTHETIC PEPTIDE FOR EVALUATING PROTEIN SEQUENCER AND AMINO ACID ANALYZER PERFORMANCE IN CORE FACILITIES: DESIGN AND RESULTS , 1989 .
[29] Alexa B. R. McIntyre,et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials , 2015, Scientific Data.
[30] D G Myszka,et al. The ABRF-MIRG'02 study: assembly state, thermodynamic, and kinetic analysis of an enzyme/inhibitor interaction. , 2003, Journal of biomolecular techniques : JBT.
[31] David L Tabb,et al. Quality assessment for clinical proteomics. , 2013, Clinical biochemistry.
[32] Gregory K. Farber,et al. Core Facilities: Maximizing the Return on Investment , 2011, Science Translational Medicine.
[33] William Arbuthnot Sir Lane,et al. ABRF-97 SEQ: Sequencing results of a low-level sample , 1999 .
[34] I. Apostol,et al. The hydrolysis process and the quality of amino acid analysis: ABRF-94AAA collaborative trial , 1995 .
[35] I. Apostol,et al. Cysteine and Tryptophan Amino Acid Analysis of ABRF92-AAA , 1993 .
[36] G. Shipley,et al. Evaluation of dual-labeled fluorescent DNA probe purity versus performance in real-time PCR. , 2004, BioTechniques.
[37] S. Cohen,et al. Using quaternary high-performance liquid chromatography eluent systems for separating 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate-derivatized amino acid mixtures , 1997 .
[38] Christoph Endrullat,et al. Standardization and quality management in next-generation sequencing , 2016, Applied & translational genomics.
[39] Lennart Martens,et al. iPRG 2011: A Study on the Identification of Electron Transfer Dissociation (ETD) Mass Spectra , 2011 .
[40] Christopher E Mason,et al. Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications. , 2017, Journal of biomolecular techniques : JBT.
[41] Michael J MacCoss,et al. ABRF-PRG07: advanced quantitative proteomics study. , 2011, Journal of biomolecular techniques : JBT.
[42] J. Rush,et al. Design and analysis of ABRF-95SEQ, a recombinant protein with sequence heterogeneity , 1996 .
[43] Christopher E. Mason,et al. The ABRF Next Generation Sequencing Study: Multi-platform and Cross-methodological Reproducibility of Transcriptome Profiling by RNA-seq , 2014 .
[44] K. Knudtson,et al. DNA SEQUENCING RESEARCH GROUP (DSRG) 2003—A GENERAL SURVEY OF CORE DNA SEQUENCING FACILITIES. , 2003 .
[45] D. J. Strydom,et al. Amino acid analysis utilizing phenylisothiocyanate derivatives. , 1988, Analytical biochemistry.
[46] R. DeSalle,et al. Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing , 2017, Scientific Reports.
[47] C. Mason,et al. The impact of read length on quantification of differentially expressed genes and splice junction detection , 2015, Genome Biology.
[48] Samuel H Payne,et al. A protein standard that emulates homology for the characterization of protein inference algorithms , 2017, bioRxiv.
[49] Heike Sichtig,et al. Single-molecule sequencing detection of N6-methyladenine in microbial reference materials , 2019, Nature Communications.
[50] William Arbuthnot Sir Lane,et al. Evaluation of ABRF-96SEQ: A sequence assignment exercise , 1997 .
[51] Henry H N Lam,et al. iPRG 2012 Study: Detecting Modified Peptides in a Complex Mixture , 2012 .
[52] M. Zianni,et al. Identification of optimal protocols for sequencing difficult templates: results of the 2008 ABRF DNA Sequencing Research Group difficult template study 2008. , 2009, Journal of biomolecular techniques : JBT.
[53] Simon Bergqvist,et al. Conclusions from the MIRG 2010 Benchmark Study: Molecular Interactions in a Three Component System and Presentation of 2011 Survey Results on Label-Free Technologies. , 2011 .
[54] Robert L. Moritz,et al. PRG-2011: Defining the Interaction Between Users and Suppliers of Proteomics Services/Facilities , 2011 .
[55] Hendrik Weisser,et al. Targeted Feature Detection for Data-Dependent Shotgun Proteomics , 2017, Journal of proteome research.
[56] Thomas A Neubert,et al. The ABRF Metabolomics Research Group 2013 Study: Investigation of Spiked Compound Differences in a Human Plasma Matrix. , 2015, Journal of biomolecular techniques : JBT.
[57] Reality check on reproducibility , 2016, Nature.
[58] Noah Alexander,et al. Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance. , 2017, Journal of biomolecular techniques : JBT.
[59] Alexa B. R. McIntyre,et al. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). , 2017, Journal of biomolecular techniques : JBT.
[60] Lynda F. Bonewald,et al. Correlation of cleavage techniques with side-reactions following solid-phase peptide synthesis , 1995 .
[61] P. Hunziker,et al. Identification of proteins electroblotted to polyvinylidene difluoride membrane by combined amino acid analysis and bioinformatics: An ABRF multicenter study. , 1999, Journal of biomolecular techniques : JBT.
[62] C. Turck,et al. The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 Study , 2007, Molecular & Cellular Proteomics.
[63] Jeroen Krijgsveld,et al. The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomic analyses , 2011, Proteomics.
[64] L. C. Williams,et al. Variable Success of Peptide-Resin Cleavage and Deprotection Following Solid-Phase Synthesis , 1994 .
[65] K. Knudtson,et al. Evaluation of methods for sequence analysis of highly repetitive DNA templates. , 2006, Journal of biomolecular techniques : JBT.
[66] Henry H N Lam,et al. Proteome Informatics Research Group (iPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture* , 2013, Molecular & Cellular Proteomics.
[67] James M. Anderson,et al. U.S. National Institutes of Health core consolidation-investing in greater efficiency. , 2015, Journal of biomolecular techniques : JBT.
[68] Peter Lopez,et al. The New ABRF Flow Cytometry Research Group (FCRG). , 2013 .
[69] A. Yamniuk,et al. Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions. , 2015, Journal of biomolecular techniques : JBT.
[70] Anne-Marie Girard,et al. Quality assurance testing for modern optical imaging systems. , 2011, Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada.
[71] W. Sandoval,et al. The ABRF Edman Sequencing Research Group 2008 Study: investigation into homopolymeric amino acid N-terminal sequence tags and their effects on automated Edman degradation. , 2009, Journal of biomolecular techniques : JBT.
[73] Lloyd M. Smith,et al. How many human proteoforms are there? , 2018, Nature chemical biology.
[74] Douglas J. Botkin,et al. Nanopore DNA Sequencing and Genome Assembly on the International Space Station , 2016, bioRxiv.
[75] R. Paxton,et al. Collaborative Trial Analyses of ABRF-91AAA , 1992 .
[76] Samuel H Payne,et al. ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data. , 2018, Journal of biomolecular techniques : JBT.
[77] Thomas A Neubert,et al. ABRF-PRG03: phosphorylation site determination. , 2003, Journal of biomolecular techniques : JBT.
[78] Ekaterina V. Poverennaya,et al. The Size of the Human Proteome: The Width and Depth , 2016, International journal of analytical chemistry.
[79] Robert G. Steen,et al. Comparison of commercially available target enrichment methods for next-generation sequencing. , 2013, Journal of biomolecular techniques : JBT.
[80] Sheng Li,et al. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study , 2014, Nature Biotechnology.
[81] Brendan MacLean,et al. ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments. , 2017, Journal of proteome research.
[82] P S Adams,et al. Design strategies and performance of custom DNA sequencing primers. , 1999, BioTechniques.
[83] Claire M Brown,et al. International Test Results for Objective Lens Quality, Resolution, Spectral Accuracy and Spectral Separation for Confocal Laser Scanning Microscopes , 2013, Microscopy and Microanalysis.
[84] Brendan MacLean,et al. ABRF Research Group Development and Characterization of a Proteomics Normalization Standard Consisting of 1,000 Stable Isotope Labeled Peptides , 2014 .
[85] G A Buck,et al. A survey of nucleic acid services in core laboratories. , 1994, BioTechniques.
[86] W. T. Moore,et al. Analysis of racemization during "Standard" solid phase peptide synthesis: a multicenter study , 1997 .
[87] N M Ritter,et al. Analytical laboratory quality: Part I. General quality practices. , 2001, Journal of biomolecular techniques : JBT.
[88] Emmanuel Dias-Neto,et al. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report , 2016, Microbiome.
[89] I. Cockburn,et al. The Economics of Reproducibility in Preclinical Research , 2015, PLoS biology.
[90] Howard Gadlin,et al. Collaboration and Team Science , 2012, Journal of Investigative Medicine.
[91] Brian A. Nosek,et al. Promoting an open research culture , 2015, Science.
[92] J. Ioannidis,et al. Reproducibility in Science: Improving the Standard for Basic and Preclinical Research , 2015, Circulation research.
[93] R. Thoma,et al. ABRF ESRG 2006 study: Edman sequencing as a method for polypeptide quantitation. , 2007, Journal of biomolecular techniques : JBT.
[94] P. Urban,et al. Quantitative mass spectrometry: an overview , 2016, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[95] S. Carr,et al. ABRF-98SEQ: Evaluation of peptide sequencing at high sensitivity. , 2000, Journal of biomolecular techniques : JBT.
[96] F. Collins,et al. Policy: NIH plans to enhance reproducibility , 2014, Nature.
[97] A. Viale,et al. Big results from small samples: evaluation of amplification protocols for gene expression profiling. , 2007, Journal of biomolecular techniques : JBT.
[98] Journals unite for reproducibility , 2014, Nature.
[99] P. Andrews,et al. PROTEIN SEQUENCING OF POST-TRANSLATIONALLY MODIFIED PEPTIDES and PROTEINS: DESIGN, CHARACTERIZATION AND RESULTS OF ABRF-92SEQ , 1993 .
[100] F. Grieder,et al. Sharing Core Facilities and Research Resources--An Investment in Accelerating Scientific Discoveries. , 2016, Journal of biomolecular techniques : JBT.
[101] D. J. Strydom,et al. Comparison of amino acid analyses by phenylisothiocyanate and 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate precolumn derivatization. , 1994, Analytical biochemistry.
[102] John M. Asara,et al. Metabolomics Research Group 2011 Study. , 2011 .
[103] R. Cook,et al. ABRF-ESRG'03: analysis of a PVDF-bound known protein with a homogeneous amino-terminus. , 2003, Journal of biomolecular techniques : JBT.
[104] John P. A. Ioannidis,et al. What does research reproducibility mean? , 2016, Science Translational Medicine.
[105] Karl Mechtler,et al. Interlaboratory studies and initiatives developing standards for proteomics , 2013, Proteomics.
[106] S. Green,et al. Next Generation Sequencing and the Extreme Microbiome Project (XMP) , 2015 .
[107] Christopher E. Mason,et al. The ABRF-Next Generation Sequencing Study: A Five-Platform, Cross-site, Cross-Protocol Examination of RNA Sequencing , 2013 .
[108] P. Andrews,et al. A Synthetic Peptide for Evaluating Protein Sequencing Capabilities: Design of ABRF-93SEQ and Results , 1994 .
[109] K. Dewar,et al. Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities. , 2013, Journal of biomolecular techniques : JBT.
[110] I. Apostol,et al. Amino Acid Analysis of Phospho-Peptides: Abrf-93AAA , 1994 .
[111] Frederick J. Manning,et al. Resource Sharing in Biomedical Research , 1996 .
[112] S A Cohen,et al. Applications of amino acid derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. Analysis of feed grains, intravenous solutions and glycoproteins. , 1994, Journal of chromatography. A.
[113] H Shindo,et al. Nucleic Acids , 1932, Nature.
[114] Michael Zianni,et al. A Methodology Study for Metagenomics Using Next Generation Sequencers , 2011 .
[115] James Inglese,et al. The increasing urgency for standards in basic biologic research. , 2014, Cancer research.
[116] J. McMurray,et al. Study on the synthesis and characterization of peptides containing phosphorylated tyrosine. , 1999, The journal of peptide research : official journal of the American Peptide Society.
[117] David W. Speicher,et al. 15 – Design, Characterization and Results of ABRF-89SEQ: A Test Sample For Evaluating Protein Sequencer Performance in Protein Microchemistry Core Facilities , 1990 .
[118] William Arbuthnot Sir Lane,et al. ABRF ESRG 2005 study: identification of seven modified amino acids by Edman sequencing. , 2006, Journal of biomolecular techniques : JBT.
[119] Scott D Buckel,et al. ABRF-2002ESRG, a difficult sequence: Analysis of a PVDF-bound known protein with a heterogeneous amino-terminus. , 2002, Journal of biomolecular techniques : JBT.
[120] David P. Kreil,et al. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium , 2014, Nature Biotechnology.
[121] William Arbuthnot Sir Lane,et al. Proteomics in mixtures: Study results of ABRF-PRG02. , 2002, Journal of biomolecular techniques : JBT.
[122] Haixu Tang,et al. Interlaboratory Study on Differential Analysis of Protein Glycosylation by Mass Spectrometry: The ABRF Glycoprotein Research Multi-Institutional Study 2012* , 2013, Molecular & Cellular Proteomics.
[123] J. McMurray,et al. 1997 ABRF Peptide synthesis research committee study on a peptide containing a phosphorylated tyrosine , 2002 .
[124] John P. A. Ioannidis,et al. A manifesto for reproducible science , 2017, Nature Human Behaviour.
[125] Rebecca L Hegstad-Davies,et al. Survey on Scientific Shared Resource Rigor and Reproducibility. , 2019, Journal of biomolecular techniques : JBT.
[126] R. Angeletti,et al. Research Technologies: Fulfilling the Promise 1 , 1999, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[127] K. Williams,et al. INTERNAL PROTEIN SEQUENCING OF SDS PAGE-SEPARATED PROTEINS: A COLLABORATIVE ABRF STUDY , 1997 .
[128] K. Williams,et al. Amino Acid Analysis and Sequencing — What is State-of-the-Art? , 1991 .
[129] J. W. Fox,et al. Amino acid analysis—recovery from PVDF membranes: ABRF-95AAA collaborative trial , 1996 .
[130] N. Steneck. ORI Introduction to Responsible Conduct of Research , 2007 .
[131] Claire M. Brown,et al. Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control , 2011, Nature Protocols.
[132] C. Slaughter,et al. Evaluation of Protein Sequencing Core Facilities: Design, Characterization, and Results from a Test Sample (ABRF-91SEQ) , 1992 .
[133] Cassandra Willyard. New human gene tally reignites debate , 2018, Nature.