Marc Salit

Marc Salit

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Marc Salit

Publications by authors named "Marc Salit"

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54Publications

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CrowdVariant: a crowdsourcing approach to classify copy number variants.

Pac Symp Biocomput 2019 ;24:224-235

Biomedical Informatics, Stanford University, Stanford, CA 94305, USA,

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August 2019

Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer.

Lab Chip 2019 Aug 22;19(16):2741-2749. Epub 2019 Jul 22.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78705, USA.

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http://dx.doi.org/10.1039/c9lc00311hDOI Listing
August 2019

High-coverage, long-read sequencing of Han Chinese trio reference samples.

Sci Data 2019 06 14;6(1):91. Epub 2019 Jun 14.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L Levy Pl, New York, NY, 10029, USA.

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http://dx.doi.org/10.1038/s41597-019-0098-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6572837PMC
June 2019

A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing.

J Mol Diagn 2019 Mar 3;21(2):318-329. Epub 2019 Jan 3.

Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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http://dx.doi.org/10.1016/j.jmoldx.2018.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629256PMC
March 2019

A minimum information standard for reproducing bench-scale bacterial cell growth and productivity.

Commun Biol 2018 6;1:219. Epub 2018 Dec 6.

Joint Initiative for Metrology in Biology, 443 Via Ortega, Room 325, Stanford, CA 94305 USA.

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http://dx.doi.org/10.1038/s42003-018-0220-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283831PMC
December 2018

Unbiased Fitness Estimation of Pooled Barcode or Amplicon Sequencing Studies.

Cell Syst 2018 11 1;7(5):521-525.e4. Epub 2018 Nov 1.

Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA; National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712183039
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http://dx.doi.org/10.1016/j.cels.2018.09.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265064PMC
November 2018

Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials.

J Mol Diagn 2018 09 26;20(5):583-590. Epub 2018 Jun 26.

Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland.

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http://dx.doi.org/10.1016/j.jmoldx.2018.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172655PMC
September 2018

Cell-based reference samples designed with specific differences in microRNA biomarkers.

BMC Biotechnol 2018 03 20;18(1):17. Epub 2018 Mar 20.

Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s12896-018-0423-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859499PMC
March 2018

Genome-wide reconstruction of complex structural variants using read clouds.

Nat Methods 2017 Sep 17;14(9):915-920. Epub 2017 Jul 17.

Joint Initiative for Metrology in Biology, Stanford, California, USA.

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http://dx.doi.org/10.1038/nmeth.4366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578891PMC
September 2017

Measurements of translation initiation from all 64 codons in E. coli.

Nucleic Acids Res 2017 04;45(7):3615-3626

Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/nar/gkx070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397182PMC
April 2017

Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships.

Ann Lab Med 2016 Nov;36(6):513-20

Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea.

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http://dx.doi.org/10.3343/alm.2016.36.6.513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011103PMC
November 2016

When Wavelengths Collide: Bias in Cell Abundance Measurements Due to Expressed Fluorescent Proteins.

ACS Synth Biol 2016 09 6;5(9):1024-7. Epub 2016 Jun 6.

Joint Initiative for Metrology in Biology, Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acssynbio.6b00072DOI Listing
September 2016

External RNA Controls Consortium Beta Version Update.

J Genomics 2016 26;4:19-22. Epub 2016 Jul 26.

Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.7150/jgen.16082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978944PMC
August 2016

In Vivo Site-Specific Protein Tagging with Diverse Amines Using an Engineered Sortase Variant.

J Am Chem Soc 2016 06 9;138(24):7496-9. Epub 2016 Jun 9.

Departments of Bioengineering and Chemical Engineering, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.6b03836DOI Listing
June 2016

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design.

BMC Biotechnol 2016 Jun 24;16(1):54. Epub 2016 Jun 24.

Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s12896-016-0281-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921035PMC
June 2016

Microarray Scanner Performance Over a Five-Week Period as Measured With Cy5 and Cy3 Serial Dilution Slides.

J Res Natl Inst Stand Technol 2008 May-Jun;113(3):157-74. Epub 2008 Jun 1.

National Institute of Standards and Technology, Gaithersburg, MD 20899.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654599PMC
April 2016

PEPR: pipelines for evaluating prokaryotic references.

Anal Bioanal Chem 2016 Apr 2;408(11):2975-83. Epub 2016 Mar 2.

Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.

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http://dx.doi.org/10.1007/s00216-015-9299-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819933PMC
April 2016

Medical implications of technical accuracy in genome sequencing.

Genome Med 2016 Mar 2;8(1):24. Epub 2016 Mar 2.

Department of Medicine, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s13073-016-0269-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4774017PMC
March 2016

svclassify: a method to establish benchmark structural variant calls.

BMC Genomics 2016 Jan 16;17:64. Epub 2016 Jan 16.

Genome-Scale Measurements Group, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8313, Gaithersburg, MD, 20899, USA.

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http://dx.doi.org/10.1186/s12864-016-2366-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715349PMC
January 2016

svviz: a read viewer for validating structural variants.

Bioinformatics 2015 Dec 18;31(24):3994-6. Epub 2015 Aug 18.

Department of Genetics, Stanford University, Department of Pathology, Stanford University.

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http://dx.doi.org/10.1093/bioinformatics/btv478DOI Listing
December 2015

Unmet needs: Research helps regulators do their jobs.

Sci Transl Med 2015 Nov;7(315):315ps22

Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA 94143-2911, USA. Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1126/scitranslmed.aac4369DOI Listing
November 2015

Using mixtures of biological samples as process controls for RNA-sequencing experiments.

BMC Genomics 2015 Sep 17;16:708. Epub 2015 Sep 17.

Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA.

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http://dx.doi.org/10.1186/s12864-015-1912-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574543PMC
September 2015

Advancing Benchmarks for Genome Sequencing.

Cell Syst 2015 Sep 23;1(3):176-7. Epub 2015 Sep 23.

Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2015.09.004DOI Listing
September 2015

Best practices for evaluating single nucleotide variant calling methods for microbial genomics.

Front Genet 2015 7;6:235. Epub 2015 Jul 7.

Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, MD, USA.

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http://dx.doi.org/10.3389/fgene.2015.00235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493402PMC
July 2015

Use of Cause-and-Effect Analysis to Design a High-Quality Nanocytotoxicology Assay.

Chem Res Toxicol 2015 Jan 6;28(1):21-30. Epub 2015 Jan 6.

Materials-Biology Interactions Laboratory, and ‡International Research Cooperations Manager, Swiss Federal Laboratories for Material Testing and Research (Empa) , CH-9014 St. Gallen, Switzerland.

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http://dx.doi.org/10.1021/tx500327yDOI Listing
January 2015

Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films.

Biomaterials 2014 Aug 17;35(25):6716-26. Epub 2014 May 17.

Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA. Electronic address:

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http://dx.doi.org/10.1016/j.biomaterials.2014.04.075DOI Listing
August 2014

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Nat Biotechnol 2014 Mar 16;32(3):246-51. Epub 2014 Feb 16.

Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.2835DOI Listing
March 2014

Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing.

PLoS One 2012 31;7(7):e41356. Epub 2012 Jul 31.

Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041356PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409179PMC
April 2013

Characterization of in vitro transcription amplification linearity and variability in the low copy number regime using External RNA Control Consortium (ERCC) spike-ins.

Anal Bioanal Chem 2013 Jan 20;405(1):315-20. Epub 2012 Oct 20.

Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.

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http://dx.doi.org/10.1007/s00216-012-6445-1DOI Listing
January 2013

Mediation of Drosophila autosomal dosage effects and compensation by network interactions.

Genome Biol 2012 Apr 24;13(4):r28. Epub 2012 Apr 24.

Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1186/gb-2012-13-4-r28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446302PMC
April 2012

Synthetic spike-in standards for RNA-seq experiments.

Genome Res 2011 Sep 4;21(9):1543-51. Epub 2011 Aug 4.

Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1101/gr.121095.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166838PMC
September 2011

Contributions of the EMERALD project to assessing and improving microarray data quality.

Biotechniques 2011 Jan;50(1):27-31

Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.

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https://www.future-science.com/doi/10.2144/000113591
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http://dx.doi.org/10.2144/000113591DOI Listing
January 2011

Exploring the use of internal and externalcontrols for assessing microarray technical performance.

BMC Res Notes 2010 Dec 28;3:349. Epub 2010 Dec 28.

Chemical Science and Technology Laboratory,National Institute of Standards and Technology (NIST) Gaithersburg, Maryland 20899 USA.

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https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-
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http://dx.doi.org/10.1186/1756-0500-3-349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020182PMC
December 2010

Image-based feedback control for real-time sorting of microspheres in a microfluidic device.

Lab Chip 2010 Sep 30;10(18):2402-10. Epub 2010 Jun 30.

National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.

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http://xlink.rsc.org/?DOI=c004708b
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http://dx.doi.org/10.1039/c004708bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928395PMC
September 2010

Learning from microarray interlaboratory studies: measures of precision for gene expression.

BMC Genomics 2009 Apr 8;10:153. Epub 2009 Apr 8.

Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8390, USA.

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http://dx.doi.org/10.1186/1471-2164-10-153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679054PMC
April 2009

Use of Standard Reference Material 2242 (Relative Intensity Correction Standard for Raman Spectroscopy) for microarray scanner qualification.

Biotechniques 2008 Aug;45(2):143-4, 148, 150 passim

Biochemical Science Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8313, Gaithersburg, MD 20899, USA.

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https://www.future-science.com/doi/10.2144/000112818
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http://dx.doi.org/10.2144/000112818DOI Listing
August 2008

Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays.

BMC Bioinformatics 2007 Mar 29;8:108. Epub 2007 Mar 29.

Genomics Core Laboratory, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA.

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http://dx.doi.org/10.1186/1471-2105-8-108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853115PMC
March 2007

Standards in gene expression microarray experiments.

Authors:
Marc Salit

Methods Enzymol 2006 ;411:63-78

Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.

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http://dx.doi.org/10.1016/S0076-6879(06)11005-8DOI Listing
December 2006