High-throughput automated microfluidic sample preparation for accurate microbial genomics
Abstract
Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (B10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence B400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.
- Authors:
-
[4];
[6];
- The Broad Inst. of MIT and Harvard, Cambridge, MA (United States); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Biological Engineering
- The Broad Inst. of MIT and Harvard, Cambridge, MA (United States); Univ. of Cambridge (United Kingdom). Dept. of Biochemistry
- The Broad Inst. of MIT and Harvard, Cambridge, MA (United States); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Physics
- The Broad Inst. of MIT and Harvard, Cambridge, MA (United States); Aalto Univ., Otaniemi (Finland). Dept. of Computer Science
- The Broad Inst. of MIT and Harvard, Cambridge, MA (United States); Massachusetts General Hospital, Boston, MA (United States). Division of Infectious Diseases
- Northeastern Univ., Boston, MA (United States). Dept. of Biology
- The Broad Inst. of MIT and Harvard, Cambridge, MA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1623869
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Science & Technology - Other Topics
Citation Formats
Kim, Soohong, De Jonghe, Joachim, Kulesa, Anthony B., Feldman, David, Vatanen, Tommi, Bhattacharyya, Roby P., Berdy, Brittany, Gomez, James, Nolan, Jill, Epstein, Slava, and Blainey, Paul C. High-throughput automated microfluidic sample preparation for accurate microbial genomics. United States: N. p., 2017.
Web. doi:10.1038/ncomms13919.
Kim, Soohong, De Jonghe, Joachim, Kulesa, Anthony B., Feldman, David, Vatanen, Tommi, Bhattacharyya, Roby P., Berdy, Brittany, Gomez, James, Nolan, Jill, Epstein, Slava, & Blainey, Paul C. High-throughput automated microfluidic sample preparation for accurate microbial genomics. United States. https://doi.org/10.1038/ncomms13919
Kim, Soohong, De Jonghe, Joachim, Kulesa, Anthony B., Feldman, David, Vatanen, Tommi, Bhattacharyya, Roby P., Berdy, Brittany, Gomez, James, Nolan, Jill, Epstein, Slava, and Blainey, Paul C. Fri .
"High-throughput automated microfluidic sample preparation for accurate microbial genomics". United States. https://doi.org/10.1038/ncomms13919. https://www.osti.gov/servlets/purl/1623869.
@article{osti_1623869,
title = {High-throughput automated microfluidic sample preparation for accurate microbial genomics},
author = {Kim, Soohong and De Jonghe, Joachim and Kulesa, Anthony B. and Feldman, David and Vatanen, Tommi and Bhattacharyya, Roby P. and Berdy, Brittany and Gomez, James and Nolan, Jill and Epstein, Slava and Blainey, Paul C.},
abstractNote = {Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (B10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence B400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.},
doi = {10.1038/ncomms13919},
journal = {Nature Communications},
number = 1,
volume = 8,
place = {United States},
year = {Fri Jan 27 00:00:00 EST 2017},
month = {Fri Jan 27 00:00:00 EST 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
journal, March 2015
- Brooks, J. Paul; Edwards, David J.; Harwich, Michael D.
- BMC Microbiology, Vol. 15, Issue 1
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
journal, July 2012
- Ramsköld, Daniel; Luo, Shujun; Wang, Yu-Chieh
- Nature Biotechnology, Vol. 30, Issue 8
Thermoplastic Microfluidic Device for On-Chip Purification of Nucleic Acids for Disposable Diagnostics
journal, February 2006
- Bhattacharyya, Arpita; Klapperich, Catherine M.
- Analytical Chemistry, Vol. 78, Issue 3
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome
journal, March 2013
- Fitzsimons, M. S.; Novotny, M.; Lo, C. -C.
- Genome Research, Vol. 23, Issue 5
Whole-Genome Sequencing for National Surveillance of Shiga Toxin–Producing Escherichia coli O157
journal, April 2015
- Dallman, Timothy J.; Byrne, Lisa; Ashton, Philip M.
- Clinical Infectious Diseases, Vol. 61, Issue 3
Quake: quality-aware detection and correction of sequencing errors
journal, January 2010
- Kelley, David R.; Schatz, Michael C.; Salzberg, Steven L.
- Genome Biology, Vol. 11, Issue 11
Carbapenem Resistance Mechanisms in Pseudomonas aeruginosa Clinical Isolates
journal, February 2001
- Pai, Hyunjoo; Kim, Jong-Won; Kim, Jungmin
- Antimicrobial Agents and Chemotherapy, Vol. 45, Issue 2
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014
- Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.
- BMC Biology, Vol. 12, Issue 1
Synthetic biology to access and expand nature's chemical diversity
journal, February 2016
- Smanski, Michael J.; Zhou, Hui; Claesen, Jan
- Nature Reviews Microbiology, Vol. 14, Issue 3
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
journal, October 2013
- Buenrostro, Jason D.; Giresi, Paul G.; Zaba, Lisa C.
- Nature Methods, Vol. 10, Issue 12
A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps
journal, July 2013
- Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael
- PLoS ONE, Vol. 8, Issue 7
Simple Bulk Readout of Digital Nucleic Acid Quantification Assays
journal, January 2015
- Morinishi, Leanna S.; Blainey, Paul
- Journal of Visualized Experiments, Issue 103
Ciprofloxacin susceptibility of Pseudomonas aeruginosa isolates from keratitis
journal, October 2003
- Lomholt, J. A.
- British Journal of Ophthalmology, Vol. 87, Issue 10
Microfluidic Large-Scale Integration: The Evolution of Design Rules for Biological Automation
journal, June 2007
- Melin, Jessica; Quake, Stephen R.
- Annual Review of Biophysics and Biomolecular Structure, Vol. 36, Issue 1
The future is now: single-cell genomics of bacteria and archaea
journal, May 2013
- Blainey, Paul C.
- FEMS Microbiology Reviews, Vol. 37, Issue 3
Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat
journal, July 2005
- Balagadde, F. K.
- Science, Vol. 309, Issue 5731
Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis
journal, November 2014
- Marvig, Rasmus Lykke; Sommer, Lea Mette; Molin, Søren
- Nature Genetics, Vol. 47, Issue 1
Dense genomic sampling identifies highways of pneumococcal recombination
journal, February 2014
- Chewapreecha, Claire; Harris, Simon R.; Croucher, Nicholas J.
- Nature Genetics, Vol. 46, Issue 3
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database
journal, November 2015
- Winsor, Geoffrey L.; Griffiths, Emma J.; Lo, Raymond
- Nucleic Acids Research, Vol. 44, Issue D1
Human gut microbiome viewed across age and geography
journal, May 2012
- Yatsunenko, Tanya; Rey, Federico E.; Manary, Mark J.
- Nature, Vol. 486, Issue 7402
A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods
journal, August 2014
- de Bourcy, Charles F. A.; De Vlaminck, Iwijn; Kanbar, Jad N.
- PLoS ONE, Vol. 9, Issue 8
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
journal, June 2014
- Naccache, S. N.; Federman, S.; Veeraraghavan, N.
- Genome Research, Vol. 24, Issue 7
Effects of Diet on Mercury Metabolism and Excretion in Mice Given Methylmercury: Role of Gut Flora
journal, November 1984
- Rowland, I. R.; Robinson, R. D.; Doherty, R. A.
- Archives of Environmental Health: An International Journal, Vol. 39, Issue 6
The role of replicates for error mitigation in next-generation sequencing
journal, December 2013
- Robasky, Kimberly; Lewis, Nathan E.; Church, George M.
- Nature Reviews Genetics, Vol. 15, Issue 1
Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
journal, November 2011
- Parkinson, N. J.; Maslau, S.; Ferneyhough, B.
- Genome Research, Vol. 22, Issue 1
Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients
journal, May 2006
- Smith, E. E.; Buckley, D. G.; Wu, Z.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 22
High-throughput single-molecule optofluidic analysis
journal, February 2011
- Kim, Soohong; Streets, Aaron M.; Lin, Ron R.
- Nature Methods, Vol. 8, Issue 3
Detection of ultra-rare mutations by next-generation sequencing
journal, August 2012
- Schmitt, M. W.; Kennedy, S. R.; Salk, J. J.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 36
Is exposure to mercury a driving force for the carriage of antibiotic resistance genes?
journal, March 2010
- Skurnik, D.; Ruimy, R.; Ready, D.
- Journal of Medical Microbiology, Vol. 59, Issue 7
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
journal, June 2007
- Robertson, Gordon; Hirst, Martin; Bainbridge, Matthew
- Nature Methods, Vol. 4, Issue 8
Library preparation methodology can influence genomic and functional predictions in human microbiome research
journal, October 2015
- Jones, Marcus B.; Highlander, Sarah K.; Anderson, Ericka L.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 45
Antibiotic Susceptibility Testing by a Standardized Single Disk Method
journal, April 1966
- Bauer, A. W.; Kirby, W. M. M.; Sherris, J. C.
- American Journal of Clinical Pathology, Vol. 45, Issue 4_ts
PhyloSift: phylogenetic analysis of genomes and metagenomes
journal, January 2014
- Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric
- PeerJ, Vol. 2
Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing
journal, August 2012
- Snitkin, E. S.; Zelazny, A. M.; Thomas, P. J.
- Science Translational Medicine, Vol. 4, Issue 148
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
journal, May 2015
- Weber, Tilmann; Blin, Kai; Duddela, Srikanth
- Nucleic Acids Research, Vol. 43, Issue W1
Shotgun DNA sequencing using cloned DNase I-generated fragments
journal, January 1981
- Anderson, Stephen
- Nucleic Acids Research, Vol. 9, Issue 13
Solid-phase reversible immobilization for the isolation of PCR products
journal, January 1995
- DeAngelis, Margaret M.; Wang, David G.; Hawkins, Trevor L.
- Nucleic Acids Research, Vol. 23, Issue 22
A new antibiotic kills pathogens without detectable resistance
journal, January 2015
- Ling, Losee L.; Schneider, Tanja; Peoples, Aaron J.
- Nature, Vol. 517, Issue 7535
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
journal, November 2014
- Walker, Bruce J.; Abeel, Thomas; Shea, Terrance
- PLoS ONE, Vol. 9, Issue 11
Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species
journal, February 2010
- Nichols, D.; Cahoon, N.; Trakhtenberg, E. M.
- Applied and Environmental Microbiology, Vol. 76, Issue 8
Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures
journal, December 2013
- Lieberman, Tami D.; Flett, Kelly B.; Yelin, Idan
- Nature Genetics, Vol. 46, Issue 1
Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences
journal, April 2014
- Nasser, W.; Beres, S. B.; Olsen, R. J.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 17
Clinical use of whole genome sequencing for Mycobacterium tuberculosis
journal, March 2016
- Witney, Adam A.; Cosgrove, Catherine A.; Arnold, Amber
- BMC Medicine, Vol. 14, Issue 1
Natural Products As Sources of New Drugs over the 30 Years from 1981 to 2010
journal, January 2012
- Newman, David J.; Cragg, Gordon M.
- Journal of Natural Products, Vol. 75, Issue 3
A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing
journal, July 2013
- Kim, Hanyoup; Jebrail, Mais J.; Sinha, Anupama
- PLoS ONE, Vol. 8, Issue 7
Thermoplastic Microfluidic Device for On-Chip Purification of Nucleic Acids for Disposable Diagnostics
journal, February 2006
- Bhattacharyya, Arpita; Klapperich, Catherine M.
- Analytical Chemistry, Vol. 78, Issue 3
Natural Products As Sources of New Drugs over the 30 Years from 1981 to 2010
journal, January 2012
- Newman, David J.; Cragg, Gordon M.
- Journal of Natural Products, Vol. 75, Issue 3
Human gut microbiome viewed across age and geography
journal, May 2012
- Yatsunenko, Tanya; Rey, Federico E.; Manary, Mark J.
- Nature, Vol. 486, Issue 7402
A new antibiotic kills pathogens without detectable resistance
journal, January 2015
- Ling, Losee L.; Schneider, Tanja; Peoples, Aaron J.
- Nature, Vol. 517, Issue 7535
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
journal, July 2012
- Ramsköld, Daniel; Luo, Shujun; Wang, Yu-Chieh
- Nature Biotechnology, Vol. 30, Issue 8
Dense genomic sampling identifies highways of pneumococcal recombination
journal, February 2014
- Chewapreecha, Claire; Harris, Simon R.; Croucher, Nicholas J.
- Nature Genetics, Vol. 46, Issue 3
High-throughput single-molecule optofluidic analysis
journal, February 2011
- Kim, Soohong; Streets, Aaron M.; Lin, Ron R.
- Nature Methods, Vol. 8, Issue 3
The role of replicates for error mitigation in next-generation sequencing
journal, December 2013
- Robasky, Kimberly; Lewis, Nathan E.; Church, George M.
- Nature Reviews Genetics, Vol. 15, Issue 1
Synthetic biology to access and expand nature's chemical diversity
journal, February 2016
- Smanski, Michael J.; Zhou, Hui; Claesen, Jan
- Nature Reviews Microbiology, Vol. 14, Issue 3
Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing
journal, June 2014
- Wilson, Michael R.; Naccache, Samia N.; Samayoa, Erik
- New England Journal of Medicine, Vol. 370, Issue 25
Evolving stealth: Genetic adaptation of
Pseudomonas aeruginosa
during cystic fibrosis infections
journal, May 2006
- Nguyen, Dao; Singh, Pradeep K.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 22
Sequence error storms and the landscape of mutations in cancer
journal, August 2012
- Kirsch, Stefan; Klein, Christoph A.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 36
Library preparation methodology can influence genomic and functional predictions in human microbiome research
journal, October 2015
- Jones, Marcus B.; Highlander, Sarah K.; Anderson, Ericka L.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 45
Effects of Diet on Mercury Metabolism and Excretion in Mice Given Methylmercury: Role of Gut Flora
journal, November 1984
- Rowland, I. R.; Robinson, R. D.; Doherty, R. A.
- Archives of Environmental Health: An International Journal, Vol. 39, Issue 6
Solid-phase reversible immobilization for the isolation of PCR products
journal, January 1995
- DeAngelis, Margaret M.; Wang, David G.; Hawkins, Trevor L.
- Nucleic Acids Research, Vol. 23, Issue 22
Shotgun DNA sequencing using cloned DNase I-generated fragments
journal, January 1981
- Anderson, Stephen
- Nucleic Acids Research, Vol. 9, Issue 13
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database
journal, November 2015
- Winsor, Geoffrey L.; Griffiths, Emma J.; Lo, Raymond
- Nucleic Acids Research, Vol. 44, Issue D1
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
journal, May 2015
- Weber, Tilmann; Blin, Kai; Duddela, Srikanth
- Nucleic Acids Research, Vol. 43, Issue W1
Is exposure to mercury a driving force for the carriage of antibiotic resistance genes?
journal, March 2010
- Skurnik, D.; Ruimy, R.; Ready, D.
- Journal of Medical Microbiology, Vol. 59, Issue 7
Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
journal, November 2011
- Parkinson, N. J.; Maslau, S.; Ferneyhough, B.
- Genome Research, Vol. 22, Issue 1
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
journal, June 2014
- Naccache, S. N.; Federman, S.; Veeraraghavan, N.
- Genome Research, Vol. 24, Issue 7
The future is now: single-cell genomics of bacteria and archaea
journal, May 2013
- Blainey, Paul C.
- FEMS Microbiology Reviews, Vol. 37, Issue 3
Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing
journal, August 2012
- Snitkin, E. S.; Zelazny, A. M.; Thomas, P. J.
- Science Translational Medicine, Vol. 4, Issue 148
Quantitative Contributions of Target Alteration and Decreased Drug Accumulation to Pseudomonas aeruginosa Fluoroquinolone Resistance
journal, December 2012
- Bruchmann, Sebastian; Dötsch, Andreas; Nouri, Bianka
- Antimicrobial Agents and Chemotherapy, Vol. 57, Issue 3
Rich Medium Composition Affects Escherichia coli Survival, Glycation, and Mutation Frequency during Long-Term Batch Culture
journal, April 2015
- Kram, Karin E.; Finkel, Steven E.
- Applied and Environmental Microbiology, Vol. 81, Issue 13
Microfluidic Large-Scale Integration: The Evolution of Design Rules for Biological Automation
journal, June 2007
- Melin, Jessica; Quake, Stephen R.
- Annual Review of Biophysics and Biomolecular Structure, Vol. 36, Issue 1
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
journal, March 2015
- Brooks, J. Paul; Edwards, David J.; Harwich, Michael D.
- BMC Microbiology, Vol. 15, Issue 1
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014
- Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.
- BMC Biology, Vol. 12, Issue 1
Clinical use of whole genome sequencing for Mycobacterium tuberculosis
journal, March 2016
- Witney, Adam A.; Cosgrove, Catherine A.; Arnold, Amber
- BMC Medicine, Vol. 14, Issue 1
A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps
journal, July 2013
- Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael
- PLoS ONE, Vol. 8, Issue 7
A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing
journal, July 2013
- Kim, Hanyoup; Jebrail, Mais J.; Sinha, Anupama
- PLoS ONE, Vol. 8, Issue 7
A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods
journal, August 2014
- de Bourcy, Charles F. A.; De Vlaminck, Iwijn; Kanbar, Jad N.
- PLoS ONE, Vol. 9, Issue 8
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
journal, November 2014
- Walker, Bruce J.; Abeel, Thomas; Shea, Terrance
- PLoS ONE, Vol. 9, Issue 11
Simple Bulk Readout of Digital Nucleic Acid Quantification Assays
journal, September 2015
- Morinishi, Leanna S.; Blainey, Paul
- Journal of Visualized Experiments, Issue 103
PhyloSift: phylogenetic analysis of genomes and metagenomes
journal, January 2014
- Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric
- PeerJ, Vol. 2
Works referencing / citing this record:
Sample preparation in foodomic analyses
journal, May 2018
- Martinović, Tamara; Šrajer Gajdošik, Martina; Josić, Djuro
- ELECTROPHORESIS, Vol. 39, Issue 13
The trajectory of microbial single-cell sequencing
journal, October 2017
- Woyke, Tanja; Doud, Devin F. R.; Schulz, Frederik
- Nature Methods, Vol. 14, Issue 11
Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations
journal, March 2018
- Salk, Jesse J.; Schmitt, Michael W.; Loeb, Lawrence A.
- Nature Reviews Genetics, Vol. 19, Issue 5
Microfluidic curved-channel centrifuge for solution exchange of target microparticles and their simultaneous separation from bacteria
journal, January 2018
- Bayat, Pouriya; Rezai, Pouya
- Soft Matter, Vol. 14, Issue 26
On-ratio PDMS bonding for multilayer microfluidic device fabrication
journal, August 2019
- Lai, Andre; Altemose, Nicolas; White, Jonathan A.
- Journal of Micromechanics and Microengineering, Vol. 29, Issue 10
RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates
journal, August 2019
- Palace, Samantha G.; Wang, Yi; Rubin, Daniel H. F.
- eLife
Quantification of somatic mutation flow across individual cell division events by lineage sequencing
journal, November 2018
- Brody, Yehuda; Kimmerling, Robert J.; Maruvka, Yosef E.
- Genome Research, Vol. 28, Issue 12
Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures
journal, January 2019
- Reyes, Miguel; Vickers, Dwayne; Billman, Kianna
- Science Advances, Vol. 5, Issue 1
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
journal, October 2019
- Sanders, Jon G.; Nurk, Sergey; Salido, Rodolfo A.
- Genome Biology, Vol. 20, Issue 1
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
journal, November 2017
- Hall, Andrew Brantley; Yassour, Moran; Sauk, Jenny
- Genome Medicine, Vol. 9, Issue 1
Evaluation of a novel micro/nanofluidic chip platform for the detection of influenza A and B virus in patients with influenza-like illness
journal, May 2019
- Li, Runqing; Gai, Wei; Zhu, Dong
- AMB Express, Vol. 9, Issue 1
Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level
journal, September 2017
- Chen, Zixi; Chen, Lei; Zhang, Weiwen
- Frontiers in Microbiology, Vol. 8
Carbapenemases in Enterobacteriaceae: Detection and Antimicrobial Therapy
journal, August 2019
- Cui, Xiaoyan; Zhang, Haifang; Du, Hong
- Frontiers in Microbiology, Vol. 10
Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology
journal, June 2019
- Gorgannezhad, Lena; Stratton, Helen; Nguyen, Nam-Trung
- Micromachines, Vol. 10, Issue 6
Salivary Exosome and Cell-Free DNA for Cancer Detection
journal, July 2018
- Hyun, Kyung-A; Gwak, Hogyeong; Lee, Jaehun
- Micromachines, Vol. 9, Issue 7
On-ratio PDMS bonding for multilayer microfluidic device fabrication
journal, October 2018
- Lai, Andre; Altemose, Nicolas; White, Jonathan A.
- Journal of Micromechanics and Microengineering
Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures
text, January 2019
- K., Billman,; M., Reyes,; T., Eisenhaure,
- American Association for the Advancement of Science
RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates
journal, February 2020
- Palace, Samantha G.; Wang, Yi; Rubin, Daniel HF
- eLife, Vol. 9
A Controllable and Integrated Pump-enabled Microfluidic Chip and Its Application in Droplets Generating
journal, September 2017
- Zhao, Bei; Cui, Xingye; Ren, Wei
- Scientific Reports, Vol. 7, Issue 1
Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures
journal, January 2019
- Reyes, Miguel; Vickers, Dwayne; Billman, Kianna
- Science Advances, Vol. 5, Issue 1
Trends in Antibiotic Susceptibility in Staphylococcus aureus in Boston, Massachusetts, from 2000 to 2014
journal, January 2018
- Kanjilal, Sanjat; Sater, Mohamad R. Abdul; Thayer, Maile
- Journal of Clinical Microbiology, Vol. 56, Issue 1
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
journal, November 2017
- Hall, Andrew Brantley; Yassour, Moran; Sauk, Jenny
- Genome Medicine, Vol. 9, Issue 1
Evaluation of a novel micro/nanofluidic chip platform for the detection of influenza A and B virus in patients with influenza-like illness
journal, May 2019
- Li, Runqing; Gai, Wei; Zhu, Dong
- AMB Express, Vol. 9, Issue 1
Shared and organism-specific host responses to childhood diarrheal diseases revealed by whole blood transcript profiling
journal, January 2018
- DeBerg, Hannah A.; Zaidi, Mussaret B.; Altman, Matthew C.
- PLOS ONE, Vol. 13, Issue 1
Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level
journal, September 2017
- Chen, Zixi; Chen, Lei; Zhang, Weiwen
- Frontiers in Microbiology, Vol. 8
Salivary Exosome and Cell-Free DNA for Cancer Detection
journal, July 2018
- Hyun, Kyung-A; Gwak, Hogyeong; Lee, Jaehun
- Micromachines, Vol. 9, Issue 7