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68 entries « 1 of 2 »

2023

Reyes, Miguel; Leff, Samantha M; Gentili, Matteo; Hacohen, Nir; Blainey, Paul C

Microscale combinatorial stimulation of human myeloid cells reveals inflammatory priming by viral ligands Journal Article

In: Sci Adv, vol. 9, no. 8, pp. eade5090, 2023, ISSN: 2375-2548.

Abstract | Links | BibTeX

2022

Funk, Luke; Su, Kuan-Chung; Ly, Jimmy; Feldman, David; Singh, Avtar; Moodie, Brittania; Blainey, Paul C; Cheeseman, Iain M

The phenotypic landscape of essential human genes Journal Article

In: Cell, vol. 185, no. 24, pp. 4634–4653.e22, 2022, ISSN: 1097-4172.

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Walton, Russell T; Singh, Avtar; Blainey, Paul C

Pooled genetic screens with image-based profiling Journal Article

In: Mol Syst Biol, vol. 18, no. 11, pp. e10768, 2022, ISSN: 1744-4292.

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Metsky, Hayden C; Welch, Nicole L; Pillai, Priya P; Haradhvala, Nicholas J; Rumker, Laurie; Mantena, Sreekar; Zhang, Yibin B; Yang, David K; Ackerman, Cheri M; Weller, Juliane; Blainey, Paul C; Myhrvold, Cameron; Mitzenmacher, Michael; Sabeti, Pardis C

Designing sensitive viral diagnostics with machine learning Journal Article

In: Nat Biotechnol, vol. 40, no. 7, pp. 1123–1131, 2022, ISSN: 1546-1696.

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Quan, Kathleen A; Sater, Mohamad R A; Uy, Cherry; Clifton-Koeppel, Robin; Dickey, Linda L; Wilson, William; Patton, Pat; Chang, Wayne; Samuelson, Pamela; Lagoudas, Georgia K; Allen, Teri; Merchant, Lenny; Gannotta, Rick; Bittencourt, Cassiana E; Soto, J C; Evans, Kaye D; Blainey, Paul C; Murray, John; Shelton, Dawn; Lee, Helen S; Zahn, Matthew; Wolfe, Julia; Madey, Keith; Yim, Jennifer; Gohil, Shruti K; Grad, Yonatan H; Huang, Susan S

Epidemiology and genomics of a slow outbreak of methicillin-resistant (MRSA) in a neonatal intensive care unit: Successful chronic decolonization of MRSA-positive healthcare personnel Journal Article

In: Infect Control Hosp Epidemiol, pp. 1–8, 2022, ISSN: 1559-6834.

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Welch, Nicole L; Zhu, Meilin; Hua, Catherine; Weller, Juliane; Mirhashemi, Marzieh Ezzaty; Nguyen, Tien G; Mantena, Sreekar; Bauer, Matthew R; Shaw, Bennett M; Ackerman, Cheri M; Thakku, Sri Gowtham; Tse, Megan W; Kehe, Jared; Uwera, Marie-Martine; Eversley, Jacqueline S; Bielwaski, Derek A; McGrath, Graham; Braidt, Joseph; Johnson, Jeremy; Cerrato, Felecia; Moreno, Gage K; Krasilnikova, Lydia A; Petros, Brittany A; Gionet, Gabrielle L; King, Ewa; Huard, Richard C; Jalbert, Samantha K; Cleary, Michael L; Fitzgerald, Nicholas A; Gabriel, Stacey B; Gallagher, Glen R; Smole, Sandra C; Madoff, Lawrence C; Brown, Catherine M; Keller, Matthew W; Wilson, Malania M; Kirby, Marie K; Barnes, John R; Park, Daniel J; Siddle, Katherine J; Happi, Christian T; Hung, Deborah T; Springer, Michael; MacInnis, Bronwyn L; Lemieux, Jacob E; Rosenberg, Eric; Branda, John A; Blainey, Paul C; Sabeti, Pardis C; Myhrvold, Cameron

Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants Journal Article

In: Nat Med, vol. 28, no. 5, pp. 1083–1094, 2022, ISSN: 1546-170X.

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Thakku, Sri Gowtham; Ackerman, Cheri M; Myhrvold, Cameron; Bhattacharyya, Roby P; Livny, Jonathan; Ma, Peijun; Gomez, Giselle Isabella; Sabeti, Pardis C; Blainey, Paul C; Hung, Deborah T

Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays Journal Article

In: PNAS Nexus, vol. 1, no. 1, pp. pgac021, 2022, ISSN: 2752-6542.

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Feldman, David; Funk, Luke; Le, Anna; Carlson, Rebecca J; Leiken, Michael D; Tsai, FuNien; Soong, Brian; Singh, Avtar; Blainey, Paul C

Pooled genetic perturbation screens with image-based phenotypes Journal Article

In: Nat Protoc, vol. 17, no. 2, pp. 476–512, 2022, ISSN: 1750-2799.

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2021

Kehe, Jared; Ortiz, Anthony; Kulesa, Anthony; Gore, Jeff; Blainey, Paul C; Friedman, Jonathan

Positive interactions are common among culturable bacteria Journal Article

In: Sci Adv, vol. 7, no. 45, pp. eabi7159, 2021, ISSN: 2375-2548.

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Banal, James L; Shepherd, Tyson R; Berleant, Joseph; Huang, Hellen; Reyes, Miguel; Ackerman, Cheri M; Blainey, Paul C; Bathe, Mark

Random access DNA memory using Boolean search in an archival file storage system Journal Article

In: Nat Mater, vol. 20, no. 9, pp. 1272–1280, 2021, ISSN: 1476-4660.

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Zhu, Meilin; Tse, Megan W; Weller, Juliane; Chen, Julie; Blainey, Paul C

The future of antibiotics begins with discovering new combinations Journal Article

In: Ann N Y Acad Sci, vol. 1496, no. 1, pp. 82–96, 2021, ISSN: 1749-6632.

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Reyes, Miguel; Filbin, Michael R; Bhattacharyya, Roby P; Sonny, Abraham; Mehta, Arnav; Billman, Kianna; Kays, Kyle R; Pinilla-Vera, Mayra; Benson, Maura E; Cosimi, Lisa A; Hung, Deborah T; Levy, Bruce D; Villani, Alexandra-Chloe; Sade-Feldman, Moshe; Baron, Rebecca M; Goldberg, Marcia B; Blainey, Paul C; Hacohen, Nir

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro Journal Article

In: Sci Transl Med, vol. 13, no. 598, 2021, ISSN: 1946-6242.

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Elacqua, Joshua J; Ranu, Navpreet; DiIorio, Sarah E; Blainey, Paul C

DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution Journal Article

In: Genome Res, vol. 31, no. 1, pp. 75–87, 2021, ISSN: 1549-5469.

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Al’Khafaji, Aziz M.; Smith, Jonathan T.; Garimella, Kiran V; Babadi, Mehrtash; Sade-Feldman, Moshe; Gatzen, Michael; Sarkizova, Siranush; Schwartz, Marc A.; Popic, Victoria; Blaum, Emily M.; Day, Allyson; Costello, Maura; Bowers, Tera; Gabriel, Stacey; Banks, Eric; Philippakis, Anthony A.; Boland, Genevieve M.; Blainey, Paul C.; Hacohen, Nir

High-throughput RNA isoform sequencing using programmable cDNA concatenation Unpublished

2021.

Abstract | Links | BibTeX

2020

Shand, Megan; Soto, Jose; Lichtenstein, Lee; Benjamin, David; Farjoun, Yossi; Brody, Yehuda; Maruvka, Yosef; Blainey, Paul C; Banks, Eric

A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis Journal Article

In: Commun Biol, vol. 3, no. 1, pp. 744, 2020, ISSN: 2399-3642.

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Feldman, David; Tsai, FuNien; Garrity, Anthony J; O'Rourke, Ryan; Brenan, Lisa; Ho, Patricia; Gonzalez, Elizabeth; Konermann, Silvana; Johannessen, Cory M; Beroukhim, Rameen; Bandopadhayay, Pratiti; Blainey, Paul C

CloneSifter: enrichment of rare clones from heterogeneous cell populations Journal Article

In: BMC Biol, vol. 18, no. 1, pp. 177, 2020, ISSN: 1741-7007.

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Ackerman, Cheri M; Myhrvold, Cameron; Thakku, Sri Gowtham; Freije, Catherine A; Metsky, Hayden C; Yang, David K; Ye, Simon H; Boehm, Chloe K; Kosoko-Thoroddsen, Tinna-Sólveig F; Kehe, Jared; Nguyen, Tien G; Carter, Amber; Kulesa, Anthony; Barnes, John R; Dugan, Vivien G; Hung, Deborah T; Blainey, Paul C; Sabeti, Pardis C

Massively multiplexed nucleic acid detection with Cas13 Journal Article

In: Nature, vol. 582, no. 7811, pp. 277–282, 2020, ISSN: 1476-4687.

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Reyes, Miguel; Filbin, Michael R; Bhattacharyya, Roby P; Billman, Kianna; Eisenhaure, Thomas; Hung, Deborah T; Levy, Bruce D; Baron, Rebecca M; Blainey, Paul C; Goldberg, Marcia B; Hacohen, Nir

An immune-cell signature of bacterial sepsis Journal Article

In: Nat Med, vol. 26, no. 3, pp. 333–340, 2020, ISSN: 1546-170X.

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Ysasi, Alexandra B; Bennett, Robert D; Wagner, Willi; Valenzuela, Cristian D; Servais, Andrew B; Tsuda, Akira; Pyne, Saumyadipta; Li, Shuqiang; Grimsby, Jonna; Pokharel, Prapti; Livak, Kenneth J; Ackermann, Maximilian; Blainey, Paul C; Mentzer, Steven J

Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts Journal Article

In: Front Med (Lausanne), vol. 7, pp. 112, 2020, ISSN: 2296-858X.

Abstract | Links | BibTeX

Peters, Joshua M.; Blainey, Paul C.; Bryson, Bryan D.

Consensus transcriptional states describe human mononuclear phagocyte diversity in the lung across health and disease Unpublished

2020.

Abstract | Links | BibTeX

2019

Schmidt, Stephanie Tzouanas; Yu, Feiqiao Brian; Blainey, Paul C; May, Andrew P; Quake, Stephen R

Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium Journal Article

In: Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23100–23105, 2019, ISSN: 1091-6490.

Abstract | Links | BibTeX

Reyes, Miguel; Billman, Kianna; Hacohen, Nir; Blainey, Paul C

Simultaneous profiling of gene expression and chromatin accessibility in single cells Journal Article

In: Adv Biosyst, vol. 3, no. 11, 2019, ISSN: 2366-7478.

Abstract | Links | BibTeX

Feldman, David; Singh, Avtar; Schmid-Burgk, Jonathan L; Carlson, Rebecca J; Mezger, Anja; Garrity, Anthony J; Zhang, Feng; Blainey, Paul C

Optical Pooled Screens in Human Cells Journal Article

In: Cell, vol. 179, no. 3, pp. 787–799.e17, 2019, ISSN: 1097-4172.

Abstract | Links | BibTeX

Guo, Syuan-Ming; Veneziano, Remi; Gordonov, Simon; Li, Li; Danielson, Eric; de Arce, Karen Perez; Park, Demian; Kulesa, Anthony B; Wamhoff, Eike-Christian; Blainey, Paul C; Boyden, Edward S; Cottrell, Jeffrey R; Bathe, Mark

Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes Journal Article

In: Nat Commun, vol. 10, no. 1, pp. 4377, 2019, ISSN: 2041-1723.

Abstract | Links | BibTeX

Kehe, Jared; Kulesa, Anthony; Ortiz, Anthony; Ackerman, Cheri M; Thakku, Sri Gowtham; Sellers, Daniel; Kuehn, Seppe; Gore, Jeff; Friedman, Jonathan; Blainey, Paul C

Massively parallel screening of synthetic microbial communities Journal Article

In: Proc Natl Acad Sci U S A, vol. 116, no. 26, pp. 12804–12809, 2019, ISSN: 1091-6490.

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Järvenpää, Marko; Sater, Mohamad R Abdul; Lagoudas, Georgia K; Blainey, Paul C; Miller, Loren G; McKinnell, James A; Huang, Susan S; Grad, Yonatan H; Marttinen, Pekka

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation Journal Article

In: PLoS Comput Biol, vol. 15, no. 4, pp. e1006534, 2019, ISSN: 1553-7358.

Abstract | Links | BibTeX

Berghuis, Bojk A; Yu, Feiqiao Brian; Schulz, Frederik; Blainey, Paul C; Woyke, Tanja; Quake, Stephen R

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens Journal Article

In: Proc Natl Acad Sci U S A, vol. 116, no. 11, pp. 5037–5044, 2019, ISSN: 1091-6490.

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Jin, Chengcheng; Lagoudas, Georgia K; Zhao, Chen; Bullman, Susan; Bhutkar, Arjun; Hu, Bo; Ameh, Samuel; Sandel, Demi; Liang, Xu Sue; Mazzilli, Sarah; Whary, Mark T; Meyerson, Matthew; Germain, Ronald; Blainey, Paul C; Fox, James G; Jacks, Tyler

Commensal Microbiota Promote Lung Cancer Development via γδ T Cells Journal Article

In: Cell, vol. 176, no. 5, pp. 998–1013.e16, 2019, ISSN: 1097-4172.

Abstract | Links | BibTeX

Reyes, Miguel; Vickers, Dwayne; Billman, Kianna; Eisenhaure, Thomas; Hoover, Paul; Browne, Edward P; Rao, Deepak A; Hacohen, Nir; Blainey, Paul C

Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures Journal Article

In: Sci Adv, vol. 5, no. 1, pp. eaau9223, 2019, ISSN: 2375-2548.

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Ranu, Navpreet; Villani, Alexandra-Chloé; Hacohen, Nir; Blainey, Paul C

Targeting individual cells by barcode in pooled sequence libraries Journal Article

In: Nucleic Acids Res, vol. 47, no. 1, pp. e4, 2019, ISSN: 1362-4962.

Abstract | Links | BibTeX

2018

Brody, Yehuda; Kimmerling, Robert J; Maruvka, Yosef E; Benjamin, David; Elacqua, Joshua J; Haradhvala, Nicholas J; Kim, Jaegil; Mouw, Kent W; Frangaj, Kristjana; Koren, Amnon; Getz, Gad; Manalis, Scott R; Blainey, Paul C

Quantification of somatic mutation flow across individual cell division events by lineage sequencing Journal Article

In: Genome Res, vol. 28, no. 12, pp. 1901–1918, 2018, ISSN: 1549-5469.

Abstract | Links | BibTeX

Kulesa, Anthony; Kehe, Jared; Hurtado, Juan E; Tawde, Prianca; Blainey, Paul C

Combinatorial drug discovery in nanoliter droplets Journal Article

In: Proc Natl Acad Sci U S A, vol. 115, no. 26, pp. 6685–6690, 2018, ISSN: 1091-6490.

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Vestergaard, Christian L; Blainey, Paul C; Flyvbjerg, Henrik

Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA Journal Article

In: Nucleic Acids Res, vol. 46, no. 5, pp. 2446–2458, 2018, ISSN: 1362-4962.

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Kanjilal, Sanjat; Sater, Mohamad R Abdul; Thayer, Maile; Lagoudas, Georgia K; Kim, Soohong; Blainey, Paul C; Grad, Yonatan H

Trends in Antibiotic Susceptibility in Staphylococcus aureus in Boston, Massachusetts, from 2000 to 2014 Journal Article

In: J Clin Microbiol, vol. 56, no. 1, 2018, ISSN: 1098-660X.

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2017

Xiong, Kan; Blainey, Paul C

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA Journal Article

In: J Vis Exp, no. 128, 2017, ISSN: 1940-087X.

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Yu, Feiqiao Brian; Blainey, Paul C; Schulz, Frederik; Woyke, Tanja; Horowitz, Mark A; Quake, Stephen R

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples Journal Article

In: Elife, vol. 6, 2017, ISSN: 2050-084X.

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Brito, I L; Yilmaz, S; Huang, K; Xu, L; Jupiter, S D; Jenkins, A P; Naisilisili, W; Tamminen, M; Smillie, C S; Wortman, J R; Birren, B W; Xavier, R J; Blainey, P C; Singh, A K; Gevers, D; Alm, E J

Corrigendum: Mobile genes in the human microbiome are structured from global to individual scales Journal Article

In: Nature, vol. 544, no. 7648, pp. 124, 2017, ISSN: 1476-4687.

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Kim, Soohong; Jonghe, Joachim De; 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 Journal Article

In: Nat Commun, vol. 8, pp. 13919, 2017, ISSN: 2041-1723.

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2016

Xiong, Kan; Erwin, Graham S; Ansari, Aseem Z; Blainey, Paul C

Sliding on DNA: From Peptides to Small Molecules Journal Article

In: Angew Chem Int Ed Engl, vol. 55, no. 48, pp. 15110–15114, 2016, ISSN: 1521-3773.

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Xu, Liyi; Brito, Ilana L; Alm, Eric J; Blainey, Paul C

Virtual microfluidics for digital quantification and single-cell sequencing Journal Article

In: Nat Methods, vol. 13, no. 9, pp. 759–762, 2016, ISSN: 1548-7105.

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Blainey, Paul C

Funding: Interdisciplinary challenges Journal Article

In: Nat Microbiol, vol. 1, no. 8, pp. 16118, 2016, ISSN: 2058-5276.

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Brito, I L; Yilmaz, S; Huang, K; Xu, L; Jupiter, S D; Jenkins, A P; Naisilisili, W; Tamminen, M; Smillie, C S; Wortman, J R; Birren, B W; Xavier, R J; Blainey, P C; Singh, A K; Gevers, D; Alm, E J

Mobile genes in the human microbiome are structured from global to individual scales Journal Article

In: Nature, vol. 535, no. 7612, pp. 435–439, 2016, ISSN: 1476-4687.

Abstract | Links | BibTeX

Xiong, Kan; Blainey, Paul C

Molecular sled sequences are common in mammalian proteins Journal Article

In: Nucleic Acids Res, vol. 44, no. 5, pp. 2266–2273, 2016, ISSN: 1362-4962.

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Mangel, Walter F; McGrath, William J; Xiong, Kan; Graziano, Vito; Blainey, Paul C

Molecular sled is an eleven-amino acid vehicle facilitating biochemical interactions via sliding components along DNA Journal Article

In: Nat Commun, vol. 7, pp. 10202, 2016, ISSN: 2041-1723.

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Biteen, Julie S; Blainey, Paul C; Cardon, Zoe G; Chun, Miyoung; Church, George M; Dorrestein, Pieter C; Fraser, Scott E; Gilbert, Jack A; Jansson, Janet K; Knight, Rob; Miller, Jeff F; Ozcan, Aydogan; Prather, Kimberly A; Quake, Stephen R; Ruby, Edward G; Silver, Pamela A; Taha, Sharif; van den Engh, Ger; Weiss, Paul S; Wong, Gerard C L; Wright, Aaron T; Young, Thomas D

Tools for the Microbiome: Nano and Beyond Journal Article

In: ACS Nano, vol. 10, no. 1, pp. 6–37, 2016, ISSN: 1936-086X.

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Kimmerling, Robert J; Szeto, Gregory Lee; Li, Jennifer W; Genshaft, Alex S; Kazer, Samuel W; Payer, Kristofor R; de Riba Borrajo, Jacob; Blainey, Paul C; Irvine, Darrell J; Shalek, Alex K; Manalis, Scott R

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages Journal Article

In: Nat Commun, vol. 7, pp. 10220, 2016, ISSN: 2041-1723.

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2014

Vestergaard, Christian L; Blainey, Paul C; Flyvbjerg, Henrik

Optimal estimation of diffusion coefficients from single-particle trajectories Journal Article

In: Phys Rev E Stat Nonlin Soft Matter Phys, vol. 89, no. 2, pp. 022726, 2014, ISSN: 1550-2376.

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Bennett, Robert D; Ysasi, Alexandra B; Belle, Janeil M; Wagner, Willi L; Konerding, Moritz A; Blainey, Paul C; Pyne, Saumyadipta; Mentzer, Steven J

Laser microdissection of the alveolar duct enables single-cell genomic analysis Journal Article

In: Front Oncol, vol. 4, pp. 260, 2014, ISSN: 2234-943X.

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Blainey, Paul C; Quake, Stephen R

Dissecting genomic diversity, one cell at a time Journal Article

In: Nat Methods, vol. 11, no. 1, pp. 19–21, 2014, ISSN: 1548-7105.

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2013

Blainey, Paul C

The future is now: single-cell genomics of bacteria and archaea Journal Article

In: FEMS Microbiol Rev, vol. 37, no. 3, pp. 407–427, 2013, ISSN: 1574-6976.

Abstract | Links | BibTeX

68 entries « 1 of 2 »