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Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms.
Published in:
European Journal of Clinical Microbiology & Infectious Diseases, 2021, v. 40, n. 1, p. 95, doi. 10.1007/s10096-020-03996-4
By:
- Yee, Rebecca;
- Breitwieser, Florian P.;
- Hao, Stephanie;
- Opene, Belita N.A.;
- Workman, Rachael E.;
- Tamma, Pranita D.;
- Dien-Bard, Jennifer;
- Timp, Winston;
- Simner, Patricia J.
Publication type:
Article
Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization.
Published in:
Nucleic Acids Research, 2017, v. 45, n. 14, p. 1, doi. 10.1093/nar/gkx471
By:
- Credle, Joel J.;
- Itoh, Christopher Y.;
- Yuan, Tiezheng;
- Sharma, Rajni;
- Scott, Erick R.;
- Workman, Rachael E.;
- Yunfan Fan;
- Housseau, Franck;
- Llosa, Nicolas J.;
- Bell, W. Robert.;
- Miller, Heather;
- Zhang, Sean X.;
- Timp, Winston;
- Larman, H. Benjamin
Publication type:
Article
Plasma virome and the risk of blood-borne infection in persons with substance use disorder.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26980-8
By:
- Kandathil, Abraham J.;
- Cox, Andrea L.;
- Page, Kimberly;
- Mohr, David;
- Razaghi, Roham;
- Ghanem, Khalil G.;
- Tuddenham, Susan A.;
- Hsieh, Yu-Hsiang;
- Evans, Jennifer L.;
- Coller, Kelly E.;
- Timp, Winston;
- Celentano, David D.;
- Ray, Stuart C.;
- Thomas, David L.
Publication type:
Article
Epigenetically regulated digital signaling defines epithelial innate immunity at the tissue level.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22070-x
By:
- Clark, Helen R.;
- McKenney, Connor;
- Livingston, Nathan M.;
- Gershman, Ariel;
- Sajjan, Seema;
- Chan, Isaac S.;
- Ewald, Andrew J.;
- Timp, Winston;
- Wu, Bin;
- Singh, Abhyudai;
- Regot, Sergi
Publication type:
Article
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.
Published in:
Nature Biotechnology, 2021, v. 39, n. 4, p. 431, doi. 10.1038/s41587-020-0731-9
By:
- Kovaka, Sam;
- Fan, Yunfan;
- Ni, Bohan;
- Timp, Winston;
- Schatz, Michael C.
Publication type:
Article
Targeted nanopore sequencing with Cas9-guided adapter ligation.
Published in:
Nature Biotechnology, 2020, v. 38, n. 4, p. 433, doi. 10.1038/s41587-020-0407-5
By:
- Gilpatrick, Timothy;
- Lee, Isac;
- Graham, James E.;
- Raimondeau, Etienne;
- Bowen, Rebecca;
- Heron, Andrew;
- Downs, Bradley;
- Sukumar, Saraswati;
- Sedlazeck, Fritz J;
- Timp, Winston
Publication type:
Article
Increased methylation variation in epigenetic domains across cancer types.
Published in:
Nature Genetics, 2011, v. 43, n. 8, p. 768, doi. 10.1038/ng.865
By:
- Hansen, Kasper Daniel;
- Timp, Winston;
- Bravo, Héctor Corrada;
- Sabunciyan, Sarven;
- Langmead, Benjamin;
- McDonald, Oliver G.;
- Bo Wen;
- Hao Wu;
- Yun Liu;
- Dinh Diep;
- Briem, Eirikur;
- Kun Zhang;
- Irizarry, Rafael A.;
- Feinberg, Andrew P.
Publication type:
Article
Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy.
Published in:
Nature Methods, 2007, v. 4, n. 7, p. 567, doi. 10.1038/nmeth1053
By:
- Zeskind, Benjamin J.;
- Jordan, Caroline D.;
- Timp, Winston;
- Trapani, Linda;
- Waller, Guichy;
- Horodincu, Victor;
- Ehrlich, Daniel J.;
- Matsudaira, Paul
Publication type:
Article
Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition.
Published in:
Nature Structural & Molecular Biology, 2011, v. 18, n. 8, p. 867, doi. 10.1038/nsmb.2084
By:
- McDonald, Oliver G.;
- Hao Wu;
- Timp, Winston;
- Doi, Akiko;
- Feinberg, Andrew P.
Publication type:
Article
Characterization of human telomerase reverse transcriptase promoter methylation and transcription factor binding in differentiated thyroid cancer cell lines.
Published in:
Genes, Chromosomes & Cancer, 2019, v. 58, n. 8, p. 530, doi. 10.1002/gcc.22735
By:
- Avin, Brittany A.;
- Wang, Yongchun;
- Gilpatrick, Timothy;
- Workman, Rachael E.;
- Lee, Isac;
- Timp, Winston;
- Umbricht, Christopher B.;
- Zeiger, Martha A.
Publication type:
Article
FrameD: framework for DNA-based data storage design, verification, and validation.
Published in:
Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad572
By:
- Volkel, Kevin D;
- Lin, Kevin N;
- Hook, Paul W;
- Timp, Winston;
- Keung, Albert J;
- Tuck, James M
Publication type:
Article
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome.
Published in:
GigaScience, 2020, v. 9, n. 5, p. N.PAG, doi. 10.1093/gigascience/giaa050
By:
- Marrano, Annarita;
- Britton, Monica;
- Zaini, Paulo A;
- Zimin, Aleksey V;
- Workman, Rachael E;
- Puiu, Daniela;
- Bianco, Luca;
- Pierro, Erica Adele Di;
- Allen, Brian J;
- Chakraborty, Sandeep;
- Troggio, Michela;
- Leslie, Charles A;
- Timp, Winston;
- Dandekar, Abhaya;
- Salzberg, Steven L;
- Neale, David B
Publication type:
Article
PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02486-w
By:
- Mahmoud, Medhat;
- Doddapaneni, Harshavardhan;
- Timp, Winston;
- Sedlazeck, Fritz J.
Publication type:
Article
A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor.
Published in:
PLoS Pathogens, 2021, v. 17, n. 4, p. 1, doi. 10.1371/journal.ppat.1009537
By:
- Vornhagen, Jay;
- Bassis, Christine M.;
- Ramakrishnan, Srividya;
- Hein, Robert;
- Mason, Sophia;
- Bergman, Yehudit;
- Sunshine, Nicole;
- Fan, Yunfan;
- Holmes, Caitlyn L.;
- Timp, Winston;
- Schatz, Michael C.;
- Young, Vincent B.;
- Simner, Patricia J.;
- Bachman, Michael A.
Publication type:
Article
Epigenetic comparison of CHO hosts and clones reveals divergent methylation and transcription patterns across lineages.
Published in:
Biotechnology & Bioengineering, 2022, v. 119, n. 4, p. 1062, doi. 10.1002/bit.28036
By:
- Chang, Meiping;
- Kumar, Amit;
- Kumar, Swetha;
- Huhn, Steven;
- Timp, Winston;
- Betenbaugh, Michael;
- Du, Zhimei
Publication type:
Article
Characterization of Allele-Specific Regulation of Telomerase Reverse Transcriptase in Promoter Mutant Thyroid Cancer Cell Lines.
Published in:
Thyroid, 2020, v. 30, n. 10, p. 1470, doi. 10.1089/thy.2020.0055
By:
- McKelvey, Brittany A.;
- Gilpatrick, Timothy;
- Wang, Yongchun;
- Timp, Winston;
- Umbricht, Christopher B.;
- Zeiger, Martha A.
Publication type:
Article
Transposon-sequencing (Tn-seq) of the Candida glabrata reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin.
Published in:
G3: Genes | Genomes | Genetics, 2024, v. 14, n. 9, p. 1, doi. 10.1093/g3journal/jkae173
By:
- Nickels, Timothy J;
- Gale, Andrew N;
- Harrington, Abigail A;
- Timp, Winston;
- Cunningham, Kyle W
Publication type:
Article
A genome sequence for the threatened whitebark pine.
Published in:
G3: Genes | Genomes | Genetics, 2024, v. 14, n. 5, p. 1, doi. 10.1093/g3journal/jkae061
By:
- Neale, David B;
- Zimin, Aleksey V;
- Meltzer, Amy;
- Bhattarai, Akriti;
- Amee, Maurice;
- Corona, Laura Figueroa;
- Allen, Brian J;
- Puiu, Daniela;
- Wright, Jessica;
- Torre, Amanda R De La;
- McGuire, Patrick E;
- Timp, Winston;
- Salzberg, Steven L;
- Wegrzyn, Jill L
Publication type:
Article
Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin.
Published in:
G3: Genes | Genomes | Genetics, 2022, v. 12, n. 1, p. 1, doi. 10.1093/g3journal/jkab380
By:
- Neale, David B.;
- Zimin, Aleksey V.;
- Zaman, Sumaira;
- Scott, Alison D.;
- Shrestha, Bikash;
- Workman, Rachael E.;
- Puiu, Daniela;
- Allen, Brian J.;
- Moore, Zane J.;
- Sekhwal, Manoj K.;
- De La Torre, Amanda R.;
- McGuire, Patrick E.;
- Burns, Emily;
- Timp, Winston;
- Wegrzyn, Jill L.;
- Salzberg, Steven L.
Publication type:
Article
Genome and transcriptome of a pathogenic yeast, Candida nivariensis.
Published in:
G3: Genes | Genomes | Genetics, 2021, v. 11, n. 7, p. 1, doi. 10.1093/g3journal/jkab137
By:
- Yunfan Fan;
- Gale, Andrew N.;
- Bailey, Anna;
- Barnes, Kali;
- Colotti, Kiersten;
- Mass, Michal;
- Morina, Luke B.;
- Robertson, Bailey;
- Schwab, Remy;
- Tselepidakis, Niki;
- Timp, Winston
Publication type:
Article
De novo genome assembly of the tobacco hornworm moth (Manduca sexta) .
Published in:
G3: Genes | Genomes | Genetics, 2021, v. 11, n. 1, p. 1, doi. 10.1093/g3journal/jkaa047
By:
- Gershman, Ariel;
- Romer, Tatiana G.;
- Fan, Yunfan;
- Razaghi, Roham;
- Smith, Wendy A.;
- Timp, Winston
Publication type:
Article
Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions.
Published in:
G3: Genes | Genomes | Genetics, 2020, v. 10, n. 10, p. 3859, doi. 10.1534/g3.120.401595
By:
- Gale, Andrew N.;
- Sakhawala, Rima M.;
- Levitan, Anton;
- Sharan, Roded;
- Berman, Judith;
- Timp, Winston;
- Cunningham, Kyle W.
Publication type:
Article
A Reference Genome Sequence for Giant Sequoia.
Published in:
G3: Genes | Genomes | Genetics, 2020, v. 10, n. 11, p. 3907, doi. 10.1534/g3.120.401612
By:
- Scott, Alison D.;
- Zimin, Aleksey V.;
- Puiu, Daniela;
- Workman, Rachael;
- Britton, Monica;
- Zaman, Sumaira;
- Caballero, Madison;
- Read, Andrew C.;
- Bogdanove, Adam J.;
- Burns, Emily;
- Wegrzyn, Jill;
- Timp, Winston;
- Salzberg, Steven L.;
- Neale, David B.
Publication type:
Article
First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans).
Published in:
G3: Genes | Genomes | Genetics, 2017, v. 7, n. 11, p. 3831, doi. 10.1534/g3.117.300107
By:
- Ruibang Luo;
- Zimin, Aleksey;
- Workman, Rachael;
- Yunfan Fan;
- Pertea, Geo;
- Grossman, Nina;
- Wear, Maggie P.;
- Bei Jia;
- Miller, Heather;
- Casadevall, Arturo;
- Timp, Winston;
- Zhang, Sean X.;
- Salzberg, Steven L.
Publication type:
Article
Long-Read Nanopore-Based Sequencing of Anelloviruses.
Published in:
Viruses (1999-4915), 2024, v. 16, n. 5, p. 723, doi. 10.3390/v16050723
By:
- Anantharam, Raghavendran;
- Duchen, Dylan;
- Cox, Andrea L.;
- Timp, Winston;
- Thomas, David L.;
- Clipman, Steven J.;
- Kandathil, Abraham J.
Publication type:
Article
Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like bla<sub>KPC</sub> bearing plasmids.
Published in:
JAC-Antimicrobial Resistance, 2023, v. 5, n. 3, p. 1, doi. 10.1093/jacamr/dlad061
By:
- Simner, Patricia J.;
- Bergman, Yehudit;
- Fan, Yunfan;
- Jacobs, Emily B.;
- Ramakrishnan, Srividya;
- Lu, Jennifer;
- Lewis, Shawna;
- Hanlon, Ann;
- Tamma, Pranita D.;
- Schatz, Michael C.;
- Timp, Winston;
- Carroll, Karen C.
Publication type:
Article
Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries.
Published in:
Nucleic Acids Research, 2021, v. 49, n. 12, p. 6687, doi. 10.1093/nar/gkab505
By:
- Lietard, Jory;
- Leger, Adrien;
- Erlich, Yaniv;
- Sadowski, Norah;
- Timp, Winston;
- Somoza, Mark M
Publication type:
Article
Molecular diagnostics for personal medicine using a nanopore.
Published in:
WIREs: Nanomedicine & Nanobiotechnology, 2010, v. 2, n. 4, p. 367, doi. 10.1002/wnan.86
By:
- Mirsaidov, Utkur M.;
- Wang, Deqiang;
- Timp, Winston;
- Timp, Gregory
Publication type:
Article
Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification.
Published in:
Plant Physiology, 2023, v. 193, n. 2, p. 1016, doi. 10.1093/plphys/kiad409
By:
- Junhui Zhou;
- Muzi Li;
- Yongping Li;
- Yuwei Xiao;
- Xi Luo;
- Shenglan Gao;
- Zhimin Ma;
- Sadowski, Norah;
- Timp, Winston;
- Dardick, Chris;
- Callahan, Ann;
- Mount, Stephen M.;
- Zhongchi Liu
Publication type:
Article
Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs.
Published in:
Annals of Internal Medicine, 2017, v. 167, n. 1, p. 1, doi. 10.7326/M17-0085
By:
- Kandathil, Abraham J.;
- Breitwieser, Florian P.;
- Sachithanandham, Jaiprasath;
- Robinson, Matthew;
- Mehta, Shruti H.;
- Timp, Winston;
- Salzberg, Steven L.;
- Thomas, David L.;
- Balagopal, Ashwin
Publication type:
Article
Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs.
Published in:
2017
By:
- Kandathil, Abraham J;
- Breitwieser, Florian P;
- Sachithanandham, Jaiprasath;
- Robinson, Matthew;
- Mehta, Shruti H;
- Timp, Winston;
- Salzberg, Steven L;
- Thomas, David L;
- Balagopal, Ashwin
Publication type:
journal article
Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.
Published in:
Genome Medicine, 2014, v. 6, n. 8, p. 32, doi. 10.1186/s13073-014-0061-y
By:
- Timp, Winston;
- Bravo, Hector;
- McDonald, Oliver;
- Goggins, Michael;
- Umbricht, Chris;
- Zeiger, Martha;
- Feinberg, Andrew;
- Irizarry, Rafael
Publication type:
Article
Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria.
Published in:
PLoS ONE, 2018, v. 13, n. 12, p. 1, doi. 10.1371/journal.pone.0209408
By:
- Xiong, Tina;
- Rohm, Dahlia;
- Workman, Rachael E.;
- Roundtree, Lauren;
- Novina, Carl D.;
- Timp, Winston;
- Ostermeier, Marc
Publication type:
Article
Subcloning induces changes in the DNA‐methylation pattern of outgrowing Chinese hamster ovary cell colonies.
Published in:
Biotechnology Journal, 2021, v. 16, n. 6, p. 1, doi. 10.1002/biot.202000350
By:
- Weinguny, Marcus;
- Klanert, Gerald;
- Eisenhut, Peter;
- Lee, Isac;
- Timp, Winston;
- Borth, Nicole
Publication type:
Article
Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae.
Published in:
2018
By:
- Simner, Patricia J.;
- Antar, Annukka A. R.;
- Hao, Stephanie;
- Gurtowski, James;
- Tamma, Pranita D.;
- Rock, Clare;
- Opene, Belita N. A.;
- Tekle, Tsigereda;
- Carroll, Karen C.;
- Schatz, Michael C.;
- Timp, Winston
Publication type:
journal article
Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host.
Published in:
Nature Reviews Cancer, 2013, v. 13, n. 7, p. 497, doi. 10.1038/nrc3486
By:
- Timp, Winston;
- Feinberg, Andrew P.
Publication type:
Article
Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging.
Published in:
Aging Cell, 2023, v. 22, n. 6, p. 1, doi. 10.1111/acel.13842
By:
- Vandiver, Amy R.;
- Hoang, Austin N.;
- Herbst, Allen;
- Lee, Cathy C.;
- Aiken, Judd M.;
- McKenzie, Debbie;
- Teitell, Michael A.;
- Timp, Winston;
- Wanagat, Jonathan
Publication type:
Article
A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.
Published in:
Microbiome, 2020, v. 8, n. 1, p. 1, doi. 10.1186/s40168-020-00812-1
By:
- Olson, Nathan D.;
- Kumar, M. Senthil;
- Li, Shan;
- Braccia, Domenick J.;
- Hao, Stephanie;
- Timp, Winston;
- Salit, Marc L.;
- Stine, O. Colin;
- Bravo, Hector Corrada
Publication type:
Article
A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.
Published in:
Microbiome, 2020, v. 8, n. 1, p. N.PAG, doi. 10.1186/s40168-020-00812-1
By:
- Olson, Nathan D.;
- Kumar, M. Senthil;
- Li, Shan;
- Braccia, Domenick J.;
- Hao, Stephanie;
- Timp, Winston;
- Salit, Marc L.;
- Stine, O. Colin;
- Bravo, Hector Corrada
Publication type:
Article

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