Publications

2020

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

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms Journal Article

European Journal of Clinical Microbiology & Infectious Diseases, 2020, ISSN: 1435-4373.

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Miga, Karen H; Koren, Sergey; Rhie, Arang; Vollger, Mitchell R; Gershman, Ariel; Bzikadze, Andrey; Brooks, Shelise; Howe, Edmund; Porubsky, David; Logsdon, Glennis A; Schneider, Valerie A; Potapova, Tamara; Wood, Jonathan; Chow, William; Armstrong, Joel; Fredrickson, Jeanne; Pak, Evgenia; Tigyi, Kristof; Kremitzki, Milinn; Markovic, Christopher; Maduro, Valerie; Dutra, Amalia; Bouffard, Gerard G; Chang, Alexander M; Hansen, Nancy F; Wilfert, Amy B; Thibaud-Nissen, Françoise; Schmitt, Anthony D; Belton, Jon-Matthew; Selvaraj, Siddarth; Dennis, Megan Y; Soto, Daniela C; Sahasrabudhe, Ruta; Kaya, Gulhan; Quick, Josh; Loman, Nicholas J; Holmes, Nadine; Loose, Matthew; Surti, Urvashi; ana Risques, Rosa; Lindsay, Tina Graves A; Fulton, Robert; Hall, Ira; Paten, Benedict; Howe, Kerstin; Timp, Winston; Young, Alice; Mullikin, James C; Pevzner, Pavel A; Gerton, Jennifer L; Sullivan, Beth A; Eichler, Evan E; Phillippy, Adam M

Telomere-to-telomere assembly of a complete human X chromosome Journal Article

Nature, pp. 1–9, 2020, ISSN: 1476-4687, (Publisher: Nature Publishing Group).

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McKelvey, Brittany A; Gilpatrick, Timothy; Wang, Yongchun; Timp, Winston; Umbricht, Christopher B; Zeiger, Martha A

Characterization of Allele-Specific Regulation of Telomerase Reverse Transcriptase in Promoter Mutant Thyroid Cancer Cell Lines Journal Article

Thyroid, 2020, ISSN: 1050-7256, (Publisher: Mary Ann Liebert, Inc., publishers).

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Olson, Nathan D; Kumar, Senthil M; Li, Shan; Braccia, Domenick J; Hao, Stephanie; Timp, Winston; Salit, Marc L; Stine, Colin O; Bravo, Hector Corrada

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures. Journal Article

Microbiome, 8 (1), pp. 35, 2020, ISSN: 2049-2618.

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Gilpatrick, Timothy; Lee, Isac; Graham, James E; Raimondeau, Etienne; Bowen, Rebecca; Heron, Andrew; Downs, Bradley; Sukumar, Saraswati; Sedlazeck, Fritz J; Timp, Winston

Targeted nanopore sequencing with Cas9-guided adapter ligation Journal Article

Nature Biotechnology, 2020, ISSN: 1546-1696.

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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

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome Journal Article

GigaScience, 9 (5), 2020, ISSN: 2047-217X, (giaa050).

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Gale, Andrew N; Sakhawala, Rima M; Levitan, Anton; Sharan, Roded; Berman, Judith; Timp, Winston; Cunningham, Kyle W

Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions Journal Article

G3: Genes, Genomes, Genetics, 2020.

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Kovaka, Sam; Fan, Yunfan; Ni, Bohan; Timp, Winston; Schatz, Michael C

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED Journal Article

bioRxiv, 2020.

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Roach, Nathan P; Sadowski, Norah; Alessi, Amelia F; Timp, Winston; Taylor, James; Kim, John K

The full-length transcriptome of C. elegans using direct RNA sequencing Journal Article

Genome Research, 2020.

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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

The giant sequoia genome and proliferation of disease resistance genes Journal Article

bioRxiv, 2020.

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Stephenson, William; Razaghi, Roham; Busan, Steven; Weeks, Kevin M; Timp, Winston; Smibert, Peter

Direct detection of RNA modifications and structure using single molecule nanopore sequencing Journal Article

bioRxiv, 2020.

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Thielen, Peter M; Wohl, Shirlee; Mehoke, Thomas; Ramakrishnan, Srividya; Kirsche, Melanie; Falade-Nwulia, Oluwaseun; Trovao, Nidia S; Erlund, Amanda; Howser, Craig; Sadowski, Norah; Morris, Paul; Hopkins, Mark; Schwartz, Matthew; Fan, Yunfan; Gniazdowski, Victoria; Lessler, Justin; Sauer, Lauren; Schatz, Michael C; Evans, Jared D; Ray, Stuart C; Timp, Winston; Mostafa, Heba H

Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region Journal Article

medRxiv, 2020.

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Timp, Winston; Timp, Gregory

Beyond mass spectrometry, the next step in proteomics Journal Article

Science Advances, 6 (2), 2020.

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Vornhagen, Jay; Bassis, Christine M; Ramakrishnan, Srividya; Hein, Robert; Mason, Sophia; Bergman, Yehudit; Sunshine, Nicole; Fan, Yunfan; Timp, Winston; Schatz, Michael C; Young, Vincent B; Simner, Patricia J; Bachman, Michael A

A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor Journal Article

bioRxiv, 2020.

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2019

Aganezov, Sergey; Goodwin, Sara; Sherman, Rachel; Sedlazeck, Fritz J; Arun, Gayatri; Bhatia, Sonam; Lee, Isac; Kirsche, Melanie; Wappel, Robert; Kramer, Melissa; Kostroff, Karen; Spector, David L; Timp, Winston; McCombie, Richard W; Schatz, Michael C

Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing Journal Article

bioRxiv, 2019.

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Workman, Rachael E; Tang, Alison D; Tang, Paul S; Jain, Miten; Tyson, John R; Razaghi, Roham; Zuzarte, Philip C; Gilpatrick, Timothy; Payne, Alexander; Quick, Joshua; Sadowski, Norah; Holmes, Nadine; de Jesus, Jaqueline Goes; Jones, Karen L; Soulette, Cameron M; Snutch, Terrance P; Loman, Nicholas; Paten, Benedict; Loose, Matthew; Simpson, Jared T; Olsen, Hugh E; Brooks, Angela N; Akeson, Mark; Timp, Winston

Nanopore native RNA sequencing of a human poly(A) transcriptome Journal Article

Nature Methods, pp. 1–9, 2019, ISSN: 1548-7105.

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Sakowski, Eric; Uritskiy, Gherman; Cooper, Rachel; Gomes, Maya; McLaren, Michael R; Meisel, Jacquelyn S; Mickol, Rebecca L; Mintz, David C; Mongodin, Emmanuel F; Pop, Mihai; Rahman, Mohammad Arifur; Sanchez, Alvaro; Timp, Winston; Vela, Jeseth Delgado; Wolz, Carly Muletz; Zackular, Joseph P; Chopyk, Jessica; Commichaux, Seth; Davis, Meghan; Dluzen, Douglas; Ganesan, Sukirth M; Haruna, Muyideen; Nasko, Dan; Regan, Mary J; Sarria, Saul; Shah, Nidhi; Stacy, Brook; Taylor, Dylan; DiRuggiero, Jocelyne; Preheim, Sarah P

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019 Journal Article

mSystems, 4 (5), 2019.

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Tiek, Deanna M; Razaghi, Roham; Jin, Lu; Sadowski, Norah; Alamillo-Ferrer, Carla; Hogg, Robert J; Haddad, Bassem R; Drewry, David H; Wells, Carrow I; Pickett, Julie E; Zuercher, William J; Timp, Winston; Riggins, Rebecca B

Targeting destabilized DNA G-quadruplexes and aberrant splicing in drug-resistant glioblastoma Journal Article

bioRxiv, 2019.

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Allen, Jawara; Hao, Stephanie; Sears, Cynthia L; Timp, Winston

Epigenetic changes induced by Bacteroides fragilis toxin (BFT) Journal Article

Infection and Immunity, 2019, ISSN: 0019-9567, 1098-5522.

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Briem, Eirikur; Budkova, Zuzana; Sigurdardottir, Anna Karen; Hilmarsdottir, Bylgja; Kricker, Jennifer; Timp, Winston; Magnusson, Magnus Karl; Traustadottir, Gunnhildur Asta; Gudjonsson, Thorarinn

MiR-203a is differentially expressed during branching morphogenesis and EMT in breast progenitor cells and is a repressor of peroxidasin Journal Article

Mechanisms of Development, 155 , pp. 34–47, 2019, ISSN: 0925-4773.

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Drewes, Julia L; Corona, Alina; Sanchez, Uriel; Fan, Yunfan; Hourigan, Suchitra K; Weidner, Melissa; Sidhu, Sarah D; Simner, Patricia J; Wang, Hao; Timp, Winston; Oliva-Hemker, Maria; Sears, Cynthia L

Transmission and clearance of potential procarcinogenic bacteria during fecal microbiota transplantation for recurrent Clostridioides difficile Journal Article

JCI Insight, 4 (19), 2019.

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Avin, Brittany A; Wang, Yongchun; Gilpatrick, Timothy; Workman, Rachael E; Lee, Isac; Timp, Winston; Umbricht, Christopher B; Zeiger, Martha A

Characterization of human telomerase reverse transcriptase promoter methylation and transcription factor binding in differentiated thyroid cancer cell lines Journal Article

Genes, Chromosomes & Cancer, 2019, ISSN: 1098-2264.

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Tamma, Pranita D; Fan, Yunfan; Bergman, Yehudit; Pertea, Geo; Kazmi, Abida; Lewis, Shawna; Carroll, Karen C; Schatz, Michael C; Timp, Winston; Simner, Patricia J

Applying Rapid Whole Genome Sequencing to Predict Phenotypic Antimicrobial Susceptibility Testing Results Among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates Journal Article

Antimicrobial Agents and Chemotherapy, 63 (1), pp. e01923–18, 2019, ISSN: 0066-4804.

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2018

Vanaja, Kiran G; Timp, Winston; Feinberg, Andrew P; Levchenko, Andre

A Loss of Epigenetic Control Can Promote Cell Death through Reversing the Balance of Pathways in a Signaling Network Journal Article

Molecular Cell, 72 (1), pp. 60–70.e3, 2018, ISSN: 1097-4164.

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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

Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae Journal Article

The Journal of Antimicrobial Chemotherapy, 2018, ISSN: 1460-2091.

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Tamma, Pranita D; Fan, Yunfan; Bergman, Yehudit; Sick-Samuels, Anna C; Hsu, Alice J; Timp, Winston; Simner, Patricia J

Successful Treatment of Persistent Burkholderia cepacia Complex Bacteremia with Ceftazidime-Avibactam Journal Article

Antimicrobial Agents and Chemotherapy, 62 (4), 2018, ISSN: 1098-6596.

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Workman, Rachael; Fedak, Renee; Kilburn, Duncan; Hao, Stephanie; Liu, Kelvin; Timp, Winston

High Molecular Weight DNA Extraction from Recalcitrant Plant Species for Third Generation Sequencing Journal Article

Nature Protocols Exchange, 2018.

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Workman, Rachael E; Myrka, Alexander M; Wong, William G; Tseng, Elizabeth; Welch, Kenneth C; Timp, Winston

Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris Journal Article

GigaScience, 7 (3), 2018.

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Xiong, Tina; Rohm, Dahlia; Workman, Rachael E; Roundtree, Lauren; Novina, Carl D; Timp, Winston; Ostermeier, Marc

Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria Journal Article

PLoS One, 13 (12), pp. 1-18, 2018.

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Lee, Isac; Razaghi, Roham; Gilpatrick, Timothy; Sadowski, Norah; Sedlazeck, Fritz; Timp, Winston

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing Journal Article

bioRxiv, 2018.

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2017

Lee, Isac; Rasoul, Bejan A; Holub, Ashton S; Lejeune, Alannah; Enke, Raymond A; Timp, Winston

Whole genome DNA methylation sequencing of the chicken retina, cornea and brain Journal Article

Scientific Data, 4 , pp. sdata2017148, 2017, ISSN: 2052-4463.

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Xiong, Tina; Meister, Glenna E; Workman, Rachael E; Kato, Nathaniel C; Spellberg, Michael J; Turker, Fulya; Timp, Winston; Ostermeier, Marc; Novina, Carl D

Targeted DNA methylation in human cells using engineered dCas9-methyltransferases Journal Article

Scientific Reports, 7 , 2017, ISSN: 2045-2322.

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Kandathil, Abraham J; Breitwieser, Florian P; Sachithanandham, Jaiprasath; Robinson, Matthew; Mehta, Shruti H; Timp, Winston; Salzberg, Steven L; Thomas, David L; Balagopal, Ashwin

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs Journal Article

Annals of Internal Medicine, 167 (1), pp. 1–7, 2017, ISSN: 1539-3704.

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Simpson, Jared T; Workman, Rachael E; Zuzarte, P C; David, Matei; Dursi, L J; Timp, Winston

Detecting DNA cytosine methylation using nanopore sequencing Journal Article

Nature Methods, 14 (4), pp. 407–410, 2017, ISSN: 1548-7091.

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Credle, Joel J; Itoh, Christopher Y; Yuan, Tiezheng; Sharma, Rajni; Scott, Erick R; Workman, Rachael E; Fan, Yunfan; Housseau, Franck; Llosa, Nicolas J; Bell, Robert W; Miller, Heather; Zhang, Sean X; Timp, Winston; Larman, Benjamin H

Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization Journal Article

Nucleic Acids Research, 45 (14), pp. e128–e128, 2017.

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Luo, Ruibang; Zimin, Aleksey; Workman, Rachael; Fan, Yunfan; Pertea, Geo; Grossman, Nina; Wear, Maggie P; Jia, Bei; Miller, Heather; Casadevall, Arturo; Timp, Winston; Zhang, Sean X; Salzberg, Steven L

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans) Journal Article

G3: Genes, Genomes, Genetics, 7 (11), pp. 3831–3836, 2017.

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2016

Norris, Alexis L; Workman, Rachael E; Fan, Yunfan; Eshleman, James R; Timp, Winston

Nanopore sequencing detects structural variants in cancer Journal Article

Cancer Biology & Therapy, 17 (3), pp. 246–253, 2016, ISSN: 1555-8576.

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2014

Timp, Winston; Nice, Allison M; Nelson, E M; Kurz, V; McKelvey, K; Timp, Gregory

Think Small: Nanopores for Sensing and Synthesis Journal Article

IEEE Access, 2 , pp. 1396–1408, 2014, ISSN: 2169-3536.

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Timp, Winston; Bravo, Hector Corrada; McDonald, Oliver G; Goggins, Michael; Umbricht, Chris; Zeiger, Martha; Feinberg, Andrew P; Irizarry, Rafael A

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors Journal Article

Genome Medicine, 6 (8), pp. 61, 2014, ISSN: 1756-994X.

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2013

Kurz, Volker; Nelson, Edward M; Perry, Nicolas; Timp, Winston; Timp, Gregory

Epigenetic Memory Emerging from Integrated Transcription Bursts Journal Article

Biophysical Journal, 105 (6), pp. 1526–1532, 2013, ISSN: 0006-3495.

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Timp, Winston; Feinberg, Andrew P

Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host Journal Article

Nature Reviews Cancer, 13 (7), pp. 497–510, 2013, ISSN: 1474-1768.

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2012

Nelson, Edward M; Kurz, Volker; Shim, Jiwook; Timp, Winston; Timp, Gregory

Using a Nanopore for Single Molecule Detection and Single Cell Transfection Journal Article

The Analyst, 137 (13), pp. 3020–3027, 2012, ISSN: 0003-2654.

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Timp, Winston; Comer, Jeffrey; Aksimentiev, Aleksei

DNA base-calling from a nanopore using a Viterbi algorithm Journal Article

Biophysical Journal, 102 (10), pp. L37–39, 2012, ISSN: 1542-0086.

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2011

McDonald, Oliver G; Wu, Hao; Timp, Winston; Doi, Akiko; Feinberg, Andrew P

Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition Journal Article

Nature Structural & Molecular Biology, 18 (8), pp. 867–874, 2011, ISSN: 1545-9985.

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Hansen, Kasper Daniel; Timp, Winston; Bravo, Héctor Corrada; Sabunciyan, Sarven; Langmead, Benjamin; McDonald, Oliver G; Wen, Bo; Wu, Hao; Liu, Yun; Diep, Dinh; Briem, Eirikur; Zhang, Kun; Irizarry, Rafael A; Feinberg, Andrew P

Increased methylation variation in epigenetic domains across cancer types Journal Article

Nature Genetics, 43 (8), pp. 768–775, 2011, ISSN: 1061-4036.

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2010

Timp, Winston; Mirsaidov, Utkur M; Wang, Deqiang; Comer, Jeff; Aksimentiev, Aleksei; Timp, Gregory

Nanopore Sequencing: Electrical Measurements of the Code of Life Journal Article

IEEE Transactions on Nanotechnology, 9 (3), pp. 281–294, 2010, ISSN: 1536-125X.

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2009

Timp, Winston; Mirsaidov, Utkur; Matsudaira, Paul; Timp, Gregory

Jamming prokaryotic cell-to-cell communications in a model biofilm Journal Article

Lab on a Chip, 9 (7), pp. 925–934, 2009, ISSN: 1473-0197.

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Mirsaidov, U; Timp, W; Zou, X; Dimitrov, V; Schulten, K; Feinberg, A P; Timp, G

Nanoelectromechanics of methylated DNA in a synthetic nanopore Journal Article

Biophysical Journal, 96 (4), pp. L32–34, 2009, ISSN: 1542-0086.

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Timp, Winston; Levchenko, Andre; Feinberg, Andrew P

A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction Journal Article

Cell Cycle (Georgetown, Tex.), 8 (3), pp. 383–390, 2009, ISSN: 1551-4005.

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2008

Mirsaidov, Utkur; Scrimgeour, Jan; Timp, Winston; Beck, Kaethe; Mir, Mustafa; Matsudaira, Paul; Timp, Gregory

Live cell lithography: using optical tweezers to create synthetic tissue Journal Article

Lab on a Chip, 8 (12), pp. 2174–2181, 2008, ISSN: 1473-0197.

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