Papers
Under Review
Enabling Non-invasive Detection of Pancreatic Ductal Adenocarcinoma in Pre-diagnostic High-risk and De-novo Symptomatic Patients
Under Revision in Nature Communications
Travis W. Moore, Elias Spiliotopoulos, Rowan Callahan, C. Ward Kirschbaum, Hyun Ji Kim, Breeshey Roskams-Hieter, Florian Goncalves, Dove Keith, Aaron Grossberg, Paul T. Spellman, Gordon B. Mills, Rosalie Sears, Terry K. Morgan, Thuy T. M. Ngo*
2024
Dependence of Nucleosome Mechanical Stability on DNA Mismatches
Elife; 13; RP95514 (2024)
Thuy T. M. Ngo, Bailey Liu, Feng Wang, Aakash Basu, Carl Wu, Taekjip Ha
Analysis Methods and Clinical Applications of Circulating Cell-free DNA and RNA in Human Blood
Cutting-edge Technology in Biological Sensing and Analysis 33 (2024) - Book Chapter
Josiah T. Wagner, Josephine Briand, Thuy T. M. Ngo*
Activation of coagulation FXI promotes endothelial inflamation and amplifies platelet activation in a nonhuman primate model of hyperlipidemia
Research and Practice in Thrombosis and Haemostasis 8 (1), 102276 (2024)
Tia CL Kohs, Helen H Vu, Kelley R Jordan, Ivan Parra-Izquierdo, Monica Hinds, Joseph J Shatzel, Paul Kievit, Terry K Morgan, Samuel Tassi Yunga, Thuy T. M. Ngo, Joseph E Aslan, Michael Wallisch, Christina U Lorentz, Erik I Tucker, David Gailani, Jonathan R Lindner, Cristina Puy, & Owen JT McCarty
2023
Selective enrichment of plasma cell-free messnger RNA in cancer-associated extracellular vesicles
Communications Biology 6, 885 (2023)
Hyun Ji Kim, Matthew J. Rames, Florian Goncalves, C. Ward Kirschbaum, Breeshey Roskams-Hieter, Elias Spiliotopoulos, Josephine Briand, Aaron Doe, Joseph Estabrook, Josiah T. Wagner, Emek Demir, Gordon Mills, Thuy T. M. Ngo*
2022
Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies
npj Precision Oncology 6, 28 (2022)
Breeshey Roskams-Hieter, Hyun Ji Kim, Pavana Anur, Josiah T. Wagner, Rowan Callahan, Elias Spiliotopoulos, Charles Ward Kirschbaum, Fehmi Civitci, Paul Spellman, Reid F. Thompson, Khashayar Farsad, Willscott E. Naugler, Thuy T. M. Ngo*
Irreversible alteration of extracellular vesicle and cell-free messenger RNA profiles in human plasma associated with blood processing and storage
Scientific Reports 12:2099 (2022)
Hyun Ji Kim, Matthew Rames, Samuel Tassi Yunga, Randall Armstrong, Mayu Morita, Anh T.P. Ngo, Owen J.T. McCarty, Fehmi Civitci, Terry K. Morgan, and Thuy T. M. Ngo*
2021
Measuring DNA mechanics on the genome scale
Nature 589 (7842), 462-467 (2021)
Aakash Basu, Dmitriy G. Bobrovnikov, Zan Qureshi, Tunc Kayikcioglu, Thuy T.M. Ngo, Anand Ranjan, Sebastian Eustermann, Basilio Cieza, Michael T. Morgan, Miroslav Hejna, H. Tomas Rube, Karl-Peter Hopfner, Cynthia Wolberger, Jun S Song, Taekjip Ha
Longitudinal analysis of human pancreatic adenocarcinoma development reveals transient gene expression signatures
Molecular Cancer Research 19, 1854-67 (2021)
Jungsun Kim, Taelor Ekstrom, Wenli Yang, Greg Donahue, Dmytro Grygoryev, Thuy T.M. Ngo, John L. Muschler, Terry Morgan, and Kenneth S. Zaret
2020
Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples
Scientific Reports 10 (1), 1-8 (2020)
Josiah T. Wagner, Hyun Ji Kim, Katie C. Johnson-Camacho, Taylor Keley, Laura F. Newell, Paul T. Spellman, Thuy T. M. Ngo*
2019
Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy
PNAS, Vol. 116 (17) pp. 8350-8359 (2019)
Jaba Mitra, Monika Makurath, Thuy T.M. Ngo, Alice Troitskaia, Yann R. Chemla and Taekjip Ha
Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy
Bioinformatics, Vol 35 (1), pp 95-103 (2019)
Mohammad Sajjad Ghaemi, Daniel B. DiGiulio, Kévin Contrepois, Benjamin Callahan, Thuy T. M. Ngo, Brittany Lee-McMullen, Benoit Lehallier, Anna Robaczewska, David Mcilwain, Yael Rosenberg-Hasson, Ronald J Wong, Cecele Quaintance, Anthony Culos, Athena Tanada, Amy Tsai, Dyani Gaudilliere, Edward Ganio, Xiaoyuan Han, Kazuo Ando, Leslie McNeil, Martha Tingle, Paul Wise, Ivana Maric, Marina Sirota, Tony Wyss-Coray, Virginia D Winn, Maurice L. Druzin, Ronald Gibbs, Gary L Darmstadt, David B Lewis, Vahid Partovi Nia, Bruno Agard, Robert Tibshirani, Garry Nolan, Michael P. Snyder, David A. Relman, Stephen R. Quake, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour
2018
Noninvasive blood tests for fetal development predict gestational age and preterm delivery
Science, Vol. 360, Issue 6393, pp. 1133-1136 (2018)
Thuy T. M. Ngo, Mira N. Moufarrej, Marie-Louise H. Rasmussen, Joan Camunas-Soler, Wenying Pan, Jennifer Okamoto, Norma F. Neff, Keli Liu, Ronald J. Wong, Katheryne Downes, Robert Tibshirani, Gary M. Shaw, Line Skotte, David K. Steveson, Joseph R. Biggio, Michal A. Elowitz, Mads Melbye and Stephen R. Quake
Features: NYTimes, CNN, BBC, Time, abcnews, The Guardian, USnews, National Geographic, Daily Mail
Precision and accuracy of single-molecule FRET measurements – a worldwide benchmark study
Nature Methods, Vol. 15, pp. 669–676 (2018)
Björn Hellenkamp, Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth, Soheila Rezaei Adariani, Anders Barth, Victoria Birkedal, Mark E. Bowen, Hongtao Chen, Thorben Cordes, Tobias Eilert, Carel Fijen, Markus Götz, Giorgos Gouridis, Enrico Gratton, Taekjip Ha, Christian A. Hanke, Andreas Hartmann, Jelle Hendrix, Lasse L. Hildebrandt, Johannes Hohlbein, Christian G. Hübner, Eleni Kallis, Achillefs N. Kapanidis, Jae-Yeol Kim, Georg Krainer, Don C. Lamb, Nam Ki Lee, Edward A. Lemke, Brié Levesque, Marcia Levitus, James J. McCann, Nikolaus Naredi-Rainer, Daniel Nettels, Thuy Ngo, Ruoyi Qiu, Carlheinz Röcker, Hugo Sanabria, Michael Schlierf, Benjamin Schuler, Henning Seidel, Lisa Streit, Philip Tinnefeld, Swati Tyagi, Niels Vandenberk, Keith R. Weninger, Bettina Wünsch, Inna S. Yanez-Orozco, Jens Michaelis, Claus A.M. Seidel, Timothy D. Craggs, Thorsten Hugel
2017
Simultaneously Monitoring Immune Response and Microbial Infections during Pregnancy through Plasma cfRNA Sequencing
Clinical Chemistry 63:11 (2017)
Wenying Pan, Thuy T. M. Ngo, Joan Camunas-Soler, Chunxiao Song, Mark Alec Kowarsky, Yair J Blumenfeld, Ronald J, Wong, Gary M. Shaw, David K. Stevenson, and Stephen Quake
Prior to 2017
Defining single molecular forces required for Notch activation using nano yoyo
Nano Letters, 16 (6), pp 3892–3897, (2016)
Farhan Chowdhury, Isaac T. S. Li, Thuy T. M. Ngo, Ben J. Leslie, Byoung Choul Kim, Xuefeng Wang, Yann R. Chemla, Timothy M. Lohman, Taekjip Ha
Effects of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability
Nature Communications, 7, 10813 (2016)
Thuy T. M. Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei Askimentiev, Taekjip Ha
Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Flexibility
Cell, 160 (6), 1135-1144 (2015)
Thuy T. M. Ngo, Qiucen Zhang, Ruobo Zhou, Jaya Yodh, Taekjip Ha
Featured in News and Views: Moevus and Greene, Cell, 160 (6), 1039-1040 (2015)
Nucleosomes Undergo Slow Spontaneous Gaping
Nucleic Acids Research, 43 (8), 3964-3971 (2015)
Thuy T. M. Ngo, Taekjip Ha
A Coarse-grained Model of Unstructured Single-stranded DNA Derived from Atomistic Simulation and Single-molecule Experiment
Journal of Chemical Theory and Computation, 10, 2891-2896 (2014)
Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, Aleksei Aksimentiev
Molecular Restructuring of Water and Lipids upon the Interaction of DNA with Lipids Monolayers
Journal of American Chemical Society, 132, 8037-8047 (2010)
R. Kramer Campen, Thuy T. M. Ngo, Maria Sovago, Jean-Marie Ruysschaert and Mischa Bonn
Enabling Non-invasive Detection of Pancreatic Ductal Adenocarcinoma in Pre-diagnostic High-risk and De-novo Symptomatic Patients
Under Revision in Nature Communications
Travis W. Moore, Elias Spiliotopoulos, Rowan Callahan, C. Ward Kirschbaum, Hyun Ji Kim, Breeshey Roskams-Hieter, Florian Goncalves, Dove Keith, Aaron Grossberg, Paul T. Spellman, Gordon B. Mills, Rosalie Sears, Terry K. Morgan, Thuy T. M. Ngo*
2024
Dependence of Nucleosome Mechanical Stability on DNA Mismatches
Elife; 13; RP95514 (2024)
Thuy T. M. Ngo, Bailey Liu, Feng Wang, Aakash Basu, Carl Wu, Taekjip Ha
Analysis Methods and Clinical Applications of Circulating Cell-free DNA and RNA in Human Blood
Cutting-edge Technology in Biological Sensing and Analysis 33 (2024) - Book Chapter
Josiah T. Wagner, Josephine Briand, Thuy T. M. Ngo*
Activation of coagulation FXI promotes endothelial inflamation and amplifies platelet activation in a nonhuman primate model of hyperlipidemia
Research and Practice in Thrombosis and Haemostasis 8 (1), 102276 (2024)
Tia CL Kohs, Helen H Vu, Kelley R Jordan, Ivan Parra-Izquierdo, Monica Hinds, Joseph J Shatzel, Paul Kievit, Terry K Morgan, Samuel Tassi Yunga, Thuy T. M. Ngo, Joseph E Aslan, Michael Wallisch, Christina U Lorentz, Erik I Tucker, David Gailani, Jonathan R Lindner, Cristina Puy, & Owen JT McCarty
2023
Selective enrichment of plasma cell-free messnger RNA in cancer-associated extracellular vesicles
Communications Biology 6, 885 (2023)
Hyun Ji Kim, Matthew J. Rames, Florian Goncalves, C. Ward Kirschbaum, Breeshey Roskams-Hieter, Elias Spiliotopoulos, Josephine Briand, Aaron Doe, Joseph Estabrook, Josiah T. Wagner, Emek Demir, Gordon Mills, Thuy T. M. Ngo*
2022
Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies
npj Precision Oncology 6, 28 (2022)
Breeshey Roskams-Hieter, Hyun Ji Kim, Pavana Anur, Josiah T. Wagner, Rowan Callahan, Elias Spiliotopoulos, Charles Ward Kirschbaum, Fehmi Civitci, Paul Spellman, Reid F. Thompson, Khashayar Farsad, Willscott E. Naugler, Thuy T. M. Ngo*
Irreversible alteration of extracellular vesicle and cell-free messenger RNA profiles in human plasma associated with blood processing and storage
Scientific Reports 12:2099 (2022)
Hyun Ji Kim, Matthew Rames, Samuel Tassi Yunga, Randall Armstrong, Mayu Morita, Anh T.P. Ngo, Owen J.T. McCarty, Fehmi Civitci, Terry K. Morgan, and Thuy T. M. Ngo*
2021
Measuring DNA mechanics on the genome scale
Nature 589 (7842), 462-467 (2021)
Aakash Basu, Dmitriy G. Bobrovnikov, Zan Qureshi, Tunc Kayikcioglu, Thuy T.M. Ngo, Anand Ranjan, Sebastian Eustermann, Basilio Cieza, Michael T. Morgan, Miroslav Hejna, H. Tomas Rube, Karl-Peter Hopfner, Cynthia Wolberger, Jun S Song, Taekjip Ha
Longitudinal analysis of human pancreatic adenocarcinoma development reveals transient gene expression signatures
Molecular Cancer Research 19, 1854-67 (2021)
Jungsun Kim, Taelor Ekstrom, Wenli Yang, Greg Donahue, Dmytro Grygoryev, Thuy T.M. Ngo, John L. Muschler, Terry Morgan, and Kenneth S. Zaret
2020
Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples
Scientific Reports 10 (1), 1-8 (2020)
Josiah T. Wagner, Hyun Ji Kim, Katie C. Johnson-Camacho, Taylor Keley, Laura F. Newell, Paul T. Spellman, Thuy T. M. Ngo*
2019
Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy
PNAS, Vol. 116 (17) pp. 8350-8359 (2019)
Jaba Mitra, Monika Makurath, Thuy T.M. Ngo, Alice Troitskaia, Yann R. Chemla and Taekjip Ha
Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy
Bioinformatics, Vol 35 (1), pp 95-103 (2019)
Mohammad Sajjad Ghaemi, Daniel B. DiGiulio, Kévin Contrepois, Benjamin Callahan, Thuy T. M. Ngo, Brittany Lee-McMullen, Benoit Lehallier, Anna Robaczewska, David Mcilwain, Yael Rosenberg-Hasson, Ronald J Wong, Cecele Quaintance, Anthony Culos, Athena Tanada, Amy Tsai, Dyani Gaudilliere, Edward Ganio, Xiaoyuan Han, Kazuo Ando, Leslie McNeil, Martha Tingle, Paul Wise, Ivana Maric, Marina Sirota, Tony Wyss-Coray, Virginia D Winn, Maurice L. Druzin, Ronald Gibbs, Gary L Darmstadt, David B Lewis, Vahid Partovi Nia, Bruno Agard, Robert Tibshirani, Garry Nolan, Michael P. Snyder, David A. Relman, Stephen R. Quake, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour
2018
Noninvasive blood tests for fetal development predict gestational age and preterm delivery
Science, Vol. 360, Issue 6393, pp. 1133-1136 (2018)
Thuy T. M. Ngo, Mira N. Moufarrej, Marie-Louise H. Rasmussen, Joan Camunas-Soler, Wenying Pan, Jennifer Okamoto, Norma F. Neff, Keli Liu, Ronald J. Wong, Katheryne Downes, Robert Tibshirani, Gary M. Shaw, Line Skotte, David K. Steveson, Joseph R. Biggio, Michal A. Elowitz, Mads Melbye and Stephen R. Quake
Features: NYTimes, CNN, BBC, Time, abcnews, The Guardian, USnews, National Geographic, Daily Mail
Precision and accuracy of single-molecule FRET measurements – a worldwide benchmark study
Nature Methods, Vol. 15, pp. 669–676 (2018)
Björn Hellenkamp, Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth, Soheila Rezaei Adariani, Anders Barth, Victoria Birkedal, Mark E. Bowen, Hongtao Chen, Thorben Cordes, Tobias Eilert, Carel Fijen, Markus Götz, Giorgos Gouridis, Enrico Gratton, Taekjip Ha, Christian A. Hanke, Andreas Hartmann, Jelle Hendrix, Lasse L. Hildebrandt, Johannes Hohlbein, Christian G. Hübner, Eleni Kallis, Achillefs N. Kapanidis, Jae-Yeol Kim, Georg Krainer, Don C. Lamb, Nam Ki Lee, Edward A. Lemke, Brié Levesque, Marcia Levitus, James J. McCann, Nikolaus Naredi-Rainer, Daniel Nettels, Thuy Ngo, Ruoyi Qiu, Carlheinz Röcker, Hugo Sanabria, Michael Schlierf, Benjamin Schuler, Henning Seidel, Lisa Streit, Philip Tinnefeld, Swati Tyagi, Niels Vandenberk, Keith R. Weninger, Bettina Wünsch, Inna S. Yanez-Orozco, Jens Michaelis, Claus A.M. Seidel, Timothy D. Craggs, Thorsten Hugel
2017
Simultaneously Monitoring Immune Response and Microbial Infections during Pregnancy through Plasma cfRNA Sequencing
Clinical Chemistry 63:11 (2017)
Wenying Pan, Thuy T. M. Ngo, Joan Camunas-Soler, Chunxiao Song, Mark Alec Kowarsky, Yair J Blumenfeld, Ronald J, Wong, Gary M. Shaw, David K. Stevenson, and Stephen Quake
Prior to 2017
Defining single molecular forces required for Notch activation using nano yoyo
Nano Letters, 16 (6), pp 3892–3897, (2016)
Farhan Chowdhury, Isaac T. S. Li, Thuy T. M. Ngo, Ben J. Leslie, Byoung Choul Kim, Xuefeng Wang, Yann R. Chemla, Timothy M. Lohman, Taekjip Ha
Effects of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability
Nature Communications, 7, 10813 (2016)
Thuy T. M. Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei Askimentiev, Taekjip Ha
Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Flexibility
Cell, 160 (6), 1135-1144 (2015)
Thuy T. M. Ngo, Qiucen Zhang, Ruobo Zhou, Jaya Yodh, Taekjip Ha
Featured in News and Views: Moevus and Greene, Cell, 160 (6), 1039-1040 (2015)
Nucleosomes Undergo Slow Spontaneous Gaping
Nucleic Acids Research, 43 (8), 3964-3971 (2015)
Thuy T. M. Ngo, Taekjip Ha
A Coarse-grained Model of Unstructured Single-stranded DNA Derived from Atomistic Simulation and Single-molecule Experiment
Journal of Chemical Theory and Computation, 10, 2891-2896 (2014)
Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, Aleksei Aksimentiev
Molecular Restructuring of Water and Lipids upon the Interaction of DNA with Lipids Monolayers
Journal of American Chemical Society, 132, 8037-8047 (2010)
R. Kramer Campen, Thuy T. M. Ngo, Maria Sovago, Jean-Marie Ruysschaert and Mischa Bonn
Patents
Cell-free Biomarkers for the Detection of Cancer and Predisposition to Cancer
[Provisional Filed] Application Number 63/303,970, Attorney Docket Tech 2851-1
Biomarkers for Detection and Treatment of Cirrhosis and Hepatocellular Carcinoma
[Provisional Filed] Application Number 63074738, Attorney Docket 52193-506P01US
Licensed to Ymir Genomics.
A noninvasive Molecular Clock for Fetal Development Predicts Gestational Age and Preterm Birth
International Patent Number WO2017096405A1
Licensed to Mirvie
[Provisional Filed] Application Number 63/303,970, Attorney Docket Tech 2851-1
Biomarkers for Detection and Treatment of Cirrhosis and Hepatocellular Carcinoma
[Provisional Filed] Application Number 63074738, Attorney Docket 52193-506P01US
Licensed to Ymir Genomics.
A noninvasive Molecular Clock for Fetal Development Predicts Gestational Age and Preterm Birth
International Patent Number WO2017096405A1
Licensed to Mirvie