* A complete list of publications can also be found at Prof. Iwijn De Vlaminck’s Google Scholar page.

  • Cell-Free DNA Tissues-of-Origin by Methylation Profiling Reveals Significant Cell, Tissue and Organ-Specific injury related to COVID-19 Severity.
    Alexandre Pellan Cheng, Matthew Pellan Cheng, Wei Gu, Joan Sesing Lenz, Elaine Hsu, Erwin Schurr, Guillaume Bourque, Mathieu Bourgey, Jerome Ritz, Francisco Marty, Charles Y. Chiu, Donald Cuong Vinh, Iwijn De Vlaminck.
    In press (Cell Med), preprint (2021).
  • Strength in numbers: Large-scale integration of single-cell transcriptomic data reveals rare, transient muscle progenitor cell states in muscle regeneration
    David W. McKellar, Lauren D. Walter, Leo T. Song, Madhav Mantri, Michael F.Z. Wang, Iwijn De Vlaminck*,
    and Benjamin D. Cosgrove*.  * Equal contribution.
    submitted (2020), bioRxiv preprint.
  • Fragment length biases distort measurements of cell-free DNA fragment length profiles and define the sensitivity of metagenomic cell-free DNA sequencing assays
    Adrienne Chang, Omary Mzava, Joan S. Lenz, Alexandre P. Cheng, Philip Burnham, S. Timothy Motley, Crissa Bennett, John T. Connelly, Darshana Dadhania, Manikkam Suthanthiran, John R. Lee, Amy Steadman, Iwijn De Vlaminck.
    submitted (2020).
  • Recent advances in tools to map the microbiome
    Hao Shi, Benjamin Grodner*, Iwijn De Vlaminck.  * Equal contribution.
    submitted (2020).
  • Cell-Free DNA Sequencing of Peritoneal Fluid Informs Infections within the Abdominal Cavity
    Philip Burnham, Fanny Chen, Alexandre P. Cheng, Vesh Srivatana, Lisa T. Zhang, Emmanuel Edusei, Shady Albakry, Brittany Botticelli, Xunxi Guo, Amanda Renaghan, Jeffrey Silberzweig, Darshana M. Dadhania, Joan S. Lenz, Michael Heyang, Lars Westblade, Iwijn De Vlaminck*, John R. Lee*. * Equal contribution.
    submitted (2020).
  • Dynamics of cell-free DNA and exosomes before, during, and after long duration human spaceflight
    Daniela Bezdan, Kirill Grigorev, Cem Meydan, Fanny Augusta Vatter, Michele Cioffi, Varsha Rao, Kiichi Nakahira, Philip Burnham, Ebrahim Afshinnekoo, Craig Westover, Daniel J Butler, Chris Moszary, Matthew MacKay, Jonathan Foox, Tejaswini Mishra, Serena Lucotti, Brinda K Rana, Ari M Melnick, Haiying Zhang, Irina Matei, David P Kelsen, Kenneth H Yu, Lynn Taylor, Susan Bailey, Michael Snyder, Francine Garrett-Bakelman, David C Lyden, Stephan Ossowski, Iwijn De Vlaminck, Christopher E Mason.
    iScience (2020).
  • Highly Multiplexed Spatial Mapping of Microbial Communities
    Hao Shi, Qiaojuan Shi, Benjamin Grodner, Joan Sesing Lenz, Warren Zipfel, Ilana Brito, Iwijn De Vlaminck.
    Nature (2020).
  • The proportion of donor specific cell-free DNA in blood as a marker of transplant rejection: not an absolute.
    Iwijn De Vlaminck.
    Clinical Chemistry (2020).
  • Host remodeling of vascular grafts through macrophage trans-differentiation into vascular cells.
    Jiayin Fu, Michael Wang, Chelsea E.T. Stowell, Iwijn De Vlaminck and Yadong Wang.
    Submitted (2020).
  • Uncovering Transcriptional Dark Matter via Gene Annotation Independent Single-Cell RNA Sequencing Analysis.
    Michael F.Z. Wang, Madhav Mantri, Shao-Pei Chou, Gaetano J. Scuderi, David McKellar, Jonathan T. Butcher, Charles G. Danko and Iwijn De Vlaminck.
    Submitted, bioRxiv preprint (2020).
  • Blood-borne biomarkers may help predict COVID-19 mortality.
    Iwijn De Vlaminck
    Science Translational Medicine (2020).
  • Spatiotemporal single-cell RNA sequencing of developing hearts reveals interplay between cellular differentiation and morphogenesis.
    Madhav Mantri, Gaetano J. Scuderi, Roozbeh Abedini Nassab, Michael F.Z. Wang, David McKellar, Jonathan T. Butcher, and Iwijn De Vlaminck. Submitted (2020).
    bioRxiv preprint.
  • Donor-derived Cell-free DNA is Elevated During Allograft Rejection after Lung Transplantation.
    Kiran Khush, John Beausang, Iwijn De Vlaminick, Helen Luikart, Mark Nicolls, G Dhillon, Robert Woodward, David J Ross, David Weill.
    ERJ Open Research (2020).
  • Cell-free DNA Tissues-of-Origin Profiling Predicts Graft versus Host Disease and Detects Infection after Hematopoietic Cell Transplantation.
    Alexandre Pellan Cheng, Matthew Pellan Cheng, Joan Sesing Lenz, Kaiwen Chen, Philip Burnham, Kaitlyn Marie Timblin, Jose Luis Orejas, Emily Silverman, Francisco M. Marty, Jerome Ritz, Iwijn De Vlaminck. Submitted (2020).
    bioRxiv preprint.
  • Transcriptomics of Acute Rejection in Kidney Allografts
    Akanksha Verma, Thangamani Muthukumar, Hua Yang, Michelle Lubetzky, Michael Cassidy, Darshana M. Dadhania, John R. Lee, Catherine Snopkowski, Steve P. Salvatore, Vijay K. Sharma, Jenny Z. Xiang, Iwijn De Vlaminck, Surya V. Seshan, Franco B. Mueller, Olivier Elemento, Manikkam Suthanthiran.
    JCI Insight (2020).
  • Separating the signal from the noise in metagenomic cell-free DNA sequencing
    Philip Burnham, Nardhy Gomez-Lopez, Michael Heyang, Alexandre Pellan Cheng, Joan Sesing Lenz, Darshana Dadhania, John Richard Lee, Manikkam Suthanthiran, Roberto Romero, Iwijn De Vlaminck.
    Microbiome, 8,18 (2020).
  • Single-cell analysis of the muscle stem cell hierarchy identifies heterotypic communication signals involved in skeletal muscle regeneration
    Andrea J. De Micheli, Paula Fraczek, Sharon Soueid-Baumgarten, Hiranmayi Ravichandran, Iwijn De Vlaminck, Olivier Elemento, Benjamin D. Cosgrove.
    Cell Reports (2020).
  • Adding insult on injury: immunogenic role for donor-derived cell-free DNA?
    Shamik Dholakia, Iwijn De Vlaminck, Kiran Khush.
    Transplantation, Online First (2020).
  • A cell-free DNA metagenomic sequencing assay that integrates the damage response to infection.
    Alexandre Pellan Cheng, Philip Burnham, John Richard Lee, Matthew Pellan Cheng, Manikkam Suthanthiran, Darshana Dadhania, Iwijn De Vlaminck
    Proceedings of the National Academy of Sciences (2019).
  • Gut Uropathogen Abundance is a Risk Factor for Development of Bacteriuria and Urinary Tract Infection.
    Matthew Magruder, Nidal Sholi, Catherine Gong, Lisa Zhang, Emmanuel Edusei, Jennifer Huang, Shady Albakry, Michael J Satlin, Lars F Westblade, Carl Crawford, Darshana Dadhania, Michelle Lubetzky, Lilan Ling, Philip Burnham, Iwijn De Vlaminck, Eric Pamer, John Richard Lee
    Nature Communications (2019).
  • Donor-derived cell-free DNA predicts allograft failure and mortality after lung transplantation.
    Sean Agbor-Enoh, Ilker Tunc, Andrew Davis, Iwijn De Vlaminck, Sasha Gorham, Jennifer Wylie, Natalie Goodwin, Moon Kyoo Jang, Argit Marishta, Kenneth Bhatti, Ulgen Fideli, Yanqin Yang, Kapil Patel, Helen Luikart, Jun Zhu, Stephen R. Quake, Kiran Khush, Hannah A. Valantine
    EBioMedicine (2019).
  • Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
    Mridusmita Saikia*, Philip Burnham*, Sara H. Keshavjee, Michael F. Z. Wang, Pablo Moral-Lopez, Meleana M. Hinchman, Charles G. Danko, John S. L. Parker, Iwijn De Vlaminck.
    Nature Methods (2019).
  • Biopsy-free screening for glioma
    Alexandre Cheng, Philip Burnham, Iwijn De Vlaminck
    EMBO Molecular Medicine, e9484 (2018)
  • Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract
    Philip Burnham, Darshana Dadhania, Michael Heyang, Fanny Chen, Manikkam Suthanthiran, John Richard Lee*, Iwijn De Vlaminck*
    Nature Communications (2018).
  • Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype
    Eilon Sharon, Hao Shi, Sandhya Kharbanda, Winston Koh, Lance R. Martin, Kiran K. Khush, Hannah Valantine, Jonathan K. Pritchard, Iwijn De Vlaminck
    Plos Computational Biology, 2017.
  • Humans are colonized by many uncharacterized and highly divergent microbes
    Mark Kowarsky, Joan Camunas, Michael Kertesz, Iwijn De Vlaminck,Winston Koh,Wenying Pan, Lance Martin, Norma Neff, Jennifer Okamoto, Yasser El-Sayed, Yair Blumenfeld, Kiran Khush, Hannah Valantine, David Weill, Mark Nicholls, David Cornfield, Nathan Wolfe, and Stephen R. Quake
    Proceedings of the National Academy of Sciences (2017).
  • Implementation of a comprehensive noninvasive prenatal test in the Brazilian population
    Carolina Malcher, Guilherme Lopes Yamamoto, Philip Burnham, Suzana Andreoli Marques Ezquina, David Santos Marco Antonio, Naila Cristina Vilaca Lourenco, Thomaz Gollop, Maria Rita Pavanello, Mayana Zatz, Debora Bertola, Iwijn De Vlaminck, Maria Rita Passos-Bueno
    Genetics and Molecular Biology, (2018)
  • Precision Monitoring of Immunotherapies in Solid Organ and Hematopoietic Stem Cell Transplantation
    Rose Diloreto, Kiran Khush, Iwijn De Vlaminck
    Advanced Drug Delivery Reviews, (2017)
  • Vast population genetic diversity underlies the treatment and dynamics of ETV6-RUNX|ALL
    Veronica Gonzalex, Matthew MacKay, Iwijn De Vlaminck, John Easton, Charles Gawad, submitted (2017).
    BioRxiv preprint.
  • Annealing helicase HARP closes RPA-stabilised DNA bubbles non-processively
    Daniel R Burnham, Bas Nijholt, Iwijn De Vlaminck, Jinhua Quan, Timur Yusufzai, Cees Dekker
    Nucleic Acids Research45, 4687 (2017)
  • Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation
    Sean Agbor-Enoh, Ilker Tunc, Iwijn De Vlaminck, Ulgen Fideli, Kiran Khush, Jun Zhu, and Hannah Valantine, et al
    Journal of Heart and Lung Transplantation  (2017)
  • Myriad applications of circulating cell-free DNA in precision organ transplant monitoring
    Philip Burnham, Kiran Khush, Iwijn De Vlaminck
    Annals of the American Thoracic Society, S237-241 (2017)
  • Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma
    Philip Burnham, Min Seong Kim, Sean Agbor-Enoh, Helen Luikart, Hannah A. Valantine, Kiran K. Khush, Iwijn De Vlaminck
    Scientific Reports6 (2016)
  • Monitoring pharmacologically induced immunosuppression by immune repertoire sequencing to detect acute allograft rejection in heart transplant patients: a proof-of-concept diagnostic accuracy study
    Christopher Vollmers*, Iwijn De Vlaminck*, Hannah A.Valantine, Lolita Penland, Helen Luikart, Calvin Strehl, Garrett Cohen, Kiran K. Khush, Stephen R. Quake.
    Plos Medicine (2015).
  • Single-cell Genomics-Facilitated Read-first Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes
    Wesley Swingley, Jeremy Dodsworth, Senthil Murugapiran, Jan Ohlsson, Brandon Briggs, Jad Kanbar, Iwijn De Vlaminck, Stephen Quake, Hailiang Dong, Brian Hedlund, and Eric Becraft
    Applied and Environmental Microbiology,  82 (4):992-1003 (2015)
  • Non-invasive monitoring of infection and rejection after lung transplantation
    Iwijn De Vlaminck*, Lance Martin*, Mickey Kertesz, Kapil Patel, Mark Kowarsky, Calvin Strehl, Garrett S. Cohen, Helen Luikart, Norma F. Neff, Jennifer Okamoto, Mark R. Nicolls, David N. Cornfield, David Weill, Hannah A. Valantine, Kiran K. Khush, Stephen R. Quake
    Proceedings of the National Academy of Sciences, 112, 13336 (2015)
  • Design and Implementation of the International Genetics and Translational Research in Transplantation Network (iGeneTRAiN).
    iGeneTRAiN collaboration.
    Transplantation, 99, 2401 (2015)
  • Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China.
    Qiuyuan Huang, Brandon R. Briggs, Hailiang Dong, Hongchen Jiang, Geng Wu, Christian Edwardson, Iwijn De Vlaminck, and Stephen Quake
    Plos One, 9, e111681 (2014)
  • Quantitative Comparison of Single-Cell Whole Genome Amplification Methods
    Charles de Bourcy*, Iwijn De Vlaminck*, Jad kanbar*, Jianbin Wang, Charles Gawad, Stephen R. Quake
    Plos One, 9, e105585 (2014)
  • Circulating Cell-Free DNA Enables Noninvasive Diagnosis of Heart Transplant Rejection
    Iwijn De Vlaminck, Hannah A. Valantine, Thomas M. Snyder, Calvin Strehl, Garrett Cohen, Helen Luikart, Norma F. Neff, Jennifer Okamoto, Daniel Bernstein, Dana Weisshaar, Stephen R. Quake, and Kiran K. Khush
    Science Translational Medicine, 6, 241ra77 (2014)
  • Non-normal Brownian fluctuations in magnetic tweezers and consequences for single molecule experiments
    Daniel Burnham, Iwijn De Vlaminck, Thomas Henighan and Cees Dekker
    Plos One, 9, e108271 (2014)
  • Temporal response of the human virome in response to immune modulation and antiviral therapy
    Iwijn De Vlaminck, Kiran K. Khush, Calvin Strehl, Bitika Kohli, Helen Luikart, Norma F. Neff, Jennifer Okamoto, Thomas M. Snyder, David N. Cornfield, Mark R. Nicolls, David Weill, Daniel Bernstein, Hannah A. Valantine, and Stephen R. Quake
    Cell, 155, 1178 (2013)
  • Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers
    Marijn van Loenhout, \underline{Iwijn De Vlaminck}, Benedetta Flebus, Ludovit Zweifel, Johan den Blanken, Koen Hooning, Jacob Kerssemakers, and Cees Dekker
    Plos One, 8, e65329, (2013)
  • Non-bias-limited tracking of spherical particles, enabling nanometer resolution at low magnification
    Marijn van Loenhout, Jacob Kerssemakers, Iwijn De Vlaminck, and Cees Dekker
    Biophysical Journal, (2012)
  • Magnetic forces and DNA mechanics in multiplexed magnetic tweezers
    Iwijn De Vlaminck*, Thomas Henighan*, Marijn T.J. van Loenhout, Daniel Burnham, and Cees Dekker
    Plos One, 7, e41432 (2012)
  • Mechanism of homology recognition in DNA recombination from dual molecule experiments
    Iwijn De Vlaminck, Marijn van Loenhout, Ludovit Zweifel, Johan den Blanken, Susanne Hage, Jacob Kerssemakers, and Cees Dekker
    Molecular Cell, 46, 616 (2012)
  • Recent advances in magnetic tweezers
    Iwijn De Vlaminck and Cees Dekker
    Annual Reviews of Biophysics, 41, (2012)
  • Highly Parallel Magnetic Tweezers by Targeted DNA Tethering
    Iwijn De Vlaminck, Thomas Henighan, Marijn T.J. van Loenhout, Indriati Pfeiffer, Julius Huijts, Jacob W. J. Kerssemakers, Allard J. Katan, Anja van Langen-Suurling, Emile van der Drift, Claire Wyman, and Cees Dekker
    Nano Letters, 11, 5489 (2011)
  • Torsional regulation of hRPA-induced unwinding of double stranded DNA
    Iwijn De Vlaminck, Iztok Vidic, Marijn van Loenhout, Joyce Lebbink, Roland Kanaar, and Cees Dekker
    Nucleic Acids Research, 38,4133 (2010)
  • Focusing Plasmons in Nanoslits for Surface-Enhanced Raman Scattering
    Chang Chen, James Andell Hutchison, Pol Van Dorpe, Ronald Kox, Iwijn De Vlaminck, Hiroshi Uji-i, Johan Hofkens, Liesbet Lagae, Guido Maes, and Gustaaf Borghs
    Small, 24, 2876 (2009
  • Tunable optical forces between nanophotonic waveguides
    Joris Roels, Iwijn De Vlaminck, Liesbet Lagae, Bjorn Maes, Dries Van Thourhout and Roel Baets
    Nature Nanotechnology, 4, 510 (2009)
  • Localized surface plasmon resonance biosensor integrated with microfluidic chip
    Chengjun Huang, Kristien Bonroy, Gunter Reekmans, Wim Laureyn, Katarina Verhaegen, Iwijn De Vlaminck, Liesbet Lagae and Gustaaf Borghs
    Biomedical microdevices, 11, 893 (2009)
  • Fabrication and Optical Properties of Gold Semishells
    Jian Ye, Pol Van Dorpe, Willem Van Roy, Kristof Lodewijks, Iwijn De Vlaminck, Guido Maes and Gustaaf Borghs
    Journal of Physical Chemistry C, 113, 3110 (2009)
  • Electrical detection of confined gap plasmons in metal insulator metal waveguides
    Pieter Neutens, Pol Van Dorpe, Iwijn De Vlaminck, Liesbet Lagae, Gustaaf Borghs
    Nature Photonics, 3, 283 (2009)
  • Integrated nanomechanical motion detection by means of optical evanescent wave coupling
    Iwijn De Vlaminck, Joris Roels, Dirk taillaert, Dries Van Thourhout, Liesbet Lagae, Roel Baets, Gustaaf Borghs
    Proceedings of the SPIE Photonics West conference, 6464 (2007)
  • Multifunctional nanomechanical systems via tunably-coupled piezoelectric actuation Sotiris masmanidis, Rassul Karabalin, Iwijn De Vlaminck, Gustaaf Borghs, Mark R. Freeman, Michael L. Roukes
    Science, 317, 717 (2007)
  • Local electrical detection of single nanoparticle plasmon resonance
    Iwijn De Vlaminck, Pol Van Dorpe, Liesbet Lagae, Gustaaf Borghs
    Nano Letters, 7, 703 (2007)
  • Detection of nanomechanical motion through evanescent light-wave coupling
    Iwijn De Vlaminck, Joris Roels, Dirk Taillaert, Dries Van Thourhout, Liesbet Lagae, Roel Baets, Gustaaf Borghs
    Applied Physics Letters, 90, 233116 (2007)
  • Silicon nanomechanical resonators with double-triangle cross section leading to an enhanced mass sensitivity
    Iwijn De Vlaminck, Kristiaan De Greve, Liesbet Lagae, Gustaaf Borghs
    Applied Physics Letters, 88, 063112 (2006)