A complete list of publications can also be found on Iwijn’s Google Scholar page.
2022
- Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis
Madhav Mantri, , , , , , . Nature Cardiovascular Research (2022). - Spatial mapping of the total transcriptome by in situ polyadenylation
David W. McKellar, Madhav Mantri, Meleana Hinchman, John S.L. Parker, Praveen Sethupathy, Benjamin D. Cosgrove, Iwijn De Vlaminck. Nature Biotechnology (2022). - A gene expression-based diagnostic classifier for identification of severe COVID-19 and multisystem inflammatory syndrome in children (MIS-C). Alicia Sotomayor-Gonzalez*, Conor J. Loy*, Jenny Nguyen*, Venice Servellita*, Jenny Nguyen, Joan Lenz, Sanchita Bhattacharya, Meagan Williams, Alexandre P. Cheng, Andrew Bliss, Prachi Saldhi, Noah Brazer, Jessica Streithorst, Will Suslovic, Charlotte Hsieh, Burak Bahar, Nathan Wood, Abiodun Foresythe, Amelia Gliwa, Kushmita Bhakta, Maria A. Perez, Evan J. Anderson, Ann Chahroudi, Meghan Delaney, Atul Butte, Roberta DeBiasi, Christina A. Rostad, Iwijn De Vlaminck*, Charles Y. Chiu*, submitted, medRxiv preprint (2022). *Equal contribution.
- Nucleic acid biomarkers of immune response and cell and tissue damage in COVID-19 and MIS-C. Conor J. Loy*, Alicia Sotomayor-Gonzalez*, Venice Servellita*, Jenny Nguyen, Joan Lenz, Sanchita Bhattacharya, Meagan Williams, Alexandre P. Cheng, Andrew Bliss, Prachi Saldhi, Noah Brazer, Jessica Streithorst, Will Suslovic, Charlotte Hsieh, Burak Bahar, Nathan Wood, Abiodun Foresythe, Amelia Gliwa, Kushmita Bhakta, Maria A. Perez, Evan J. Anderson, Ann Chahroudi, Meghan Delaney, Atul Butte, Roberta DeBiasi, Christina A. Rostad, Iwijn De Vlaminck*, Charles Y. Chiu*, submitted, medRxiv preprint (2022). *Equal contribution
- An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome
Shixuan Liu, Camille Ezran, Michael F.Z. Wang, Zhengda Li, The Tabula Microcebus Consortium, Jonathan Z. Long, Iwijn De Vlaminck, Sheng Wang, Christin Kuo, Jacques Epelbaum, Jeremy Terrien, Mark A. Krasnow, James E. Ferrell Jr.bioRxiv preprint , submitted (2022).
- Mouse lemur transcriptomic atlas elucidates primate genes, physiology, disease, and evolution, The Tabula Microcebus Consortium. Submitted, bioRxiv preprint (2022).
- Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism The Tabula Microcebus Consortium. Submitted, bioRxiv preprint (2022).
- A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle. Umji Lee, Pascal Stuelsatz, Sonia Karaz, David W. McKellar, Julie Russeil, Maria Deak, Iwijn De Vlaminck, Christoph Lepper, Bart Deplancke, Benjamin D. Cosgrove, and Jerome N. Feige. iScience (2022).
- A needle in a haystack: metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis
Adrienne Chang, Omary Mzava, Liz-Audrey Djomnang Kounatse, Joan Lenz, Philip Burnham, Peter Kaplinsky, Alfred Andama, John Connelly, Christine M. Bachman, Adithya Cattamanchi, Amy Steadman, Iwijn De Vlaminck. Scientific Reports, in press (2022). - A metagenomic DNA sequencing assay that is robust against environmental DNA contamination
Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Djomnang Kounatse, Joan Lenz, Randy Longman, Amy Steadman, Mirella Salvatore, Manikkam Suthanthiran, John R. Lee, Christopher E. Mason, Darshana Dadhania, Iwijn De Vlaminck. Nature Communications (2022). - Run-on sequencing reveals transcriptional dynamics within the human microbiome
Albert Vill, Edward Rice, Iwijn De Vlaminck, Charles Danko, Ilana Brito. Submitted (2022). - Cell-free DNA Profiling Informs Major Complications of 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.
Proceedings of The National Academy of Sciences (2022). - Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis
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.
Kidney Medicine (2022).
2021
- Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal 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.
Communications Biology (2021). - Measurement Biases Distort Cell-Free DNA Fragmentation 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.
Clinical Chemistry (2021). - Recent advances in tools to map the microbiome
Hao Shi*, Benjamin Grodner*, Iwijn De Vlaminck. * Equal contribution.
Current Opinion in Biomedical Engineering (2021). - Molecular approaches to transplant monitoring: is the horizon there?
Sean Agbor-Enoh, Angela Wu, Philip F Halloran, Iwijn De Vlaminck, Michael Keller.
Clinical Chemistry (2021). - 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.
Nature Communications (2021). - Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis
Madhav Mantri, Gaetano J. Scuderi, Roozbeh Abedini-Nassab, Michael F.Z. Wang, David McKellar, Hao Shi, Benjamin Grodner, Jonathan T. Butcher, and Iwijn De Vlaminck.
Nature Communications (2021). - Donor-derived, Cell-free DNA levels by Next Generation Targeted Sequencing are Elevated in Allograft Rejection after Lung Transplantation
Kiran Khush, Iwijn De Vlaminick, Helen Luikart, David J Ross, Mark Nicolls.
ERJ Open Research (2021). - 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.
Cell Med (2021).
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). - Thick PCL Fibers Improving Host Remodeling of PGS‐PCL Composite Grafts Implanted in Rat Common Carotid Arteries
Jiayin Fu, Michael Wang, Iwijn De Vlaminck, Yadong Wang.
Small (2020). - Blood-borne biomarkers may help predict COVID-19 mortality
Iwijn De Vlaminck.
Science Translational Medicine (2020). - Urinary cell transcriptomics and acute rejection in human 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).
2019
- 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).
2018
- 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). - 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).
2017
- 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). - 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 Research, 45, 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)
2016
- 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 Reports, 6 (2016) - Single-cell Genomics-Facilitated Read-first Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes
Eric Bedcraft, Jeremy Dodsworth, Senthil Murugapiran, Jan Ohlsson, Brandon Briggs, Jad Kanbar, Iwijn De Vlaminck, Stephen Quake, Hailiang Dong, Brian Hedlund, and Wesley D. Swingley
Applied and Environmental Microbiology, 82 (4):992-1003 (2016)
2015-
- 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). - 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, 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)