Publications

A complete list of publications can also be found on Iwijn’s Google Scholar page.

2025

• Single-cell transcriptomics reveals targeted modulation of inflammatory repertoire by SOCE blockers, Andreas Stephanou, Madhav Mantri1, Divya Shankaranarayanan, Carol Li, Mila Lagman, Jenny Xiang, Chendong Pan, Yanjie Sun, Thangamani Muthukumar, Khaled Machaca, Iwijn De Vlaminck, Manikkam Suthanthiran, submitted (2025).
• Pathology of the coronary arteries and myocardium in Kawasaki Disease, Chisato Shimizu1, Adrian Ruiz Villalba, Conor J. Loy, Iwijn De Vlaminck, Adriana H. Tremoulet, Jose Maria Perez Pomares, Jane C. Burns,  Annual Reviews in Pathology, in press (2025).
• Minimal correlation but complementary diagnostic utility for plasma cell-free RNA and proteins, Andrew Bliss, Conor J. Loy, Jihoon Kim, Chisato Shimizu, Joan S. Lenz, Emma Belcher, Adriana H. Tremoulet, Jane C. Burns, and Iwijn De Vlaminck, submitted (2025).
• Measuring Longitudinal Genome-wide Clonal Evolution of Pediatric Acute Lymphoblastic Leukemia at Single-Cell Resolution, Charles Gawad, Yakun Pang, Tamara Prieto, Veronica Gonzalez-Pena, Athena Aragon, Yuntao Xia, Sheng Kao, Srinivas Rajagopalan, John Zinno, Jean Quentin, Julien Laval, Dennis J Yuan, Nathaniel D. Omans, Catherine Potenski, David Klein, Matthew MacKay, Iwijn De Vlaminck, John Easton, William Evans, Dan A. Landau, submitted (2025).
• Smoothie: Efficient Inference of Spatial Co-expression Networks from Denoised Spatial Transcriptomics Data, Chase Holdener, Iwijn De Vlaminck, submitted, bioRxiv (2025).
• A temporal and spatial atlas of adaptive immune responses in the lymph node following viral infection, Shaowen Jiang, Madhav Mantri, Viviana Maymi, Scott A. Leddon, Peter Schweitzer, Subash Bhandari, Chase Holdener, Ioannis Ntekas, Christopher Vollmers, Andrew I. Flyak, Deborah J. Fowell, Brian D. Rudd, Iwijn De Vlaminck, bioRxiv (2025).
• Spatial Transcriptomics to Study Virus-Host Interactions, Chase Holdener, Shaowen Jiang, Danica M. Sutherland, Kira A. Griswold, Terence S. Dermody, John S. L. Parker, and Iwijn De Vlaminck, Annual Reviews of Virology (2025).
• Bone mineral density affects tumor growth by shaping microenvironmental heterogeneity, Matthew A. Whitman*, Madhav Mantri*, Emmanuel Spanos, Lara A. Estroff, Iwijn De Vlaminck*, Claudia Fischbach*, Biomaterials (2025). * Equal contribution
• A Peritoneal Effluent Sequencing Assay that Removes Environmental DNA Contamination in Peritoneal Dialysis Patients, Liz-Audrey Kounatse Djomnang, Vesh Srivatana, Omary Mzava, Emma Belcher, Lars F. Westblade, Darshana M. Dadhania, Carol Li, Iwijn De Vlaminck, John R. Lee, submitted (2025).
• Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids, Plansky Hoang, David McKellar, Andrew Kowalczewski, Nhu Y Mai, Meng Chai, Xiaojun Lance Lian, Yi Zheng, Jeffrey Amack, Nathan Tucker, Iwijn De Vlaminck, Huaxiao Yang, Benjamin D. Cosgrove, Zhen Ma, Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids, submitted (2025).
• Multiscale Spatial Mapping of Microbial Communities for Biotherapeutic Development, Prateek Sehgal, Andrea G. Shaw, Kevin Cutler, Bridget Letson, Gregory T. Booth, Gaetano J. Scuderi, Anjali Doshi, Peter Diebold, Hannah Bronson, Maya Trisolini, Unnati Dharaiya, Kevin Keomanee-Dizon, Seyi Jung, Jennifer Bagin, James Berleman, Aditya Bhalla, Kyle Jacoby, Steve Kujawa, Jackson Mintz, Pallavi Murugkar, Marguerite Prior, Keiramarie Robertson, Ashlie L. Burkart, Jason Pontin, Lee R. Swem, Iwijn De Vlaminck, Matthew P. Cheng, Philip Burnham, Hao Shi, Multiscale Spatial Mapping of Microbial Communities for Bio-therapeutic Development, bioRxiv 646377 (2025).
• Circulating cell-free RNA signatures towards the characterization and diagnosis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), Anne E. Gardella, Daniel Eweis-LaBolle, Conor J. Loy, Emma D. Belcher, Joan S. Lenz, Carl J. Franconi, Sally Y. Scofield, Andrew W. Grimson, Maureen R. Hanson, Iwijn De Vlaminck, Circulating cell-free RNA signatures towards the characterization and diagnosis of Myalgic  Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), Proceedings of the National Academy of Sciences, in press (2025).
• Urine Cell-Free RNA versus Plasma Cell-Free RNA for Monitoring of Kidney Injury and Systemic Complications, Omary Mzava, Conor J. Loy, Isabel Helena Gonzalez-Bocco, Liz-Audrey Djomnang Kounatse, Andrew Bliss, Sophia L. Wells, Joan Lenz, Emma Belcher, Kaiwen Chen, Sophia Koo, Lindsey Robert Baden, Tinyi Chu, Matthew Pellan Cheng, Jerome Ritz, Shruti Gupta Iwijn De Vlaminck, Clinical Chemistry, in press (2025).

2024

• Molecular characterization of Kawasaki disease subgroups using cell-free RNA profiling, Conor J. Loy, Hao Wang, Jihoon Kim, Chisato Shimizu, Joan Lenz, Emma Belcher, Adriana H. Tremoulet, Jane C. Burns, Iwijn De Vlaminck, submitted (2024). * Equal contribution
• High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing, Ioannis Ntekas*, Lena Takayasu*, DavidW. McKellar*, Benjamin M. Grodner, Chase Holdener, Peter Schweitzer, Maya Sauthoff, Qiaojuan Shi, Ilana L. Brito, Iwijn De Vlaminck, submitted, bioRxiv preprint (2024). *Equal contribution
• Microscale Spatial Dysbiosis in Oral biofilms Associated with Disease,  Benjamin Grodner*, David T. Wu*, Sumin Hahm, Lena Takayasu, Natalie Wen, David M. Kim*, Chia-Yu Chen*, Iwijn De Vlaminck*, submitted, bioRxiv preprint (2024). *Equal contribution.
• Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children. Conor J. Loy, Venice Servellita, Alicia Sotomayor-Gonzalez, Andrew Bliss, Joan Lenz, Emma Belcher, Will Suslovic, Jenny Nguyen, Meagan E. Williams, Miriam Oseguera, Michael A. Gardiner, Pediatric Emergency Medicine Kawasaki Disease Research Group (PEMKDRG), The CHARMS Study Group, Jong-Ha Choi, Hui-Mien Hsiao, Hao Wang, Jihoon Kim, Chisato Shimizu, Adriana Tremoulet, Meghan Delaney, Roberta L. DeBiasi, Christina A. Rostad, Jane C. Burns, Charles Y. Chiu, Iwijn De Vlaminck, Proceedings of the National Academy of Sciences (2024).
• Mouse lemur transcriptomic atlas elucidates primate genes, physiology, disease, and evolution, The Tabula Microcebus Consortium. Nature, in press, (2024).
• Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism The Tabula Microcebus Consortium. Nature, in press (2024).
• Circulating Cell-Free RNA in Blood as a Host Response Biomarker for the Detection of Tuberculosis. Adrienne  Chang*,  Conor  J.  Loy*,  Daniel Eweis-LaBolle*, Joan  S.  Lenz,  Amy  Steadman,  Alfred  Andgrama, Nguyen  Viet  Nhung,  Charles  Yu,  William  Worodria,  Claudia  M.  Denkinger,  Payam  Nahid, Adithya Cattamanchi, Iwijn De Vlaminck, Nature Communications. *Equal contribution
• Spatial Mapping of mobile genetic elements and their bacterial hosts in complex microbiomes,  Benjamin Grodner, Hao Shi, Owen Farchione, Albert C Vill, Ioannis Ntekas, Peter J Diebold, David T. Wu, Chia-Yu Chen, David M. Kim, Warren R. Zipfel, Ilana L. Brito, Iwijn De Vlaminck, Nature Microbiology (2024).
• Cell-free RNA Liquid Biopsy to Monitor Hematopoietic Stem Cell Transplantation, Conor Loy, Matthew P. Cheng, Isabel H. Gonzalez-Bocco, Joan Lenz, Emma Belcher, Andrew Bliss, Daniel Eweis-LaBolle, Tinyi Chu, Jerome Ritz, Iwijn De Vlaminck, submitted (2024).
• Insights, opportunities and challenges provided by large cell atlases, CZI single cell meeting participants, submitted (2024).
• Single-cell and spatial transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states associated with senescence,  Lauren D. Walter, Jessica L. Orton, Ioannis Ntekas, Ern Hwei Hannah Fong, Viviana I. Maymi, Brian D. Rudd, Iwijn De Vlaminck, Jennifer H. Elisseeff, and Benjamin D. Cosgrove, Nature Aging (2024).
  
• A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers, Liz-Audrey Djomnang, Carol Li, Omary Mzava, Alexandre Cheng, Adrienne Chang, Joan Lenz, Manikkam Suthanthiran, John Lee, Darshana Dadhania*, Iwijn De Vlaminck*, Scientific Reports (2024). *Equal contribution
• Bone mineral density affects tumor growth by shaping microenvironmental heterogeneity, Matthew A. Whitman*, Madhav Mantri*, Emmanuel Spanos, Lara A. Estroff, Iwijn De Vlaminck*, Claudia Fischbach*, Biomaterials (2024). * Equal contribution
• Spatiotemporal expression and control of haemoglobin in space, Josef Borg, Conor Loy, JangKeun Kim, Alfred Buhagiar, Christopher Chin, Namita Damle, Iwijn De Vlaminck, Alex Felice, Tammy Liu, Irina Matei, Cem Meydan, Masafumi Muratani, Omary Mzava, Eliah Overbey, Krista A. Ryon, Scott M. Smith, Braden T. Tierney, Guy Trudel, Sara R. Zwart, Afshin Beheshti, Christopher E. Mason & Joseph Borg, Nature Communications (2024)
• Single-cell multiome and immune profiles of the Inspiration4 crew reveal cell-type, sex, and microbiome-specific responses to spaceflight. JangKeun Kim, Conor Loy, …, Joan S. Lenz, Omary Mzava, Iwijn De Vlaminck, … Christopher E. Mason, Nature Communications (2024).
• The Space Omics and Medical Atlas (SOMA): A comprehensive data resource and biobank for astronauts, Eliah G. Overbey, …, Conor Loy, Omary Mzava, Joan Lenz, … Iwijn De Vlaminck,… Christopher E. Mason, The Space Omics and Medical Atlas (SOMA): A comprehensive data resource and biobank for astronauts, Nature (2024).
• The Second Space Age: Omics, Platforms, and Medicine Across Orbits, Christopher Mason , …, Iwijn De Vlaminck,…, Michael Schmidt,  Nature (2024)
• Genome and Clonal Hematopoiesis Stability Contrasts with Immune, cfDNA, mitochondrial, and telomere length changes to Short Duration Spaceflight, J.Sebastian Garcia-Medina, …, Conor Loy, Omary Mzava, Iwijn De Vlaminck, … Christopher E. Mason, Precision Clinical Medicine (2024).
• Liquid biopsy based on cell-free DNA and RNA, Conor Loy, Lauren Ahmann, Iwijn De Vlaminck*, Wei Gu*, Annual Review of Biomedical Engineering (2024). *Equal contribution
• Precision run-on sequencing for microbiome transcriptomics
  Albert Vill, Edward Rice, Iwijn De Vlaminck, Charles Danko, Ilana Brito, Nature Microbiology (2024).
• A Spatiotemporal Molecular Atlas of the Ovulating Mouse Ovary, Madhav Mantri, Hanxue Hannah Zhang, Emmanuel Spanos, Yi A Ren*, Iwijn De Vlaminck*, Proceedings of the National Academy of Sciences (2024). *Equal contribution
• Villus myofibroblasts are developmental and adult progenitors of mammalian gut lymphatic musculature. Bhargav D. Sanketi*, Madhav Mantri*, Mohammad A. Tavallaei, Shing Hu, Michael F. Z. Wang, Iwijn De Vlaminck*, Natasza A. Kurpios*. Developmental Cell (2024). *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, Christing S. Kuo, Mark A. Krasnow, James E. Ferrell Jr., Nature Communications (2024).

2023

• Spatial methods for microbiome-host interactions, Ioannis Ntekas, Iwijn De Vlaminck, Nature Biotechnology (2023).
• A novel tool to identify bactericidal compounds and vulnerable targets against drug-tolerant caseum M. tuberculosis Jansy P. Sarathy, Min Xie, Mark Jones, Adrienne Chang, Paulina Osiecki, Danielle Weiner, Tsao WenShan, Maureen Dougher, Landry Blanc, Nader Fotouhi, Laura E. Via, Clifton E. Barry, Iwijn De Vlaminck, David Sherman, Veronique A. Dartois, mBio (2023).
• Blockade of store-operated calcium entry by BTP2 preserves anti-inflammatory gene expression in human peripheral blood mononuclear cells. Divya Shankaranarayanan*, Madhav Mantri*, Mila Lagman, Carol Li, Vijay K. Sharma, Thangamani Muthukumar, Jenny Z. Xiang, Iwijn De Vlaminck, Khaled Machaca, Manikkam Suthanthiran, Human Immunology (2023). *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*, Cell Reports Medicine,  (2023). *Equal contribution
• A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients: A Pilot Study. Iman Khan, Sylvia Wu, Anika Hudson, Clayton Hughes, Gabriel Stryjniak, Lars Westblade, Michael Satlin, Anne-Catrin Uhlemann, Colleen Kraft, Darshana M. Dadhania, Jeffrey Silberzweig, Iwijn De Vlaminck, Carol Li, Vesh Srivatana, John Richard Lee, Kidney360 (2023).
• 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 (2023).

2022

• Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis
  Madhav Mantri, Meleana M. Hinchman, David W. McKellar, Michael F. Z. Wang, Shaun T. Cross, John S. L. Parker, Iwijn De Vlaminck. Nature Cardiovascular Research (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).
• 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 (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).
• Cell-free DNA Profiling Informs Major Complications of Hematopoietic Cell Transplantation
  Alexandre Pellan Cheng, Matthew Pellan Cheng, Joan Sesing Lenz, Kaiwen Chen, Sami Smalling, 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).
• Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets, Jia Zhao, Gefei Wang, Jingsi Ming, Zhixiang Lin, Yang Wang, The Tabula Microcebus Consortium, Angela Ruohao Wu & Can Yang, Nature Computational Science (2022).
• FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets, Jingsi Ming, Zhixiang Lin, Jia Zhao, Xiang Wan, Tabula Microcebus Consortium Consortium TTM Ezran C Liu S, Can Yang, Angela Ruohao Wu, Briefings in bioinformatics (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)