Jinmiao Chen obtained a Bachelor degree in Computer Science from Sun Yat-sen University, China in 2002, PhD in machine learning and artificial intelligence from Nanyang Technological University, Singapore in 2007. As a postdoctoral research fellow, she joined the Bioinformatics core of SIgN, A*STAR Singapore, analyzed microarray, next generation sequencing (RNA-seq/DNA-seq), microbiome/metagenomics, high dimensional flow/mass cytometry and single-cell RNA-sequencing data. In 2014, she became a Project Leader and established her own research lab. She is now a Principal Investigator and her lab is focusing on single-cell computational/system immunology (SCCI).

Single-cell computational/system immunology (SCCI)

Single-cell analysis technologies such as single-cell RNA-sequencing, high-dimensional flow/mass cytometry and multiplex immunohistochemistry (IHC) / Immunofluorescence (IF) allow for measurements of cellular heterogeneity at single-cell resolution with unprecedented dimensionality. We focus on developing innovative single-cell data analytic methodologies and single-cell data integration to delineate immune cell subsets, detect rare cells, construct cell lineages & identify regulators of cell fate, trace cell trafficking, infer spatial localization and infer cell-cell contact/interaction between different subsets of immune cells, pathogens and malignant cells. Using integrative single-cell analysis, we study crosstalk between tumor, immune cells and pathogens in human cancers, aiming to improve diagnosis and cancer immunotherapy. Meanwhile, we collaborate closely with biologists and clinicians, actively involved in data analysis.

 Postdocs (Ph.D) Research Officers
  • Xiaomeng ZHANG
  • Hoa TRAN
  • Kok Siong ANG
  • Hong Kai LEE
  • Michelle GOH
  • Marion CHEVRIER


2019

Janela B, Patel AA, Lau MC, Goh CC, Msallam R, Kong WT, Fehlings M, Hubert S, Lum J, Simoni Y, Malleret B, Zolezzi F, Chen J, Poidinger M, Satpathy AT, Briseno C, Wohn C, Malissen B, Murphy KM, Maini AA, Vanhoutte L, Guilliams M, Vial E, Hennequin L, Newell E, Ng LG, Musette P, Yona S, Hacini-Rachinel F, Ginhoux F. A Subset of Type I Conventional Dendritic Cells Controls Cutaneous Bacterial Infections through VEGFα-Mediated Recruitment of Neutrophils. Immunity. 2019 Mar 26. [Epub ahead of print]

Chakarov S, Lim HY, Tan L, Lim SY, See P, Lum J, Zhang XM, Foo S, Nakamizo S, Duan K, Kong WT, Gentek R, Balachander A, Carbajo D, Bleriot C, Malleret B, Tam JKC, Baig S, Shabeer M, Toh SES, Schlitzer A, Larbi A, Marichal T, Malissen B, Chen J, Poidinger M, Kabashima K, Bajenoff M, Ng LG, Angeli V, Ginhoux F. Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches. Science. 2019 Mar 15;363(6432).

Periasamy P, Hutchinson PE, Chen J, Bonne I, Shahul Hameed SS, Selvam P, Hey YY, Fink K, Irving AT, Dutertre CA, Baker M, Crameri G, Wang LF, Alonso S. Studies on B Cells in the Fruit-Eating Black Flying Fox (Pteropus alecto). Front Immunol. 2019 Mar 14;10:489.

Lachmandas E, Eckold C, Böhme J, Koeken VACM, Marzuki MB, Blok B, Arts RJW, Chen J, Teng KWW, Ratter J, Smolders EJ, van den Heuvel C, Stienstra R, Dockrell HM, Newell E, Netea MG, Singhal A, Cliff JM, van Crevel R. Metformin alters human host responses to Mycobacterium tuberculosis in healthy subjects. J Infect Dis. 2019 Feb 12. [Epub ahead of print]

Cheng Y, Zhu YO, Becht E, Aw P, Chen J, Poidinger M, de Sessions PF, Hibberd ML, Bertoletti A, Lim SG, Newell EW. Multifactorial heterogeneity of virus-specific T cells and association with the progression of human chronic hepatitis B infection. Sci Immunol. 2019 Feb 8;4(32).

Yeong J, Lim JCT, Lee B, Li H, Ong CCH, Thike AA, Yeap WH, Yang Y, Lim AYH, Tay TKY, Liu J, Wong SC, Chen J, Lim EH, Iqbal J, Dent R, Newell EW, Tan PH. Prognostic value of CD8 + PD-1+ immune infiltrates and PDCD1 gene expression in triple negative breast cancer. J Immunother Cancer. 2019 Feb 6;7(1):34.

Dick SA, Macklin JA, Nejat S, Momen A, Clemente-Casares X, Althagafi MG, Chen J, Kantores C, Hosseinzadeh S, Aronoff L, Wong A, Zaman R, Barbu I, Besla R, Lavine KJ, Razani B, Ginhoux F, Husain M, Cybulsky MI, Robbins CS, Epelman S. Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction. Nat Immunol. 2019 Jan;20(1):29-39.

2018

Hammond TR, Dufort C, Dissing-Olesen L, Giera S, Young A, Wysoker A, Walker AJ, Gergits F, Segel M, Nemesh J, Marsh SE, Saunders A, Macosko E, Ginhoux F, Chen J, Franklin RJM, Piao X, McCarroll SA, Stevens B. Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes. Immunity. 2018 Nov 21. [Epub ahead of print]

See P, Lum J, Chen J, Ginhoux F. A Single-Cell Sequencing Guide for Immunologists. Front Immunol. 2018 Oct 23;9:2425.

Gentek R, Ghigo C, Hoeffel G, Bulle MJ, Msallam R, Gautier G, Launay P, Chen J, Ginhoux F, Bajénoff M. Hemogenic Endothelial Fate Mapping Reveals Dual Developmental Origin of Mast Cells. Immunity. 2018 Jun 19;48(6):1160-1171.e5.

Wang B, Lam TH, Soh MK, Ye Z, Chen J, Ren EC. Influenza A Virus Facilitates Its Infectivity by Activating p53 to Inhibit the Expression of Interferon-Induced Transmembrane Proteins. Front Immunol. 2018 May 31;9:1193.

Chen J, Rénia L, Ginhoux F. Constructing cell lineages from single-cell transcriptomes. Mol Aspects Med. 2018 Feb;59:95-113.

Thion MS, Low D, Silvin A, Chen J, Grisel P, Schulte-Schrepping J, Blecher R, Ulas T, Squarzoni P, Hoeffel G, Coulpier F, Siopi E, David FS, Scholz C, Shihui F, Lum J, Amoyo AA, Larbi A, Poidinger M, Buttgereit A, Lledo PM, Greter M, Chan JKY, Amit I, Beyer M, Schultze JL, Schlitzer A, Pettersson S, Ginhoux F, Garel S. Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner. Cell. 2018 Jan 25;172(3):500-516.e16.

2017

He JS, Subramaniam S, Narang V, Srinivasan K, Saunders SP, Carbajo D, Wen-Shan T, Hidayah Hamadee N, Lum J, Lee A, Chen J, Poidinger M, Zolezzi F, Lafaille JJ, Curotto de Lafaille MA. IgG1 memory B cells keep the memory of IgE responses. Nat Commun. 2017 Sep 21;8(1):641.

Tan-Garcia A, Wai LE, Zheng D, Ceccarello E, Jo J, Banu N, Khakpoor A, Chia A, Y L Tham C, Tan AT, Hong M, Keng CT, Rivino L, Tan KC, Hoe Lee K, Lim SG, Newell EW, Pavelka N, Chen J, Ginhoux F, Chen Q, Bertoletti A, Dutertre CA. Intrahepatic CD206+ macrophages contribute to inflammation in advanced viral-related liver disease. J Hepatol. 2017 Sep;67(3):490-500.

See P, Dutertre CA, Chen J, Günther P, McGovern N, Irac SE, Gunawan M, Beyer M, Händler K, Duan K, Sumatoh HRB, Ruffin N, Jouve M, Gea-Mallorquí E, Hennekam RCM, Lim T, Yip CC, Wen M, Malleret B, Low I, Shadan NB, Fen CFS, Tay A, Lum J, Zolezzi F, Larbi A, Poidinger M, Chan JKY, Chen Q, Renia L, Haniffa M, Benaroch P, Schlitzer A, Schultze JL, Newell EW, Ginhoux F. Mapping the human DC lineage through the integration of high-dimensional techniques. Science.  2017 Jun 9;356(6342).

Cheng C, Gutierrez NM, Marzuki MB, Lu X, Foreman TW, Paleja B, Lee B, Balachander A, Chen J, Tsenova L, Kurepina N, Teng KWW, West K, Mehra S, Zolezzi F, Poidinger M, Kreiswirth B, Kaushal D, Kornfeld H, Newell EW, Singhal A. Host sirtuin 1 regulates mycobacterial immunopathogenesis and represents a therapeutic target against tuberculosis. Sci Immunol. 2017 Mar;2(9).

Garnelo M, Tan A, Her Z, Yeong J, Lim CJ, Chen J, Lim KH, Weber A, Chow P, Chung A, Ooi LL, Toh HC, Heikenwalder M, Ng IO, Nardin A, Chen Q, Abastado JP, Chew V. Interaction between tumour-infiltrating B cells and T cells controls the progression of hepatocellular carcinoma. Gut. 2017 Feb;66(2):342-351.

Wistuba-Hamprecht K, Martens A, Weide B, Teng KW, Zelba H, Guffart E, Chen J, Garbe C, Newell EW, Larbi A, Pawelec G. Establishing High Dimensional Immune Signatures from Peripheral Blood via Mass Cytometry in a Discovery Cohort of Stage IV Melanoma Patients. J Immunol. 2017 Jan 15;198(2):927-936.

2016


Chong SZ, Evrard M, Devi S, Chen J, Lim JY, See P, Zhang Y, Adrover JM, Lee B, Tan L, Li JL, Liong KH, Phua C, Balachander A, Boey A, Liebl D, Tan SM, Chan JK, Balabanian K, Harris JE, Bianchini M, Weber C, Duchene J, Lum J, Poidinger M, Chen Q, Rénia L, Wang CI, Larbi A, Randolph GJ, Weninger W, Looney MR, Krummel MF, Biswas SK, Ginhoux F, Hidalgo A, Bachelerie F, Ng LG. CXCR4 identifies transitional bone marrow premonocytes that replenish the mature monocyte pool for peripheral responses. J Exp Med. 2016 Oct 17;213(11):2293-2314.

Chan CY, Ng KH, Chen J, Lu J, Lee CG, Tan PH, Jordan SC, Yang HH, Yap HK. Novel role of Vav1-Rac1 pathway in actin cytoskeleton regulation in Interleukin-13-induced minimal change-like nephropathy. Clin Sci (Lond). 2016 Oct 5. [Epub ahead of print]

Chen H, Lau MC, Wong MT, Newell EW, Poidinger M, Chen J. Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline. PLoS Comput Biol. 2016 Sep 23;12(9):e1005112.

Guilliams M, Dutertre CA, Scott CL, McGovern N, Sichien D, Chakarov S, Van Gassen S, Chen J, Poidinger M, De Prijck S, Tavernier SJ, Low I, Irac SE, Mattar CN, Sumatoh HR, Low GH, Chung TJ, Chan DK, Tan KK, Hon TL, Fossum E, Bogen B, Choolani M, Chan JK, Larbi A, Luche H, Henri S, Saeys Y, Newell EW, Lambrecht BN, Malissen B, Ginhoux F. Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species. Immunity. 2016 Sep 20;45(3):669-84.

Monaco G, Chen H, Poidinger M, Chen J, de Magalhães JP, Larbi A. flowAI: automatic and interactive anomaly discerning tools for flow cytometry data. Bioinformatics. 2016 Aug 15;32(16):2473-80.

Chen J, Schlitzer A, Chakarov S, Ginhoux F, Poidinger M. Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development. Nat Commun. 2016 Jun 30;7:11988.

Yu YH, Narayanan G, Sankaran S, Ramasamy S, Chan SY, Lin S, Chen J, Yang H, Srivats H, Ahmed S. Purification, visualisation and molecular signature of neural stem cells. Stem Cells Dev. 2016 Jan 15;25(2):189-201.

2015

Zelante T, Wong AY, Ping TJ, Chen J, Sumatoh HR, Viganò E, Hong Bing Y, Lee B, Zolezzi F, Fric J, Newell EW, Mortellaro A, Poidinger M, Puccetti P, Ricciardi-Castagnoli P. CD103(+) Dendritic Cells Control Th17 Cell Function in the Lung. Cell Rep. 2015 Sep 22;12(11):1789-801.

Lim JH, Ravikumar S, Wang YM, Thamboo TP, Ong L, Chen J, Goh JG, Tay SH, Chengchen L, Win MS, Leong W, Lau T, Foo R, Mirza H, Tan KS, Sethi S, Khoo AL, Chng WJ, Motomi O, Netea MG, Wang Y, Chai LY. Bimodal Influence of Vitamin D in Host Response to Systemic Candida Infection - Vitamin D Dose Matters. J Infect Dis. 2015 Aug 15;212(4):635-44.

Schlitzer A, Sivakamasundari V, Chen J, Sumatoh HR, Schreuder J, Lum J, Malleret B, Zhang S, Larbi A, Zolezzi F, Renia L, Poidinger M, Naik S, Newell EW, Robson P, Ginhoux F. Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow. Nat Immunol. 2015 Jul;16(7):718-28.

Dang TM, Wong WC, Ong SM, Li P, Lum J, Chen J, Poidinger M, Zolezzi F, Wong SC. MicroRNA expression profiling of human blood monocyte subsets highlights functional differences. Immunology. 2015 Jul;145(3):404-16.

Wong MT, Chen J, Narayanan S, Lin W, Anicete R, Kiaang HT, De Lafaille MA, Poidinger M, Newell EW. Mapping the Diversity of Follicular Helper T Cells in Human Blood and Tonsils Using High-Dimensional Mass Cytometry Analysis. Cell Rep. 2015 Jun 23;11(11):1822-33.

Hoeffel G, Chen J, Lavin Y, Low D, Almeida FF, See P, Beaudin AE, Lum J, Low I, Forsberg EC, Poidinger M, Zolezzi F, Larbi A, Ng LG, Chan JK, Greter M, Becher B, Samokhvalov IM, Merad M, Ginhoux F. C-myb(+) erythro-myeloid progenitor-derived fetal monocytes give rise to adult tissue-resident macrophages. Immunity. 2015 Apr 21;42(4):665-78.

Shalova IN, Lim JY, Chittezhath M, Zinkernagel AS, Beasley F, Hernández-Jiménez E, Toledano V, Cubillos-Zapata C, Rapisarda A, Chen J, Duan K, Yang H, Poidinger M, Melillo G, Nizet V, Arnalich F, López-Collazo E, Biswas SK. Human Monocytes Undergo Functional Re-programming during Sepsis Mediated by Hypoxia-Inducible Factor-1α. Immunity. 2015 Mar 17;42(3):484-98.

Cottier F, Tan AS, Chen J, Lum J, Zolezzi F, Poidinger M, Pavelka N. The Transcriptional Stress Response of Candida albicans to Weak Organic Acids. G3 (Bethesda). 2015 Jan 29;5(4):497-505.

2014

Fric J, Lim CX, Mertes A, Lee BT, Viganò E, Chen J, Zolezzi F, Poidinger M, Larbi A, Strobl H, Zelante T, Ricciardi-Castagnoli P. Calcium and Calcineurin-Nfat Signaling Regulate Granulocyte-Monocyte Progenitor Cell cycle Via Flt3-L. Stem Cells. 2014 Dec;32(12):3232-44.

Becher B, Schlitzer A, Chen J, Mair F, Sumatoh HR, Teng KW, Low D, Ruedl C, Riccardi-Castagnoli P, Poidinger M, Greter M, Ginhoux F, Newell EW. High-dimensional analysis of the murine myeloid cell system. Nat Immunol. 2014 Dec;15(12):1181-9.

Chittezhath M, Dhillon MK, Lim JY, Laoui D, Shalova IN, Teo YL, Chen J, Kamaraj R, Raman L, Lum J, Thamboo TP, Chiong E, Zolezzi F, Yang H, Van Ginderachter JA, Poidinger M, Wong AS, Biswas SK. Molecular profiling reveals a tumor-promoting phenotype of monocytes and macrophages in human cancer progression. Immunity. 2014 Nov 20;41(5):815-29.

Singhal A, Jie L, Kumar P, Hong GS, Leow MKS, Paleja B, Tsenova L, Kurepina N, Chen J, Zolezzi F, Kreiswirth B, Poidinger M, Chee C, Kaplan G, Wang YT, De Libero G. Metformin as adjunct anti-tuberculosis therapy. Science Translational Medicine. 2014. 19th Nov. Vol. 6, Issue 263, p. 263ra159.

Chen J, Xue Y, Poidinger M, Lim T, Chew SH, Pang CL, Abastado JP, Thierry F. Mapping of HPV transcripts in four human cervical lesions using RNAseq suggests quantitative rearrangements during carcinogenic progression. Virology. 2014;(462-463):14-24.

Sébastien Calbo, Xavier Camous, Baptiste Janela, Kim Périchon, Jinmiao Chen, Edmond Chua, Josephine Lum, Francesca Zolezzi, Michael Poidinger, Philippe Musette, Gene profiling of B lymphoblastoid cell lines from DRESS patients after drugs incubation. Clinical and Translational Allergy. 07/2014

2013

Mertes A, Fric J, Lim C, Tay HS, Zelante T, Chen J, Ricciardi-Castagnoli P. Role of calcineurin/NFAT signalling in myeloid cell haematopoiesis and function. Frontiers in Immunology. 01/2013

2012

Narayanan G, Poonepalli A, Chen J, Sankaran S, Hariharan S, Yu YH, Robson P, Yang H, Ahmed S. Single-cell mRNA profiling identifies progenitor subclasses in neurospheres. Stem Cells Dev. vol. 21, pp. 3351-62, Dec 10 2012

Fric J, Lim CX, Koh EG, Hofmann B, Chen J, Tay HS, Mohammad Isa SA, Mortellaro A, Ruedl C, Ricciardi-Castagnoli P. Calcineurin/NFAT signalling inhibits myeloid haematopoiesis. EMBO Mol Med. 2012 Apr;4(4):269-82.

Chew V, Chen J, Lee D, Loh E, Lee J, Lim KH, Weber A, Slankamenac K, Poon RT, Yang H, Ooi LL, Toh HC, Heikenwalder M, Ng IO, Nardin A, Abastado JP. Chemokine-driven lymphocyte infiltration: an early intratumoural event determining long-term survival in resectable hepatocellular carcinoma. Gut. Mar 2012; 61(3):427-438.

Ang M, Cheung G, Vania M, Chen J, Yang H, Li J, Chee SP. Aqueous cytokine and chemokine analysis in uveitis associated with tuberculosis. Mol Vis. vol. 18, pp. 565-73, 2012.

2011

Maubach G, Lim MC, Chen J, Yang H, , ZhuoL. miRNA studies in in vitro and in vivo activated hepatic stellate cells. World J Gastroenterol. vol. 17, pp. 2748-73, Jun 14 2011.

Chow A, Her Z, Ong EK, Chen JM, Dimatatac F, Kwek DJ, Barkham T, Yang H, Renia L, Leo YS, Ng LF. Persistent Arthralgia Induced by Chikungunya Virus Infection is Associated with Interleukin-6 and Granulocyte Macrophage Colony-Stimulating Factor. J Infect Dis. Jan 2011; 203(2):149-157.

Before 2011

J. Chen and N. S. Chaudhari, "Segmented-memory recurrent neural networks" IEEE Trans Neural Network. vol. 20, pp. 1267-80, Aug 2009.

J. Chen and N. Chaudhari, "Cascaded bidirectional recurrent neural networks for protein secondary structure prediction" IEEE/ACM Trans Comput Biol Bioinform. vol. 4, pp. 572-82, Oct-Dec 2007.

J. Chen and N. S. Chaudhari, "Bidirectional segmented-memory recurrent neural network for protein secondary structure prediction" Soft Computing. vol. 10, pp. 315-324, 2006.

Conference Publications

“Single-cell analysis of crosstalk between tumor, immune cells and pathogens in gastric cancer”, Joint SGCC-CSI gastric cancer seminar, 5  April 2016, NUS, Singapore

“Single-cell computational/system immunology”, Genomic Applications of qPCR, dPCR & NGS, 26-27 May 2016, Singapore

“Single-cell analysis of myeloid lineage”, the 8th international Singapore symposium of immunology, 26-27 May 2016, Grand Copthorne Waterfront Hotel, Singapore

“Single-cell analysis of immune cell diversity and lineage development”, 5th Annual Next Generation Sequencing Asia Congress 2015, October 2015, Singapore

“Cytofkit: A BioConductor package of Integrated Mass Cytometry Data Analysis Pipeline”, GIW/InCoB 2015, September 2015, Tokyo

“Mass cytometry analysis of immune cell diversity and development”, The 12th [BC]2 - the Basel Computational Biology Conference, June 2015, Switzerland

Conference Publications


J. Chen and N. S. Chaudhari, "Statistical Analysis of Long-Range Interactions in Proteins," presented at the Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology, BIOCOMP'06, Las Vegas, Nevada, USA, 2006

J. Chen and N. S. Chaudhari, "Protein secondary structure prediction with a hybrid RNN/HMM system," presented at the 2005 IEEE International Joint Conference on Neural Networks, IJCNN  '05, Montreal, 2005.

J. Chen and N. S. Chaudhari, " Improvement of bidirectional recurrent neural network for learning long-term dependencies " presented at the The 17th International Conference on Pattern Recognition,  ICPR 2004, Cambridge, 2004.

J. Chen and N. S. Chaudhari, "Learning Long-Term Dependencies in Segmented Memory Recurrent Neural Networks," presented at the International Symposium on Neural Networks (ISNN), Lecture Notes in Computer Science, Dalian, China, 2004.

J. Chen and N. S. Chaudhari, "Protein Family Classification Using Second-Order Recurrent Neural Networks," presented at the the 14th International Conference on Genome Informatics, Pacifico Yokohama, Japan, 2003.

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