Position in Computational Biology and Digestive Disease Immunology

 CDD · IR  · 24 mois    Bac+5 / Master   CR2TI INSERM1064 - Nantes Université · NANTES (France)

 Date de prise de poste : 5 septembre 2022


singel cell RNA sequencing human gastrointestinal disease precision medicine


The Martin’s lab is seeking a computational scientist to study the cellular and molecular heterogeneity of human digestive diseases using high dimensional single-cell technologies

General context

The objective of the Martin’s lab is to harness the power offered by new single-cell technologies to deconvolute the organization and regulation of pathogenic responses driving tissue lesions in patients affected by digestive diseases. Our ultimate goal is to enhance the rational for future drug and biomarker discoveries, which are currently significantly limited by the poor understanding of disease pathophysiology. There is therefore an urgent need to gain a better knowledge of the cellular programs in normal and lesional human digestive tissues.


The applicant will be involved in two funded-projects aiming at characterizing MNP molecular programs and cellular interactions in tissues from patients with ileum Crohn’s disease, or with gastric precancerous and cancerous lesions. Using state-of-the art machine-learning and exploratory data analysis tools, the study will dissect single-cell RNA sequencing, single-cell ATACseq and spatial transcriptomics datasets. It will combine profiling microenvironments in healthy and diseased tissues with analysis of Electronic Medical Records

Martin’s lab people involved in these projects:

- Gaelle Beriou, PhD - permanent research engineer

- Aurélie Jousseaume, PhD research assistant

- Lucas Bruselle: research technician

- Thomas Laurent: PhD student

- Nicolas Chapelle: MD (digestive oncologist) - PhD student

- Pr Tamara Matysiak-Budnik: MD-PhD (digestive oncologist) – Attending Physician

Local scientific collaborators on these projects:

- Dr Jeremie Poschmann: PhD – Research team leader – Director of the singe cell facility

International scientific collaborators on these projects:

- Immunology: Pr Miriam Merad (Icahn School of Medicine at Mount Sinai, New York, NY)

- Computational biology: Dr Ephraim Kenigsberg (Icahn School of Medicine at Mount Sinai, New York, NY)

Required Qualifications: 

  • Track record demonstrating expertise in data-analysis, including scRNAseq and scATACseq
  • Candidates with a MSc demonstrating significant skills in computational biology are eligible
  • The ideal candidate will demonstrate scientific imagination, intellectual creativity, rigor, and a history of working well in teams

Appointment Terms:

  • Two years
  • Postdoc and/or research engineer position based on applicant background and expectations

Required Application Materials:

  • Curriculum vitae
  • A cover letter describing experience and research interests to be pursued during training
  • Names of two references

Contact: Applications need to be addressed at Dr Jerome Martin: jerome.martin@univ-nantes.fr



Recent publications

Uzzan M*, Martin JC*, Mesin L… Kenigsberg E, Colombel JF*, Mehandru S*. Ulcerative colitis is characterized by an intense and plasmablast skewed humoral response that associates with treatment resistance and disease complications. Nat Med. 2022 (in press)

* equal contributions

Martin JC, Chang C, Boschetti G, Ungaro R, Giri M, Grout JA, Gettler K, Chuang LS, Nayar S, Greenstein AJ, Dubinsky M, Walker L, Leader A, Fine JS, Whitehurst CE, Mbow ML, Kugathasan S, Denson LA, Hyams JS, Friedman JR, Desai PT, Ko HM, Laface I, Akturk G, Schadt EE, Salmon H, Gnjatic S, Rahman AH, Merad M, Cho JH, Kenigsberg E. Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy. Cell. 2019 5;178(6):1493-1508

Merad M & Martin JC, Pathological Inflammation in Patients With COVID-19: A Key Role for Monocytes and Macrophages, Nat Rev Immunol 2020 20(6):355-362

Martin JCJ, Bériou G, Heslan M, Chauvin C, Utriainen L, Aumeunier A, Scott CL, Mowat A, Cerovic V, Houston SA, Leboeuf M, Hubert FX, Hémont C, Merad M, Milling S, and Josien J. Mucosal Immunol. 2014. 7(1):101-113

Martin JC, Baeten DL and Josien R. Clin. Immunol. 2014. 154 (1):1-12

Martin JC, Beriou G and Josien R. Methods Mol Biol. 2016 1371:197-203

Martin JC, Beriou G, Heslan M, Bossard C, Jarry A, Abidi A, Hulin P, Ménoret S, Thinard R, Anegon I, Jacqueline C, Lardeux B, Halary F, Renauld JC, Bourreille A and Josien R. Mucosal Immunol. 2016 9(2):539-49

Martin JC*, Wolk K*, Bériou G, Abidi A, Witte-Händel E, Louvet C, Kokolakis G, Drujont L, Dumoutier L, Renauld JC, Sabat R**, Josien R**. J Immunol. 2017 198(9):3671-3678

Abidi A, Laurent A, Bériou G, Bouchet-Delbos L, Fourgeux C, Louvet C, Triki-Marrakchi R, Poschmann1* J, Josien R*, Martin JC*. Characterization of Rat ILCs Reveals ILC2 as the Dominant Intestinal Subset. Front Immunol 2020 11:255


Belarif L, Danger R, Kermarrec L, Nerrière-Daguin V, Pengam S, Durand T, Mary C, Kerdreux E, Gauttier V, Kucik A, Thepenier V, Martin JC, Chang C, Rahman A, Guen NS, Braudeau C, Abidi A, David G, Malard F, Takoudju C, Martinet B, Gérard N, Neveu I, Neunlist M, Coron E, MacDonald TT, Desreumaux P, Mai HL, Le Bas-Bernardet S, Mosnier JF, Merad M, Josien R, Brouard S, Soulillou JP, Blancho G, Bourreille A, Naveilhan P, Vanhove B, Poirier N. IL-7 receptor influences anti-TNF responsiveness and T cell gut-homing in inflammatory bowel disease, J Clin Invest. 2019 2;129(5):1910-1925

Lee JY, Hall JA, Kroehling L, Wu L, Najar T, Nguyen HH, Lin WY, Yeung ST, Moura Silva H, Li D, Hine A, Loke P, Hudesman D, Martin JC, Kenigsberg E, Merad M, Khanna KM, Littman DR. Serum Amyloid A Proteins Induce Pathogenic TH17 Cells and Promote Inflammatory Disease. Cell. 2020 180(1):79-91.

Uzzan M, Corcos O, Martin JC, Treton X, Bouhnik Y, Why is SARS-CoV-2 infection more severe in obese men? The gut lymphatics - lung axis hypothesis, Medical Hypotheses 2020 144:110023 (IF: 1.32)

Gruber C, Calis J, Buta S, Evrony G, Martin JC, Uhl S, Caron R, Jarchin L, Dunkin D, Phelps R, Webb B, Saland J, Merad M, Orange J, Mace E, Rosenberg B, Gelb B, Bogunovic D, Complex Autoinflammatory Syndrome Unveils Fundamental Principles of JAK1 Transcriptional and Biochemical Function, Immunity 2020 15;53(3):672-684

Bigenwald C, Le Bérichel J, Wilk W, Chakraborty R, Chen S, Tabachnikova A, Mancusi R, Abhyankar H, Casanova-Acebes M, Laface I, Akturk G, Jobson J, Karoulia Z, Martin JC, Grout J, Rafiei A, Lin H, Manz M, Baccarini A, Poulikakos P, Brown B, Gnjatic S, Lujambio A, McClain M, Picarsic J, Allen C, Merad M, BRAFV600E-induced senescence drives Langerhans Cell Histiocytosis pathophysiology, Nat Medicine 2021 May;27(5):851-861

Leader AM, Grout JA, Maier BB, Nabet BY, Park MD, Tabachnikova A, Chang C, Walker L, Lansky A, Le Berichel J, Troncoso L, Malissen N, Davila M, Martin JC, Magri G, Tuballes K, Zhao Z, Petralia F, Samstein R, D'Amore NR, Thurston G, Kamphorst AO, Wolf A, Flores R, Wang P, Müller S, Mellman I, Beasley MB, Salmon H, Rahman AH, Marron TU, Kenigsberg E, Merad M. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification. Cancer Cell. 2021 1535-6108(21)00560-2


Procédure : Required Application Materials: • Curriculum vitae • A cover letter describing experience and research interests to be pursued during training • Names of two references Applucations must be sent to jerome.martin@univ-nantes.fr

Date limite : 1 juillet 2022


Jerome Martin


Offre publiée le 24 février 2022, affichage jusqu'au 1 juillet 2022