My research aims at characterizing the functional impact of structural variants.

After working on their detection from sequencing data (short and long reads, pangenomes), I’m now looking for structural variants that could help us better understand complex diseases, or diagnose patients with rare undiagnosed diseases.

• Efficient indexing and querying of annotations in a pangenome graph. bioRxiv 2024.

  AM Novak, D Chung, G Hickey, S Djebali, TT Yokoyama, E Garrison, G Narzisi, B Paten, J Monlong
• Personalized pangenome references. Nature Methods 2024.

  J Sirén, P Eskandar, MT Ungaro, G Hickey, JM Eizenga, AM Novak, X Chang, PC Chang, M Kolmogorov, A Carroll, J Monlong, B Paten

  Preprint
• Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. medRxiv 2024.

  S Negi, SL Stenton, SI Berger, B McNulty, I Violich, J Gardner, …, E Vilain, A O-Luria, E Délot, KH Miga, J Monlong, B Paten
• Mapping the scientific output of organoids for animal and human modeling infectious diseases: a bibliometric assessment. Veterinary Research 2024.

  J Yan, J Monlong, C Cougoule, S Lacroix-Lamandé, A Wiedemann
• Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Research 2024.

  R Lorig-Roach, M Meredith, J Monlong, …, P Carnevali, K Miga, B Paten

  Preprint
• Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Annual Review of Genomics and Human Genetics 2024.

  DJ Taylor, JM Eizenga, Q Li, A Das, KM Jenike, EE Kenny, KH Miga, J Monlong, RC McCoy, B Paten, MC Schatz
• Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Reports 2024.

  E Kuzmin, TM Baker, T Lesluyes, J Monlong, KT Abe, PP Coelho, M Schwartz, …, J Ragoussis, G Bourque, P Van Loo, M Park
• Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nature Methods 2023.

  M Kolmogorov, KJ Billingsley, M Mastoras, M Meredith, J Monlong, …, C Blauwendraat, B Paten

  Preprint
• A draft human pangenome reference. Nature 2023.

  W Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, J Monlong, …, G Bourque, MJP Chaisson, P Flicek, AM Phillippy, JM Zook, EE Eichler, D Haussler, T Wang, ED Jarvis, KH Miga, E Garrison, T Marschall, IM Hall, H Li, B Paten

  Preprint Press
• Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology 2023.

  G Hickey*, J Monlong*, J Ebler, AM Novak, JM Eizenga, Y Gao, Human Pangenome Reference Consortium, H Li, B Paten

  Preprint Data/Code
• Glioblastoma scRNAseq Shows Treatment-induced, Immune-dependent Rise In Mesenchymal Cancer Cells, and Structural Variants in Distal Neural Stem Cells. Neuro-Oncology 2022.

  CP Couturier, J Nadaf, Z Li, S Baig, G Riva, P Le, DJ Kloosterman, J Monlong, A Nkili Meyong, R Allache, T Degenhard, M Al-Rashid, M Guiot, G Bourque, J Ragoussis, L Akkari, FJ Quintana, K Petrecca
• Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nature Biotechnology 2022.

  SD Goenka, JE Gorzynski, K Shafin, DG Fisk, T Pesout, TD Jensen, J Monlong, P Chang, G Baid, …, B Paten, EA Ashley

  PubMed Central Press
• Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock. Circulation: Genomic and Precision Medicine 2022.

  JE Gorzynski, SD Goenka, K Shafin, TD Jensen, DG Fisk, ME Grove, E Spiteri, T Pesout, J Monlong, JA Bernstein, …, B Paten, EA Ashley

  Press
• Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. New England Journal of Medicine 2022.

  JE Gorzynski, SD Goenka, K Shafin, TD Jensen, DG Fisk, ME Grove, E Spiteri, T Pesout, J Monlong, …, B Paten, EA Ashley

  Press
• Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science 2021.

  J Sirén*, J Monlong*, X Chang*, AM Novak*, JM Eizenga*, C Markello, JA Sibbesen, G Hickey, P Chang, A Carroll, N Gupta, S Gabriel, TW Blackwell, A Ratan, KD Taylor, SS Rich, JI Rotter, D Haussler, E Garrison, B Paten

  PubMed Central Preprint Data/Code Press
• Inferring Copy Number from Triple-Negative Breast Cancer Patient Derived Xenograft scRNAseq Data Using scCNA. Mapping Genetic Interactions 2021.

  E Kuzmin, J Monlong, C Martinez, H Kuasne, CL Kleinman, J Ragoussis, G Bourque, M Park
• Invasive growth associated with cold-inducible RNA-binding protein expression drives recurrence of surgically resected brain metastases. Neuro-Oncology 2021.

  M Dankner, M Caron, T Al-Saadi, W Yu, V Ouellet, R Ezzeddine, SM Maritan, MG Annis, PU Le, J Nadaf, NS Neubarth, P Savage, D Zuo, CP Couturier, J Monlong, H Djambazian, H Altoukhi, G Bourque, J Ragoussis, RJ Diaz, M Park, M Guiot, S Lam, K Petrecca, PM Siegel

  PubMed Central
• A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous RecombinationDeficient Pancreatic Cancer. Clinical Cancer Research 2020.

  Y Wang, JYP Park, A Pacis, RE Denroche, GH Jang, A Zhang, A Cuggia, C Domecq, J Monlong, …, G Zogopoulos
• Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Nature Communications 2020.

  CP Couturier, S Ayyadhury, PU Le, J Nadaf, J Monlong, …, J Antel, G Bourque, J Ragoussis, K Petrecca

  PubMed Central Preprint Press
• Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology 2020.

  K Shafin, T Pesout, R Lorig-Roach, M Haukness, HE Olsen, …, J Monlong, …, KH Miga, P Carnevali, M Jain, B Paten

  PubMed Central Preprint
• Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics 2020.

  B Rodriguez-Martin, EG Alvarez, A Baez-Ortega, …, J Monlong, …, HH Kazazian, KH Burns, PJ Campbell, JMC Tubio

  PubMed Central Preprint
• Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biology 2020.

  G Hickey*, D Heller*, J Monlong*, JA Sibbesen, J Siren, J Eizenga, ET Dawson, E Garrison, AM Novak, B Paten

  PubMed Central Preprint Data/Code Press
• Stalled developmental programs at the root of pediatric brain tumors. Nature Genetics 2019.

  S Jessa, A Blanchet-Cohen, B Krug, M Vladoiu, M Coutelier, D Faury, B Poreau, N De Jay, S Hébert, J Monlong, …, G Bourque, J Ragoussis, L Garzia, MD Taylor, N Jabado, CL Kleinman

  PubMed Central Press
• Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations. Nature Communications 2019.

  J Grajcarek, J Monlong, Y Nishinaka-Arai, M Nakamura, M Nagai, S Matsuo, D Lougheed, H Sakurai, MK Saito, G Bourque, K Woltjen

  PubMed Central Data/Code Press
• Human copy number variants are enriched in regions of low mappability. Nucleic Acids Research 2018.

  J Monlong, P Cossette, C Meloche, G Rouleau, SL Girard, G Bourque

  PubMed Central Preprint Data/Code
• Global characterization of copy number variants in epilepsy patients from whole genome sequencing. PLOS Genetics 2018.

  J Monlong*, SL Girard*, …, JL Michaud, G Rouleau, BA Minassian, G Bourque, P Cossette

  PubMed Central Preprint Data/Code
• High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies. American journal of human genetics 2017.

  F Hamdan, CT Myers, P Cossette, P Lemay, D Spiegelman, A Dionne-Laporte, C Nassif, O Diallo, J Monlong, …, BA Minassian, JL Michaud

  PubMed Central Press
• Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma. Scientific Reports 2017.

  M Arseneault*, J Monlong*, …, M Lathrop, G Bourque, Y Riazalhosseini

  PubMed Central
• The human transcriptome across tissues and individuals. Science 2015.

  M Melé, PG Ferreira, F Reverter, DS DeLuca, J Monlong, M Sammeth, …, The GTEx Consortium

  PubMed Central
• The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 2015.

  The GTEx Consortium

  PubMed Central
• Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nature Communications 2015.

  D Pervouchine, S Djebali, A Breschi, CA Davis, PP Barja, A Dobin, A Tanzer, J Lagarde, C Zaleski, L See, M Fastuca, J Drenkow, H Wang, G Bussotti, B Pei, S Balasubramanian, J Monlong, …, C Notredame, R Guigo, TR Gingeras

  PubMed Central
• Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nature Communications 2014.

  J Monlong, M Calvo, PG Ferreira, R Guigó

  PubMed Central
• Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome research 2014.

  PG Ferreira, P Jares, D Rico, G Gomez-Lopez, A Martinez-Trillos, N Villamor, S Ecker, A Gonzalez-Perez, DG Knowles, J Monlong, …, E Campo, R Guigo

  PubMed Central
• Transcriptome and genome sequencing uncovers functional variation in humans. Nature 2013.

  T Lappalainen, M Sammeth*, MR Friedlander*, PA t Hoen*, J Monlong*, MA Rivas*, et al.

  PubMed Central
• Overdiagnosis from non-progressive cancer detected by screening mammography: stochastic simulation study with calibration to population based registry data. BMJ 2011.

  A Seigneurin, O Francois, J Labarere, P Oudeville, J Monlong, M Colonna

  PubMed Central

And here is the PDF of my PhD thesis on “Population-Based Approaches to Characterize Copy Number Variation from Whole-Genome Sequencing in Healthy Individuals and Disease Cohorts” (LaTeX source).

I regularly write down notes about the tools and programming languages I use in a separate website. There are instructions to setup my working environment (Emacs-based) or things I don’t use often enough to remember but enough to collectively waste my time re-googling. I also put some exploratory analyses that might be helpful or interesting to some.

HippocamPlus: my second memory

• jean.monlong@gmail.com
• B522, INSERM IRSD U1220, CHU PURPAN, Place du Docteur Baylac, CS 60039, 31024 TOULOUSE CEDEX 3, ​FRANCE