• 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
• Personalized Pangenome References. bioRxiv 2023.

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