Publications

(Google Scholar profile)

2021

R. Zhang, L. Meng-Papaxanthos, J.-P. Vert and W. S. Noble. Semi-supervised single-cell cross-modality translation using Polarbear.
Technical report bioRxiv 2021.11.18.467517, 2021.
F. Llinares-Lopez, Q. Berthet, M. Blondel and J.-P. Vert. Deep embedding and alignment of protein sequences.
Technical report bioRxiv 2021.11.15.468653, 2021.
V. Mallet and J.-P. Vert. Reverse-complement equivariant networks for DNA sequences.
NeurIPS 2021 (in press).
[code]
A. Fermanian, P. Marion, J.-P. Vert and G. Biau. Framing RNN as a kernel method: A neural ODE approach.
NeurIPS 2021 (in press).
G. Baid, D. E. Cook, K. Shafin, T. Yun, F. Llinares-Lopez, Q. Berthet, A. M. Wenger, W. J. Rowell, M. Nattestad, H. Yang, A. Kolesnikov, A. Topfer, A. Ammar, J.-P. Vert, A. Vaswani, C. Y. McLean, P.-C. Chang and A. Carroll. DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction
Technical report bioRxiv 458403, 2021.
[code]
J. Abecassis, F. Reyal and J.-P. Vert. Clonesig can jointly infer intra-tumor heterogeneity and mutational signature activity in tumor bulk sequencing data.
Nature Communications, 12:5352, 2021.
[Code]
M. Blondel, Q. Berthet, M. Cuturi, R. Frostig, S. Hoyer, F. Llinares-Lopez, F. Pedregosa and J.-P. Vert. Efficient and modular implicit differentiation.
Technical report arXiv 2105.15183, 2021
[code]
M. Pascucci, G. Royer, J. Adamek, M. Al Asmar, D. Aristizabal, L. Blanche, A. Bezzarga, G. Boniface-Chang, A. Brunner, C. Curel, G. Dulac-Arnold, R. M. Fakhri, N. Malou, C. Nordon, V. Runge, F. Samson, E. Sebastian, D. Soukieh, J.-P. Vert, C. Ambroise and M.-A. Madoui. AI-based mobile application to fight antibiotic resistance.
Nature Communications, 12:1173, 2021.
[code]
F. Raimundo, L. Papaxanthos, C. Vallot and J.-P. Vert. Machine learning for single cell genomics data analysis
Current Opinion in Systems Biology, 25:64-71, 2021.
[Journal version]
N. Varoquaux, W. S. Noble and J.-P. Vert. Inference of genome 3D architecture by modeling overdispersion of Hi-C data
Technical report bioRxiv 429864, 2021.
M. Blondel, A. Mensch and J.-P. Vert. Differentiable divergences between time series
Proceedings of the Twenty Fourth International Conference on Artificial Intelligence and Statistics (AISTATS), PMLR 130:3853-3861, 2021.
[code]

2020

B. Colnet, I. Mayer, G. Chen, A. Dieng, R. Li, G. Varoquaux, J.-P. Vert, J. Josse and S. Yang. Causal inference methods for combining randomized trials and observational studies: a review.
Technical report arXiv 2011.08047.
L. Slim, C. Chatelain, C.-A. Azencott and J.-P. Vert. Novel Methods for Epistasis Detection in Genome-Wide Association Studies.
PLoS ONE, 15(11): e0242927, 2020.
[Code]
Q. Berthet, M. Blondel, O. Teboul, M. Cuturi, J.-P. Vert and F. Bach. Learning with differentiable perturbed optimizers.
In Advances in Neural Information Processing Systems (NeurIPS) 33, p.9508-9519, 2020.
F. Raimundo, C. Vallot and J.-P. Vert. Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Genome Biology, 21:212, 2020.
[code][data]
M. Cuturi, O. Teboul, J. Niles-Weed and J.-P. Vert. Supervised quantile normalization for low-rank matrix approximation.
In Proceedings of the 37th International Conference on Machine Learning, Vienna, Austria, PMLR 119, 2020.
[Code genomics]
L. Carratino, M. Cisse, R. Jenatton and J.-P. Vert. On mixup regularization.
Technical report arXiv 2006.06049, 2020.
P.-C. Aubin-Frankowski and J.-P. Vert. Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference.
Bioinformatics 36(18):4774-4780, 2020.
[Journal version][Code]
M. Cuturi, O. Teboul and J.-P. Vert.Noisy Adaptive Group Testing using Bayesian Sequential Experimental Design
Technical report arXiv 2004.12508, 2020
[code]
J.-P. Vert. Artificial intelligence and cancer genomics.
In Nordlinger B., Villani C., Rus D. (eds), Healthcare and Artificial Intelligence, Springer, Cham, p.165-174, 2020.
[Publisher version]
R. Menegaux and J.-P. Vert. Embedding the de Bruijn graph, and applications to metagenomics
Technical report bioRxiv 980979, 2020.
I. Mayer, J. Josse, F. Raimundo and J.-P. Vert. MissDeepCausal: Causal inference from incomplete data using deep latent variable models.
Technical report arXiv 2002.10837, 2020.
M.-M. Aynaud, O. Mirabeau, N. Gruel, S. Grossetête, V. Boeva, S. Durand, D. Surdez, O. Saulnier, S. Zaïdi, S. Gribkova, U. Kairov, V. Raynal, F. Tirode, P. Grünewald, M. Bohec, S. Baulande, I. Janoueix-Lerosey, J.-P. Vert, E. Barillot, O. Delattre and A. Zinovyev. Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution.
Cell Reports, 30(6):1767-1779.E6, 2020.
K. B. Cook, B. H. Hristov, K. G. Le Roch, J.-P. Vert and W. S. Noble. Measuring significant changes in chromatin conformation with ACCOST.
Nucleic Acids Research, 48(5):2303-2311, 2020
[Code]

2019

M. Cuturi, O. Teboul and J.-P. Vert. Differentiable ranking and sorting using optimal transport.
In Advances in Neural Information Processing Systems (NeurIPS) 32, 6858-6868, 2019.
[Code]
J. Abecassis, A.-S. Hamy, C. Laurent, B. Sadacca, H. Bonsang-Kitzis, F. Reyal and J.-P. Vert. Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data.
PLoS ONE, 14(11):e0224143, 2019.
[Code]
A. Genevay, G. Dulac-Arnold and J.-P. Vert. Differential deep clustering with cluster size contraints.
Technical report arXiv 1910.09036, 2019.
O. Collier, V. Stoven and J.-P. Vert. LOTUS: a single- and multitask machine learning algorithm for the prediction of cancer driver genes.
PLoS Computational Biology, 15(9):e1007381, 2019.
[Code]
G. Dulac-Arnold, N. Zeghidour, M. Cuturi, L. Beyer and J.-P. Vert. Deep multi-class learning from label proportions.
Technical report arXiv 1905.12909, 2019.
A. G. Cauer, G. Yardimci, J.-P. Vert, N. Varoquaux and W. S. Noble. Inferring diploid 3D chromatin structures from Hi-C data.
In K. T. Huber and D. Gusfield (Eds), Proceedings of the 19th International Workshop on Algorithms in Bioinformatics (WABI 2019), Leibniz International Proceedings in Informatics (LIPIcs) 143:11, 2019.
[Code]
J. Liu, Y. Huang, R. Singh, J.-P. Vert and W. S. Noble. Jointly embedding multiple single-cell omics measurements.
In K. T. Huber and D. Gusfield (Eds), Proceedings of the 19th International Workshop on Algorithms in Bioinformatics (WABI 2019), Leibniz International Proceedings in Informatics (LIPIcs) 143:10, 2019.
[Code]
L. Slim, C. Chatelain, C.-A. Azencott and J.-P. Vert. kernelPSI: a Post-Selection Inference Framework for Nonlinear Variable Selection.
In K. Chaudhuri and R. Salakhutdinov (Eds), Proceedings of the 36th International Conference on Machine Learning, PLMR 97:5857-5865, 2019.
[Code]
R. Menegaux and J.-P. Vert. Continuous embeddings of DNA sequencing reads, and application to metagenomics.
Journal of Computational Biology, 26(6):509-518, 2019.
[Link][Code]
B. Khalfaoui, J. Boyd and J.-P. Vert. Adaptive structured noise injection for shallow and deep neural networks.
Technical report HAL 02025929, 2019.
[Code]

2018

N. Servant, N. Varoquaux, E. Heard, J.-P. Vert and E. Barillot. Effective normalization for copy number variation in Hi-C data.
BMC Bioinformatics, 19:313, 2018.
[Code]
E. Pauwels, F. Bach and J.-P. Vert. Relating leverage scores and density using regularized Christoffel functions.
In S. Bengio, H. Wallach, H. Larochelle, K. Grauman, N. Cesa-Bianchi and R. Garnett (Eds.), Advances in Neural Information Processing Systems (NeurIPS) 31, 1670-79, 2018.
Y. Jiao and J.-P. Vert. The weighted Kendall and high-order kernels for permutations.
In J. Dy and A. Krause (Eds.), Proceedings of the 35th International Conference on Machine Learning, PMLR 80:2314-2322, 2018.
M. Le Morvan and J.-P. Vert. WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models.
In J. Dy and A. Krause (Eds.), Proceedings of the 35th International Conference on Machine Learning, PMLR 80:3635-3644, 2018.
[Code]
K. Vervier, P. Mahé and J.-P. Vert. MetaVW: Large-scale machine learning for metagenomics sequence classification.
In Mamitsuka H. (eds), Data Mining for Systems Biology. Methods in Molecular Biology, vol. 1807:9-20, Humana Press, New York, NY, 2018.
link
Y. Jiao and J.-P. Vert. The Kendall and Mallows Kernels for Permutations.
IEEE Transactions on Pattern Analysis and Machine Intelligence, 40(7):1755-1769, 2018.
[Code]
A. Recanati, N. Servant, J.-P. Vert and A. d'Aspremont. Robust Seriation and Applications to Cancer Genomics.
Technical report arXiv:1806.00664, 2018.
E. M. Bunnik, K. B. Cook, N. Varoquaux, G. Batugedara, J. Prudhomme, A. Cort, L. Shi, C. Andolina, L. S. Ross, D. Brady, D. A. Fidock, F. Nosten, R. Tewari, P. Sinnis, F. Ay, J.-P. Vert, W. Noble and K. G. Le Roch. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.
Nature Communications, 9(1):1910, 2018.
[Supplementary informations]
K. Van den Berg, F. Perraudeau, C. Soneson, M. I. Love, D. Risso, J.-P. Vert, M. D. Robinson, S. Dudoit and L. Clement. Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications.
Genome Biology, 19:24, 2018.
[Code]
B. Khalfaoui and J.-P. Vert. DropLasso: A robust variant of Lasso for single cell RNA-seq data.
Technical report HAL-01716704, 2018.
[Code]
P. Ruan, M. Hayashida, T. Akutsu and J.-P. Vert. Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.
BMC Bioinformatics, 19(Suppl 1):39, 2018.
D. Risso, F. Perraudeau, S. Gribkova, S. Dudoit and J.-P. Vert. A general and flexible method for signal extraction from single-cell RNA-seq data.
Nature Communications, 9(1):284, 2018.
[Code][Reproduce results]

2017

J.-P. Vert, "Quand les algorithmes font parler l'ADN",
La Recherche, 529:48-52, 2017.
J.-L. Plouhinec, S. Medina-Ruiz, C. Borday, E. Bernard, J.-P. Vert, M. B. Eisen, R. M. Harland and A. H. Monsoro-Burq, "A molecular atlas of the developing ectoderm defines neural, neural crest, placode and non-neural progenitor identity in vertebrates",
PLoS Biology, 15(10): e2004045, 2017.
[web site]
E. Bernard, Y. Jiao, E. Scornet, V. Stoven, T. Walter and J.-P. Vert, "Kernel multitask regression for toxicogenetics",
Molecular Informatics, 36(10), 2017.
[Link][code][Reproduce results]
M. Le Morvan and J.-P. Vert, "Supervised quantile normalization",
Technical report HAL-01525306, 2017.
M. Le Morvan, A. Zinovyev and J.-P. Vert, "NetNorM: capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis",
PLoS Computational Biology, 13(6):e1005573, 2017.
[Code]
Y. Jiao, M. R. Hidalgo, C. Cubuk, A. Amodoz, J. Carbonell-Caballero, J.-P. Vert and J. Dopazo, "Signaling pathway activities improve prognosis for breast cancer",
Technical report bioRxiv 132357, 2017.
[Code]]

2016

J.-P. Vert, "Le big data dans la recherche médicale",
Revue des Ingénieurs des Mines, 488:8-9, 2016.
S. Sieberts, F. Zhu, J. García-García, E. Stahl et al., "Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis",
Nature Communications, 7:12460, 2016.
K. Vervier, P. Mahé, M. Tournoud, J.-B. Veyrieras and J.-P. Vert, "Large-scale Machine Learning for Metagenomics Sequence Classification",
Bioinformatics, 32(7):1023-1032, 2016.
[Code]

2015

N. Servant, N. Varoquaux, B. R. Lajoie, E. Viara, C.-J. Chen, J.-P.Vert, E. Heard, J. Dekker and E. Barillot. HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.
Genome Biology, 16:259, 2015.
[Code]
M. Moarii, V. Boeva, J.-P. Vert and F. Reyal. Changes in correlation between promoter methylation and gene expression in cancer.
BMC Genomics, 16:873, 2015.
[Code]
M. Moarii, F. Reyal and J.-P. Vert, "Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype.
Human Genomics, 9:26, 2015.
[Code]
L. Guyon, C. Lajaunie, F. Fer, R. Bhajun, E. Sulpice, G. Pinna, A. Campalans, J. P. Radicella, P. Rouillier, M. Mary, S. Combe, P. Obeid, J.-P. Vert and X. Gidrol. Phi-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays.
Scientific Reports, 5:14221, 2015.
[Code]
F. Eduati, L. M. Mangravite et al. Prediction of human population responses to toxic compounds by a collaborative competition.
Nature Biotechnology, 33(9):933-940, 2015.
E. Bernard, L. Jacob, J. Mairal, E. Viara and J.-P. Vert. A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples.
BMC Bioinformatics, i16:262, 2015.
[Code]
K. Vervier, P. Mahé, J.-B. Veyrieras and J.-P. Vert. Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data.
Technical report HAL-01151889, June 2015.
Y. Jiao and J.-P. Vert. The Kendall and Mallows Kernels for Permutations.
Proceedings of the 32nd International Conference on Machine Learning, JMLR: W&CP 37, 1935-1944, 2015.
N. Varoquaux, I. Liachko, F. Ay, J. Burton, J. Shendure, M. Dunham, J.-P. Vert and W. S. Noble. Accurate identification of centromere locations in yeast genomes using Hi-C.
Nucleic Acids Research, 43(11):5331-5339, 2015.
[Supplementary information]
A. Schoenauer Sebag, S. Plancade, C. Raulet-Tomkiewicz, R. Barouki, J.-P. Vert and T. Walter. A generic methodological framework for studying single cell motility in high-throughput time-lapse data.
Bioinformatics, 31(12):i320-i328, 2015.
E. Scornet, G. Biau and J.-P. Vert. Consistency of random forests.
Annals of Statistics, 43(4):1716-1741, 2015.
[link]
A. Schoenauer Sebag, S. Plancade, C. Raulet-Tomkiewicz, R. Barouki, J.-P. Vert and T. Walter. Inferring an ontology of single cell motions from high-throughput microscopy data.
Proceedings of the 2015 IEEE 12th International Symposium on Biomedical Imaging, 160-163, 2015.
[link]
F. Ay, T. H. Vu, M. J. Zeitz, N. Varoquaux, J. E. Carette, J.-P. Vert, A. R. Hoffman and W. S. Noble. Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C.
BMC Genomics, 16:121, 2015.
F. Ay, E. Bunnik, N. Varoquaux, J.-P. Vert, W. S. Noble and K. Le Roch. Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum.
BioEssays, 37(2):182-194, 2015.
[link]

2014

E. Richard, G. Obozinski and J.-P. Vert. Tight convex relaxations for sparse matrix factorization.
In Z. Ghahramani, M. Welling, C. Cortes, N.D. Lawrence and K.Q. Weinberger (Eds.), Advances in Neural Information Processing Systems (NIPS) 27, 3284-3292, 2014.
[Technical report]
M. Moarii, A. Pinheiro, B. Sigal-Zafrani, A. Fourquet, M. Caly, N. Servant, V. Stoven J.-P. Vert and F. Reyal. Epigenomic alterations in breast carcinoma from primary tumor to locoregional recurrences.
PLoS ONE, 9(8):e103986, 2014.
J. C. Costello, L. M. Heiser, E. Georgii, M. Gönen, M. P Menden, N. J Wang, M. Bansal, M. Ammad-ud-din, P. Hintsanen, S. A Khan, J.-P. Mpindi, O. Kallioniemi, A. Honkela, T. Aittokallio, K. Wennerberg, NCI DREAM Community, J. J. Collins, D. Gallahan, D. Singer, J. Saez-Rodriguez, S. Kaski, J. W. Gray and G. Stolovitzky. A community effort to assess and improve drug sensitivity prediction algorithms.
Nature Biotechnology, 32:1202-1212, 2014.
[link]
K. Vervier, P. Mahe, A. d'Aspremont, J.-B. Veyrieras and J.-P. Vert. On learning matrices with orthogonal columns or disjoint supports.
In T. Calder et al. (Eds): ECML PKDD 2014, Part III, LNCS 8726, 274-289, Springer-Verlag Berlin Heidelberg, 2014.
[link][preprint]
E. Bernard, L. Jacob, J. Mairal and J.-P. Vert. Efficient RNA isoform identification and quantification from RNA-seq data with network flows.
Bioinformatics, 30(17):2447-2455, 2014.
[Code]
F. Ay, E. M. Bunnik, N. Varoquaux, S. M. Bol, J. Prudhomme, J.-P. Vert, W. S. Noble and K. G. Le Roch. Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.
Genome Research, 24:974-988, 2014.
[link][Supplementary material]
C. Tourette, F. Farina, R. P. Vazquez-Manrique, A.-M. Orfila, S. Hernandez, N. Offner, J. A. Parker, S. Menet, J. Kim, J. Lyu, S. H. Choi, K. Cormier, C. K. Edgerly, O. L. Bordiuk, K. Smith, A. Louise, M. Halford, S. Stacker, J.-P. Vert, R. J. Ferrante, W. Lu and C. Neri, "Increase in the Wnt receptor Ryk promotes the early stage decline of mutant polyglutamine neurons by repressing FOXO protective activity",
PLOS Biology, 12(6):e1001895, 2014.
E. Pauwels, C. Lajaunie and J.-P. Vert, "A Bayesian active learning strategy for sequential experimental design in systems biology",
BMC Systems Biology, 8:102, 2014.
[Tech report][Supplementary material]
N. Varoquaux, F. Ay, W. S. Noble and J.-P. Vert, "A statistical approach for inferring the three-dimensional structure of the genome",
Bioinformatics, 30(12):i26-i33, 2014.
[Supplementary material]
T. D. Hocking, V. Boeva, G. Rigaill, G. Schleiermacher, I. Janoueix-Lerosey, O. Delattre, W. Richer, F. Bourdeaut, M. Suguro, M. Seto, F. Bach and J.-P. Vert, "SegAnnDB: interactive web-based genomic segmentation",
Bioinformatics, 30(11):1539-1546, 2014.
J.-L. Plouhinec, D. D. Roche, C. Pegoraro, A.-L. Figueiredo, F. Maczkowiak, L. J. Brunet, M. Cecile, J.-P. Vert, N. Pollet, R. M. Harland and A.-H. Monsoro-Burq, "Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers",
Developmental Biology, 386(2):461-472, 2014.
[link]
F. Mordelet and J.-P. Vert, "A bagging SVM to learn from positive and unlabeled examples",
Pattern Recognition Letters, 37:201-209, 2014.
[link][preprint]

2013

Y. Zhao, T. Tamura, T. Akutsu and J-P. Vert, "Flux balance impact degree: A new definition of impact degree to properly treat reversible reactions in metabolic networks",
Bioinformatics, 29(17):2178-2185, 2013.
[Supplementary information]
T. D. Hocking, G. Schleiermacher, I. Janoueix-Lerosey, V. Boeva, J. Cappo, O. Delattre, F. Bach and J.-P. Vert, "Learning smoothing models of copy number profiles using breakpoint annotations",
BMC Bioinformatics, 14:164, 2013.
[R code and data][Python annotation GUI]
E. Richard, F. Bach and J.-P. Vert, "Intersecting singularities for multi-structured estimation",
In S. Dasgupta and D. McAllester (Eds.), Proceedings of the 30th International Conference on Machine Learning, JMLR W&CP 28(3):1157-1165, 2013.
G. Rigaill, T. D. Hocking, F. Bach and J.-P. Vert, "Learning sparse penalties for change-point detection using max margin interval regression",
In S. Dasgupta and D. McAllester (Eds.), Proceedings of the 30th International Conference on Machine Learning, JMLR W&CP 28(3):172-180, 2013.
E. Bernard, L. Jacob, J. Mairal and J.-P. Vert, "Efficient RNA isoform identification and quantification from RNA-seq data with network flows",
Technical report HAL-00803134, March 2013.
[link]
J.-P. Vert, "Les applications industrielles de la bio-informatique",
Annales des Mines - Realites industrielles, Feb 2013 issue, 17-23, 2013.
[preprint]
F. Mordelet and J.-P. Vert, "Supervised inference of gene regulatory networks from positive and unlabeled examples",
In H. Mamitsuka, C. DeLisi and M. Kanehisa (Eds), Data Mining for Systems Biology, Methods in Molecular Biology 939, Humana Press, p.47-58, 2013.
[link]

2012

A.-C. Haury, F. Mordelet, P. Vera-Licona and J.-P. Vert, "TIGRESS: Trustful Inference of Gene REgulation using Stability Selection"
BMC Systems Biology, 6:145, 2012.
O. Filhol, D. Ciais, C. Lajaunie, P. Charbonnier, N. Foveau, J.-P. Vert and Y. Vandenbrouck. "DSIR: Assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes"
PLOS ONE, 7(10):e48057, 2012.
D. Marbach, J.C. Costello, R. Kuffner, N. Vega, R.J. Prill, D.M. Camacho, K.R. Allison, the DREAM5 Consortium, M. Kellis, J.J. Collins, G. Stolovitzky, "Wisdom of crowds for robust gene network inference"
Nature Methods, 9, 796-804, 2012.
[link]
C. Houdayer, V. Caux-Moncoutier, S. Krieger, M. Barrois, F. Bonnet, V. Bourdon, M. Bronner, M. Buisson, F. Coulet, P. Gaildrat, C. Lefol, M. LÃ©one, S. Mazoyer, D. Muller, A. Remenieras, F. RÃ©villion, E. Rouleau, J. Sokolowska, J.-P. Vert, R. Lidereau, F. Soubrier, H. Sobol, N. Sevenet, B. Bressac de Paillerets, A. Hardouin, M. Tosi, O.M. Sinilnikova and D. Stoppa-Lyonnet, "Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico / in vitro studies on BRCA1 and BRCA2 variants"
Human Mutation, 33(8):1228-1238, 2012.
[link]
F. Lejeune, L. Mesrob, F. Parmentier, C. Bicep, R. Vazquez, A. Parker, J.-P. Vert, C. Tourette and C. Neri, "Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons"
BMC Genomics, 13:91, 2012.
K. Takemoto, T. Tamura, Y. Cong, W.-K. Ching, J.-P. Vert and T. Akutsu, "Analysis of the impact degree distribution in metabolic networks using branching process approximation",
Physica A, 391(1-2):379-387, 2012.
[html]

2011

A.-C. Haury, P. Gestraud and J.-P. Vert, "The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures",
PLOS ONE, 6(12):e28210, 2011.
[code]
F. Mordelet and J.-P. Vert, "ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples",
BMC Bioinformatics, 12:389, 2011.
[code]
G. Obozinski, L. Jacob and J.-P. Vert, "Group Lasso with Overlaps: the Latent Group Lasso approach",
Technical report HAL:inria-00628498, October, 2011.
[html]
K. Bleakley and J.-P. Vert, "The group fused Lasso for multiple change-point detection",
Technical report HAL-00602121, June, 2011.
[html][MATLAB code][Python code]
T. Matsui, M. Goto, J.-P. Vert and Y. Uchiyama, "Gradient-based musical feature extraction based on scale-invariant feature transform"
In Proceedings of the 19th European Signal Processing Conference (EUSIPCO 2011)., p.724-728, 2011.
T. Hocking, A. Joulin, F. Bach and J.-P. Vert, "Clusterpath An Algorithm for Clustering using Convex Fusion Penalties",
In L. Getoor and T. Scheffer (Eds.), Proceddings of the 28th International Conference on Machine Learning (ICML'11), p.745-752, 2011
[code]
V. Boeva, A. Zinovyev, K. Bleakley, J.-P. Vert, I. Janoueix-Lerosey, O. Delattre and E. Barillot, "Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization"
Bioinformatics, 27(2):267-268, 2011.
[code]

2010

J.-P. Vert and K. Bleakley, "Fast detection of multiple change-points shared by many signals using group LARS",
In J. Lafferty, C. K. I. Williams, J. Shawe-Taylor, R.S. Zemel and A. Culotta (Eds), Advances in Neural Information Processing Systems 23 (NIPS), p.2343-2351, 2010.
[paper][supplementary informations][poster]
F. Mordelet and J.-P. Vert, "A bagging SVM to learn from positive and unlabeled examples",
Technical report HAL-00523336, October, 2010.
[html]
J.-P. Vert, "3D ligand-based virtual screening with support vector machines",
In H. Lodhi and Y. Yamanishi (Eds.), Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques, IGI Global, p.35-45, 2010.
M. Zaslavskiy, F. Bach and J.-P. Vert, "Many-to-many graph matching: a continuous relaxation approach",
In J. Balcazar, F. Bonchi, A. Gionis and M. Sebag (Eds.), Machine Learning and Knowledge Discovery in Databases (ECML), LNCS 6323, Springer, p.515-530, 2010.
[paper][tech report][supplementary]
M. Hue and J.-P. Vert, "On learning with kernels for unordered pairs",
In J. Furnkranz and T. Joachims (Eds.), Proceedings of the 27th International Conference on Machine Learning (ICML), p.463-470, 2010.
J.-P. Vert, "Reconstruction of biological networks by supervised machine learning approaches",
in H. Lodhi and S. Muggleton (Eds.), Elements of Computational Systems Biology, Wiley, p.189-212, 2010.
[Tech report]
M. Hue, M. Riffle, J.-P. Vert and W. S. Noble, "Large-scale prediction of protein-protein interactions from structures",
BMC Bioinformatics. 11:144, 2010.
[Supplementary material]
B. Hoffmann, M. Zaslavskiy, J.-P. Vert and V. Stoven, "A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction",
BMC Bioinformatics, 11:99, 2010.
[Supplementary material]
A.-C. Haury, L. Jacob and J.-P. Vert, "Increasing stability and interpretability of gene expression signatures",
Technical report HAL-00448395, January, 2010.
[html]

2009

M. Cuturi, J.-P. Vert and A. d'Aspremont, "White Functionals for Anomaly Detection in Dynamical Systems",
In Y. Bengio, D. Schuurmans, J. Lafferty, C.K.I. Williams and A. Culotta (Eds), Advances in Neural Information Processing Systems 22 (NIPS), p.432-440, 2009
K. Bleakley and J.-P. Vert, "Joint segmentation of many aCGH profiles using fast group LARS",
Technical report HAL-00422430, October, 2009.
[html]
M. Zaslavskiy, F. Bach and J.-P. Vert, "A path following algorithm for the graph matching problem",
IEEE Transactions on Pattern Analysis and Machine Intelligence, 31(12):2227-2242, 2009.
[link][preprint][supplementary]
J.-P. Vert, T. Matsui, S. Satoh and Y. Uchiyama, "High-level feature extraction using SVM with walk-based graph kernel",
In Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2009), p.1121-1124, 2009.
[link][preprint]
L. Jacob, G. Obozinski and J.-P. Vert, "Group Lasso with Overlaps and Graph Lasso",
in L. Bottou and M. Littman, (Ed.), Proceedings of the 26th Annual International Conference on Machine Learning (ICML), 433-440, 2009.

Supplementary material

P. Mahé and J.-P. Vert, "Virtual screening with support vector machines and structure kernels",
Combinatorial Chemistry & High Throughput Screening, 12(4):409-423, 2009.
[link][Technical report]
M. Zaslavskiy, F. Bach and J.-P. Vert, "Global alignment of protein-protein interaction networks by graph matching methods",
Bioinformatics, 25(12):i259-1267, 2009.
[Supplementary material]
L. Jacob, F. Bach and J.-P. Vert, "Clustered Multi-Task Learning: A Convex Formulation",
In D. Koller, D. Schuurmans, Y. Bengio and L. Bottou (Ed.), Advances in Neural Information Processing Systems 21 (NIPS), 745-752, 2009.
[Supplementary]
J. Abernethy, F. Bach, T. Evgeniou and J.-P. Vert, "A new approach to collaborative filtering: operator estimation with spectral regularization",
Journal of Machine Learning Research, 10:803-826, 2009.
P. Mahé and J.-P. Vert, "Graph kernels based on tree patterns for molecules",
Machine Learning, 75(1):3-35, 2009.

2008

L. Jacob and J.-P. Vert, "Protein-ligand interaction prediction: an improved chemogenomics approach",
Bioinformatics, 24(19):2149-2156, 2008
L. Jacob, B. Hoffmann, V. Stoven and J.-P. Vert, "Virtual screening of GPCRs: an in silico chemogenomics approach",
BMC Bioinformatics, 9:363, 2008.
[Supplementary]
J.-P. Vert and L. Jacob, "Machine learning for in silico virtual screening and chemical genomics: new strategies",
Combinatorial Chemistry & High Throughput Screening, 11(8):677-685, 2008.
F. Mordelet and J.-P. Vert, "SIRENE: Supervised Inference of REgulatory NEtworks",
Bioinformatics, vol. 24, n.16, p.i76-i82, 2008.
[Supplementary]
M. Zaslavskiy, F. Bach and J.-P. Vert, "A path following algorithm for graph matching",
Proceedings of the 3rd International Conference on Image and Signal Processing (ICISP 2008), LNCS 5099, p.329-337, 2008.
[html]
J.-P. Vert, "The optimal assignment kernel is not positive definite",
Technical Report HAL-00218278, January, 2008.
[html]
F. Rapaport, E. Barillot and J.-P. Vert, "Classification of arrayCGH data using fused SVM",
Bioinformatics vol.24, n.13, p.i375-i382, 2008.
[Supplementary data]
J. Abernethy, T. Evgeniou, O. Toubia, and J.-P. Vert, "Eliciting Consumer Preferences using Robust Adaptive Choice Questionnaires",
IEEE Transactions on Knowledge and Data Engineering, vol. 20, n.2, p.145-155, 2008.
[link][old tech report]
L. Jacob and J.-P. Vert, "Efficient peptide-MHC-I binding prediction for alleles with few known binders",
Bioinformatics, vol.24, n.3, p.358-366, 2008.
[link][application][Old tech report]

2007

J.-P. Vert, J. Qiu and W. S. Noble, "A new pairwise kernel for biological network inference with support vector machines",
BMC Bioinformatics, 8(Suppl 10):S8, 2007.
K. Bleakley, G. Biau and J.-P. Vert, "Supervised Reconstruction of Biological Networks with Local Models",
Bioinformatics, vol.23, n.13, p.i57-i65, 2007.
[Supplementary informations]
M. Cuturi, J.-P. Vert, O. Birkenes and T. Matsui, "A kernel for time series based on global alignments",
Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2007) , Vol.2, p.II-413-II-416, 2007.
[link][Tech report][pdf][code]
Y. Yamanishi, F. Bach and J.-P. Vert, "Glycan classification with tree kernels",
Bioinformatics, vol.23, n.10, p.1211-1216, 2007.
[link][supplementary material]
J. Qiu, M. Hue, A. Ben-Hur, J.-P. Vert and W. S. Noble, "A structural alignment kernel for protein structures",
Bioinformatics, vol.23, n.9, p.1090-1098, 2007.
[link][supplementary information]
J.-P. Vert, "Kernel methods in genomics and computational biology",
in Camps-Valls, G., Rojo-Alvarez, J.-L. and Martinez-Ramon, M. (Eds.), Kernel Methods in Bioengineering, Signal and Image Processing, p.42-63, Idea Group, 2007.
[tech report]
Y. Yamanishi and J.-P. Vert, "Kernel matrix regression",
Proceedings of the 12th International Conference on Applied Stochastic Models and Data Analysis (ASMDA 2007), 2007.
[tech report]
F. Rapaport, A. Zinovyev, M. Dutreix, E. Barillot and J.-P. Vert, "Classification of microarray data using gene networks",
BMC Bioinformatics, 8:35, 2007.

2006

Y. Yamanishi and J.-P. Vert, "Estimating Protein Network from Multiple Genomic Data by Kernel Methods"
Proceedings for the Institute of Satistical Mathematics, 54(2):357-373, 2006.
[pdf]
J. Abernethy, F. Bach, T. Evgeniou and J.-P. Vert, "Low-rank matrix factorization with attributes",
Technical report N24/06/MM, Ecole des Mines de Paris, 2006.
[html]
J.-P. Vert, N. Foveau, C. Lajaunie and Y. Vandenbrouck, "An accurate and interpretable model for siRNA efficacy prediction",
BMC Bioinformatics, 7:520, 2006.
[web site]
J.-P. Vert, "Classification of biological sequences with kernel methods",
in Sakakibara et al. (Eds.), Proceedings of the 8th International Colloquium on Grammatical Inference (ICGI 2006), LNAI 4201, p.7-18, Springer Verlag, 2006.
[pdf][link]
P. Mahé, L. Ralaivola, V. Stoven and J.-P. Vert, "The pharmacophore kernel for virtual screening with support vector machines",
Journal of Chemical Information and Modeling, vol. 46, n.5, p.2003-2014, 2006.
[pdf][link][Technical report]
F. Rapaport, A. Zinovyev, E. Barillot and J.-P. Vert, "Spectral analysis of gene expression profiles using gene networks",
Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2006), vol.3, p.91-95, 2006.
[pdf]
R. Vert and J.-P. Vert, "Consistency and convergence rates of one-class SVMs and related algorithms",
Journal of Machine Learning Research, vol. 7, p.817-854, 2006.
[http][pdf]
H. Saigo, J.-P. Vert and T. Akutsu, "Optimizing amino acid substitution matrices with a local alignment kernel",
BMC Bioinformatics, 7:246, 2006.
J.-P. Vert, R. Thurman and W. S. Noble, "Kernels for gene regulatory regions",
Advances in Neural Information Processing Systems 18 (NIPS 2005), Y. Weiss, B. Schölkopf and J. Platt (Eds.), p.1401-1408, MIT Press, Cambridge, MA, 2006.
[pdf]
R. Vert and J.-P. Vert, "Consistency and convergence rates of one-class SVM and related algorithms" (short version),
Advances in Neural Information Processing Systems 18 (NIPS 2005), Y. Weiss, B. Schölkopf and J. Platt (Eds.), p.1409-1416, MIT Press, Cambridge, MA, 2006.
[pdf]

2005

S. Matsuda, J.-P. Vert, H. Saigo, N. Ueda, H. Toh, and T. Akutsu, "A novel representation of protein sequences for prediction of subcellular location using support vector machines",
Protein Science, vol.14, p.2804-2813, 2005.
[html][server]
Y. Yamanishi, J.-P. Vert and M. Kanehisa, "Supervised enzyme network inference from the integration of genomic data and chemical information",
Bioinformatics, vol. 21, p. i468-i477, 2005.
(Proceedings of ISMB 2005).
[html][pdf]
P. Mahé, N. Ueda, T. Akutsu, J.-L. Perret and J.-P. Vert, "Graph kernels for molecular structure-activity relationship analysis with support vector machines",
Journal of Chemical Information and Modeling, vol. 45, n. 4, 939 -951, 2005.
[html][pdf]
M. Cuturi and J.-P. Vert, "The Context-tree Kernel for Strings",
Neural Networks, vol.18, n.4, p.1111-1123, 2005.
[html][pdf]
M. Cuturi, K. Fukumizu and J.-P. Vert, "Semigroup kernels on measures",
Journal of Machine Learning Research, vol. 6, p. 1169-1198, 2005.
[http][pdf]
M. Cuturi and J.-P. Vert, "Semigroup kernels on finite sets",
Advances in Neural Information Processing Systems 17 (NIPS 2004), Lawrence K. Saul and Yair Weiss and Léon Bottou (Eds.), p.329-336, MIT Press, Cambridge, MA, 2005.
[ps.gz, pdf]
J.-P. Vert and Y. Yamanishi, "Supervised graph inference",
Advances in Neural Information Processing Systems 17 (NIPS 2004), Lawrence K. Saul and Yair Weiss and Léon Bottou (Eds.), p.1433-1440, MIT Press, Cambridge, MA, 2005.
[pdf]

2004

J.-P. Vert, "Kernel Methods in Computational Biology",
Habilitation's thesis, University Paris 6, 2004.
[pdf]
P. Mahé, N. Ueda, T. Akutsu, J.-L. Perret and J.-P. Vert, "Extensions of marginalized graph kernels",
Proceedings of the Twenty-First International Conference on Machine Learning (ICML 2004), R. Greiner and D. Schuurmans (Eds.), p.552-559, ACM Press, 2004..
[abstract][ps.gz][pdf][slides]
M. Cuturi, J.-P. Vert, "A mutual information kernel for strings",
Proceedings of the International Joint Conference on Neural Networks (IJCNN'04), p.1905-1910, 2004.
[pdf]
Y. Yamanishi, J.-P. Vert and M. Kanehisa, "Protein network inference from multiple genomic data: a supervised approach",
Bioinformatics, vol.20, p.i363-i370, 2004.
(Proceedings of ISMB 2004).
[abstract][pdf][local pdf][web supplement]
B. Schölkopf, K. Tsuda and J.-P. Vert (Eds.), "Kernel Methods in Computational Biology",
MIT Press, 2004.
[MIT Press]
- J.-P. Vert, K. Tsuda and B. Schölkopf, "A primer on kernel methods",
  in Kernel Methods in Computational Biology, B. Schölkopf, K. Tsuda and J.-P. Vert (Eds.), MIT Press, p.35-70, 2004.
  [pdf]
- J.-P. Vert, H. Saigo, T. Akutsu, "Local alignment kernels for biological sequences",
  in Kernel Methods in Computational Biology, B. Schölkopf, K. Tsuda and J.-P. Vert (Eds.), MIT Press, p.131-154, 2004.
  [pdf]
- R. Kondor and J.-P. Vert, "Diffusion kernels",
  in Kernel Methods in Computational Biology, B. Schölkopf, K. Tsuda and J.-P. Vert (Eds.), MIT Press, p.171-192, 2004.
  [pdf]
- Y. Yamanishi, J.-P. Vert and M. Kanehisa, "Heterogeneous data comparison and gene selection with kernel canonical correlation analysis",
  in Kernel Methods in Computational Biology, B. Schölkopf, K. Tsuda and J.-P. Vert (Eds.), MIT Press, p.209-230, 2004.
  [pdf]
H. Saigo, J.-P. Vert, T. Akutsu and N. Ueda, "Protein homology detection using string alignment kernels",
Bioinformatics, vol.20, p.1682-1689, 2004.
[local pdf][abstract][pdf][Supplementary data]

2003

J.-P. Vert and M. Kanehisa, "Extracting active pathways from gene expression data",
Bioinformatics, vol. 19, p. 238ii-244ii, 2003.
(Proceedings of ECCB 2003).
[local pdf][abstract][pdf]
Y. Yamanishi, J.-P. Vert, A. Nakaya and M. Kanehisa, "Extraction of Correlated Gene Clusters from Multiple Genomic Data by Generalized Kernel Canonical Correlation Analysis",
Bioinformatics, vol. 19, p. 323i-330i, 2003.
(Proceedings of ISMB 2003).
[ps.gz][pdf]
J.-P. Vert and M. Kanehisa, "Graph-driven features extraction from microarray data using diffusion kernels and kernel CCA",
Advances in Neural Information Processing Systems 15 (NIPS 2002), Suzanna Becker, Sebastian Thrun and Klaus Obermayer (Eds), p. 1425-1432, MIT Press, Cambridge, MA, 2003.
[paper][poster]

2002

H. Saigo, J.-P. Vert, T. Akutsu and N. Ueda, "Comparison of SVM-based methods for remote homology detection",
Genome Informatics, vol.13, p.396-397, 2004.
[pdf]
J.-P. Vert and M. Kanehisa, "Graph-driven features extraction from microarray data",
Preprint arXiv physics/0206055, June 2002.
[ps.gz][pdf]
J.-P. Vert, "A tree kernel to analyze phylogenetic profiles"
Bioinformatics, vol. 18, p. S276-S284, 2002.
(Proceedings of ISMB 2002).
[pdf][web supplement]
K. Nakai and J.-P. Vert, "Genome informatics for data-driven biology: A report on the twelfth international conference on genome informatics, Tokyo, Japan, December 17-19, 2001"
Genome Biology, 3(4):reports 4010.1-4010.3, 2002.
[pdf][Online]
J.-P. Vert, "Support vector machine prediction of signal peptide cleavage site using a new class of kernels for strings"
Proceedings of the Pacific Symposium on Biocomputing 2002, Altman, R.B., Dunker, A.K., Hunter, L., Lauerdale, K. and Klein, T.E., (Ed.), World Scientific, pp. 649-660, 2002.
[ps.gz][pdf][web supplement]

2001 and before

J.-P. Vert, "Adaptive context trees and text clustering"
IEEE Transactions on Information Theory, vol. 47, no. 5, pp. 1884-1901, July 2001
[pdf]
J.-P. Vert, "Statistical Methods for Natural Language Modelling"
PhD thesis, University Paris 6, March 2001
[ps.gz][pdf]
J.-P. Vert, "Text categorization using adaptive context trees"
Proceedings of the CICLing-2001 conference, A. Gelbukh (Ed.), LNCS 2004, Springer-Verlag Berlin Heidelberg, pp. 423-436, 2001.
[ps.gz][ pdf]
J.-P. Vert, "Double mixture and universal inference"
Technical report DMA-00-15, Ecole normale superieure, May 2000, pp. 1-27.
[ps.gz][pdf]
M. Chevrel, J.-P. Vert, "Le consensuisse"
Annales des Mines, Realites Industrielles, Feb. 1999, pp. 41-45.
[html]
J.-P. Vert, "Research in written langage processing in Japan"
MBA thesis, Corps des mines, Paris, 1998.
[ps.gz][pdf][html]
J.-P. Vert, "Panorama de la recherche en traitement automatique du langage ecrit au Japon"(in French)
MBA thesis, Corps des mines, Paris, 1998.
[ps.gz][pdf][html]

Posters / Other

J.-P. Vert, "Extracting active metabolic pathways from gene expression data using kernel CCA"
Long abstract of a talk given at the Conference Statistical Learning, Theory and Applications, CNAM, Paris, France, December 13-14, 2002.
[ps.gz][pdf]
Y. Igarashi, Y. Okuno, J.-P. Vert and M. Kanehisa, "Detecting transcriptional cis-regulation from gene expression data"
Poster presented at The Twelfth International Conference on Genome Informatics (GIW 2001), Tokyo, Japan, December 17-19, 2001.
[ps.gz][pdf]
J.-P. Vert, "Deriving kernels from probabilistic models on discrete objects"
Poster presented at the New Trends in Optimization and Computational Algorithms (NTOC2001) conference, Kyoto, Japan, December 9-13, 2001.
[ps.gz][pdf]
J.-P. Vert, "Mathematiques et post-genomique" (in French)
The abstract of a talk given at the Science and Technology conference of the French ambassy in Tokyo, November 19-20, 2001.
[ps.gz]

Last modified: Wed Oct 8 15:04:55 CEST 2008
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