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Computational Cancer Genomics

Bridging Computational Innovation and Cancer Biology

We investigate the genetic and epigenetic mechanisms driving cancer, developing computational methods—particularly machine learning and AI-driven—to analyze high-throughput sequencing data. Our work spans topics such as transcriptional remodeling, tumor microenvironment interaction, and chromatin architecture in cancer.

Selected Publications

Biological Insights

Filtering cells with high mitochondrial content depletes viable metabolically altered malignant cell populations in cancer single-cell studies, A. Kraft, J. Yates, V. Boeva. Genome Biology, 2025. Link.

Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma, J. Yates et al., V. Boeva*, E. Van Allen*. Accepted in Cell Reports Medicine, 2025. Link

DNA-methylation variability in normal mucosa: a field cancerization marker in patients with adenomatous polyps, J. Yates et al., V. Boeva. JNCI, 2024. Link.

DNA hypermethylation driven by DNMT1 and DNMT3A favors tumor immune escape contributing to the aggressiveness of adrenocortical carcinoma, G. Kerdivel et al., V. Boeva. Clinical Epigenetics, 2023. Link.

Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype (CIMP): a pan-cancer analysis J. Yates and V. Boeva. Briefings in Bioinformatics, 2022. Link.

HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia S. Gregoricchio et al., V. Boeva* and C. Guillouf*. Nucleic Acids Research, 2022, Link.

Computational Methods

Histopathological Image Classification with Cell Morphology Aware Deep Neural Networks. A. Ignatov, J. Yates, V. Boeva. CVMI proceedings of CVPR, 2024. Link.

Feature Clock: High-Dimensional Effects in Two-Dimensional Plots. O. Ovcharenko, R. Sevastjanova & V. Boeva. Proceedings of IEEE VIS, 2024. Link.

Sparsesurv: a Python package for fitting sparse survival models via knowledge distillation, D. Wissel et al., V. Boeva. Bioinformatics, 2024. Link.

Systematic comparison of multi-omics survival models reveals a widespread lack of noise resistance, D. Wissel, D. Rowson, V. Boeva. Cell Reports Methods, 2023. Link.

CHIPIN: ChIP-seq Inter-sample Normalization based on signal invariance across transcriptionally constant genes. L. Polit et al., and V. Boeva. BMC Bioinformatics, 2021. Link

QuantumClone: Clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. P. Deveauet al., and V. Boeva. Bioinformatics. 2018. Link

HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. H. Ashoor et al., and V. Boeva. Nucleic Acids Research, 2017. Link

Full List of Publications

Click to expand each year's publications. Entries include full citations and direct links to journal articles.

Publications 2025
  • Filtering cells with high mitochondrial content depletes viable metabolically altered malignant cell populations in cancer single-cell studies, A. Kraft, J. Yates, V. Boeva. Genome Biology, 2025, 26:91. Link to the paper.
  • Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection, A. Kraft, M.B. Kirschner, V. Orlowski, M. Ronner, C. Bodmer, V. Boeva, I. Opitz, M. Meerang. BMC Cancer, 2025, 25:212. Link to the paper.
  • New horizons at the interface of artificial intelligence and translational cancer research, J. Yates and E. Van Allen. Cancer Cell, 2025, 43(4): 708-727. Link to the paper.
  • Mitochondrial transfer from cancer cells induces cancer-associated fibroblast differentiation. M. Cangkrama, H. Liu, X. Wu, J. Whipman, J. Yates, C. Gabelein, M. Matsushita, L. Ferrarese, S. Sander, F. Castro-Giner, S. Asawa, M. Sznurkowska, M. Kopf, J. Dengjel, V. Boeva, N. Aceto, J. Vorholt, S. Werner. Accepted for publication in Nature Cancer.
  • Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma, J. Yates, C. Mathey-Andrews, J. Park, A. Garza, A. Gagné, S. Hoffman, K. Bi, B. Titchen, C. Hennessey, J. Remland, E. Shannon, S. Camp, S. Balamurali, S.K. Cavale, Z. Li, A.K. Raghawan, A. Kraft, G. Boland, A.J. Aguirre, N.S. Sethi, V. Boeva, E. Van Allen. Accepted for publication in Cell Reports Medicine. Link to the paper

Publications 2024
  • DNA-methylation variability in normal mucosa: a field cancerization marker in patients with adenomatous polyps. J. Yates, H. Schaufelberger, R. Steinacher, P. Schaer, K. Truninger, V. Boeva. Journal of National Cancer Institute, 2024. DOI:https://doi.org/10.1093/jnci/djae016. Link to the paper.
  • Sparsesurv: a Python package for fitting sparse survival models via knowledge distillation. D. Wissel, N. Janakarajan, J. Schulte, D. Rowson, X. Yuan, V. Boeva. Bioinformatics, 2024, 40(9):btae521. Link to the paper.
  • A Database Tool Integrating Genomic and Pharmacologic Data from Adrenocortical Carcinoma (ACC) Cell Lines, PDX, and Patient Samples. Y. Arakawa, F. Elloumi, S. Varma, P. Khandagale, U. Jo, S. Kumar, N. Roper, W. Reinhold, R. Robey, N. Takebe, M. Gottesman, C. Thomas, V. Boeva, A. Berruti, A. Abate, M. Tamburello, S. Sigala, C. Hantel, I. Weigand, M.E. Wierman, K. Kiseljak-Vassiliades, J. Del Rivero, Y. Pommier. Cancer Research Communications, 2024. 4(9):2384-2398. Link to the paper.
  • Histopathological Image Classification with Cell Morphology Aware Deep Neural Networks. A. Ignatov, J. Yates, V. Boeva. Proceedings of The 9th IEEE Workshop on Computer Vision for Microscopy Image Analysis (CVMI) of CVPR 2024. 2024. Link to the paper.
  • Feature Clock: High-Dimensional Effects in Two-Dimensional Plots. O. Ovcharenko, R. Sevastjanova & V. Boeva. Proceedings of IEEE VIS 2024. 2024. Link to the paper.
  • scTree: Discovering Cellular Hierarchies in the Presence of Batch Effects in scRNA-seq Data. M. Vandenhirtz, F. Barkmann, L. Manduchi, J.E. Vogt, V. Boeva. Proceedings of ICML 2024 Workshop on structured probabilistic inference and generative modeling (SPIGM) & the ICML 2024 Workshop on Accessible and Efficient Foundation Models for Biological Discovery (AccMLBio). 2024. Link to the paper.

Publications 2023
  • Systematic comparison of multi-omics survival models reveals a widespread lack of noise resistance. D. Wissel, D. Rowson, V. Boeva. Cell Reports Methods, 2023. DOI:https://doi.org/10.1016/j.crmeth.2023.100461. Link to the paper.
  • Reversible transitions between noradrenergic and mesenchymal tumor identities define cell plasticity in neuroblastoma. C. Thirant, A. Peltier, S. Durand, A. Kramdi, C. Louis-Brennetot, C. Pierre-Eugene, A. Costa, A. Grelier, S. Zaidi, N. Gruel, I. Jimenez, E. Lapouble, G. Pierron, H.J. Brisse, A. Gauthier, P. Freneaux, S. Grossetete-Lalami, L.G. Baudrin, V. Raynal, S. Baulande, A. Bellini, J. Bhalshankar, A.M. Carcaboso, B. Geoerger, H. Rohrer, D. Surdez, V. Boeva, G. Schleiermacher, O. Delattre, I. Janoueix-Lerosey Nature Communications, 2023, 14(1):2575. Link to the paper.
  • scROSHI: robust supervised hierarchical identification of single cells. M. Prummer, A. Bertolini, L. Bosshard, F. Barkmann, J. Yates, V. Boeva, The Tumor Profiler Consortium, D. Stekhoven, F. Singer. NAR Genomics and Bioinformatics, 2023. https://doi.org/10.1093/nargab/lqad058
  • DNA hypermethylation driven by DNMT1 and DNMT3A favors tumor immune escape contributing to the aggressiveness of adrenocortical carcinoma. G. Kerdivel, F. Amrouche, M.A. Calmejane, F. Carallis, J. Hamroune, C. Hantel, J. Bertherat, G. Assie, V. Boeva, Clinical Epigenetics, 2023. 15(1):121. Link to the paper. .

Publications 2022
  • Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype (CIMP): a pan-cancer analysis J. Yates and V. Boeva. Briefings in Bioinformatics, 2022. 23(2):bbab610. Link to the paper.
  • HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia S. Gregoricchio, L. Polit, M. Esposito, J. Berthelet, L. Delestre, E. Evanno, M. Diop, I. Gallais, H. Aleth, M. Poplineau, W. Zwart, F. Rosenbauer, F. Rodrigues Lima, E. Duprez, V. Boeva and C. Guillouf. Nucleic Acids Research, 2022, 12;50(14):7938-7958. doi: 10.1093/nar/gkac613. Link to the paper.

Publications 2021
  • Exploring pathway-based group lasso for cancer survival analysis: a special case of multi-task learning G. Malenova, D. Rowson and V. Boeva. Frontiers in Genetics. 2021. 12:771301. doi: 10.3389/fgene.2021.771301 Link to the paper.
  • CHIPIN: ChIP-seq Inter-sample Normalization based on signal invariance across transcriptionally constant genes. 2021 L. Polit, G. Kerdivel, S. Gregoricchio, M. Esposito, C. Guillouf and V. Boeva. BMC Bioinformatics. 2021. 22(1):407. doi: 10.1186/s12859-021-04320-3. Link to the paper
  • Targeted therapy of TERT-rearranged neuroblastoma with BET bromodomain inhibitor and proteasome inhibitor combination therapy. J. Chen, C. Nelson, M. Wong, A.E. Tee, P.Y. Liu, T. La, J.I. Fletcher, A. Kamili, C. Mayoh, C. Bartenhagen, T.N. Trahair, N. Xu, N. Jayatilleke, M. Wong-Erasmus, H. Peng, B. Atmadibrata, B.B. Cheung, Q. Lan, T.M. Bryan, P. Mestdagh, J. Vandesompele, V. Combaret, V. Boeva, J. Wang, I. Janoueix-Lerosey, M.J. Cowley, K.L. MacKenzie, A. Dolnikov, J. Li, P. Polly, G.M. Marshall, R.R. Redde, M.D. Norris, M. Haber, M. Fischer, X.D. Zhang, H.A. Pickett, and T. Liu. Clinical Cancer Research. 2021 (27) (5) 1438-1451.
  • Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) in Ewing sarcoma. G. Kerdivel & V. Boeva, book chapter for Methods in Molecular Biology, Springer, 2021;2226:265-284.

Publications 2020
  • CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells. A. Perez-Rathke, Q. Sun, B. Wang, V. Boeva, Z. Shao, J. Liang. Genome Biology 21 (1), 1-17. Link to the paper
  • Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single-cell resolution. M.M. Aynaud, O. Mirabeau, N. Gruel, S. Grossetete, V. Boeva, S. Durand, ..., and A. Zinovyev. Cell Reports 30 (6), 1767-1779. e6. Link to the paper

Publications 2018
  • Steroidogenic differentiation and PKA signalling are programmed by histone methyltransferase EZH2 in the adrenal cortex. M. Mathieu, C. Drelon, S. Rodriguez, H. Tabbal, A. Septier, T. Dumontet, C.Damon-Soubeyrand, A. Berthon, I. Sahut-Barnola, M. Batisse Lignier, J.C. Pointud, G. Kerdivel, M.A. Calmejane, V. Boeva, I. Tauveron, A.M. Lefran ois-Martinez, A. Martinez & P. Val. PNAS 2018 Dec 26;115(52):E12265-E12274. Link to the paper
  • Meta-mining of copy number profiles of high-risk neuroblastoma tumors. P. Depuydt, J. Koster, V. Boeva, T. Hocking, F. Speleman, G. Schleiermacher, and K. De Preter. Scientific Data. 2018 Oct 30;5:180240. Link to the paper
  • TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets. B. Decaesteker, G. Denecker, C. Van Neste, E. Dolman, M. Gartlgruber, C. Nunes, F. De Vloed, P. Depuydt, K. Verboom, D. Rombaut, S. Loontiens, J. De Wyn, B. Koopmans, A. Essing, C. Herrmann, D. Dreidax, K. Durinck, D. Deforce, F. Van Nieuwerburgh, A. Henssen, R. Versteeg, V. Boeva, G. Schleiermacher, J. van Nes, P. Mestdagh, S. Vanhauwaert, J. Schulte, F. Westermann, J. Molenaar, K. De Preter. Nature Communications. 2018 Nov 19;9(1):4866. Link to the paper
  • FUN-LDA - A latent Dirichlet allocation model for predicting tissue-specific functional effects of noncoding variation. D. Backenroth, Z. He, K. Kiryluk, V. Boeva, L. Pethukova, E. Khurana, A. Christiano, J. Buxbaum, I. Ionita-Laza. American Journal of Human Genetics. 2018. 102(5):920-942. Link to the paper
  • Genomic amplifications and distal 6q-loss: novel markers for poor survival in high-risk neuroblastoma patients. P. Depuydt, V. Boeva, T.D. Hocking, R. Cannoodt, I.M. Ambros, P.F. Ambros, S. Asgharzadeh, E.F. Attiyeh, V. Combaret, R. Defferrari, M. Fischer, B. Hero, M.D. Hogarty, M.S. Irwin, J. Koster, S. Kreissman, R. Ladenstein, E. Lapouble, G. Laureys, W.B. London, K. Mazzocco, A. Nakagawara, R. Noguera, M. Ohira, J.R. Park, U. P tschger, J. Theissen, G.P. Tonini, D. Valteau-Couanet, L. Varesio, R. Versteeg, F. Speleman, J.M. Maris, G. Schleiermacher, K. De Preter. Journal of the National Cancer Institute. 2018 Oct 1;110(10):1084-1093. PMID: 29514301 Link to the paper
  • QuantumClone: Clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. P. Deveau, L. Colmet Daage, D. Oldridge, V. Bernard, A. Bellini, M. Chicard, N. Clement, E. Lapouble, V. Combaret, A. Boland, V. Meyer, J.-F. Deleuze, I. Janoueix-Lerosey, E. Barillot, O. Delattre, J. Maris, G. Schleiermacher, and V. Boeva. Bioinformatics. 2018 Jan 12. doi: 10.1093/bioinformatics/bty016. [Epub ahead of print]. PMID: 29342233 Link to the paper
  • Activated ALK signals through the ERK-ETV5-RET pathway to drive neuroblastoma oncogenesis. L. Lopez-Delisle, C. Pierre-Eugene, C. Louis-Brennetot, D. Surdez, V. Raynal, S. Baulande, V. Boeva, S. Grossetete-Lalami, V. Combaret, M. Peuchmaur, O. Delattre, and I. Janoueix-Lerosey. Oncogene. 2018 Mar;37(11):1417-1429. doi: 10.1038/s41388-017-0039-5. PMID: 29321660 Link to the paper

Publications 2017
  • Lenalidomide-mediated erythroid improvement in non-del(5q) myelodysplastic syndromes is associated with bone marrow immuno-remodeling. G. Kerdivel, V. Chensais, E. Becht, A. Toma, N. Cagnard, F. Dumont, A. Rousseau, P. Fenaux, S. Chevret, V. Boeva, N. Chapuis, W.-H. Fridman, M. Fontenay, and O. Kosmider. Leukemia. 2017 Oct 3. doi: 10.1038/leu.2017.305. [Epub ahead of print]. PMID: 28972593
  • Calling chromosome alterations, DNA methylation statuses, and mutations in tumors by simple targeted next-generation sequencing: a solution for transferring integrated pangenomic studies into routine practice?. S. Garinet, M. Neou, B. de La Villeon, S. Faillot, J. Sakat, J.P. Da Fonseca, A. Jouinot, C. Le Tourneau, M. Kamal, W. Luscap-Rondof, V. Boeva, S. Gaujoux, M. Vidaud, E. Pasmant, F. Letourneur, J. Bertherat, G. Assie. 2017;19(5):776-787. doi: 10.1016/j.jmoldx.2017.06.005. PMID: 28826610 J Mol Diagn., 2017;19(5):776-787. doi: 10.1016/j.jmoldx.2017.06.005. PMID: 28826610
  • Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries. V. Boeva, C. Louis-Brennetot, A. Peltier, S. Durand, C. Pierre-Eugene, V. Raynal, H. Etchevers, S. Thomas, A. Lermine, E. Daudigeos-Dubus, B.Geoerger, M.F. Orth, T.G.P. Grunewald, E. Diaz, B. Ducos, D. Surdez, A.M. Carcaboso, I. Medvedeva, T. Deller, V. Combaret, E. Lapouble, G. Pierron, S. Grossetete-Lalami, S. Baulande, G. Schleiermacher, E. Barillot, H. Rohrer, O. Delattre, and I. Janoueix-Lerosey. Nature Genetics, 2017 Sep;49(9):1408-1413. PMID: 28740262. Link to the paper
  • HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. H. Ashoor, C. Louis-Brennetot, I. Janoueix-Lerosey, V.B. Bajic, and V. Boeva. Nucleic Acids Research. 2017. 45(8):e58. doi: 10.1093/nar/gkw1319, PMID: 28053124
  • Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. Y.A. Perez-Rico, V. Boeva, A.C. Mallory, A. Bitetti, S. Majello, E. Barillot, and A. Shkumatava. Genome Research, 2017. 27(2):259-268. PMID: 27965291
  • Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages. P. Deveau, E. Barillot, V. Boeva, A. Zinovyev and E. Bonnet. The R Journal, 2016. 8(2): 293-306. ISSN 2073-4859. Link to the paper

Publications 2016
  • Computational pan-genomics: status, promises and challenges. T. Marschall et al., The Computational Pan-Genomics Consortium. Briefings in Bioinformatics. 2016. pii: bbw089. [Epub ahead of print] PMID: 27769991
  • Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. S. Sieberts et al. Nature Communications. 2016; 7:12460. doi: 10.1038/ncomms12460. PMID: 27549343
  • Analysis of genomic sequence motifs for deciphering transcription factor binding and transcriptional regulation in eukaryotic cells. V. Boeva. Frontiers in Genetics. 2016. 7:24. doi: 10.3389/fgene.2016.00024. eCollection 2016. PMID: 26941778.
  • SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. D. Iakovishina, I. Janoueix-Lerosey, E. Barillot, M. Regnier and V. Boeva. Bioinformatics. 2016. 32 (7): 984-992. PMID: 26740523
  • RNF: a general framework to evaluate NGS read mappers. K. Brinda, V. Boeva, and G. Kucherov. Bioinformatics. 2016. 32(1):136-9. PMID: 26353839
  • Ovarian cancers harboring inactivating mutations in CDK12 display a distinct genomic instability pattern characterized by large tandem duplications. T. Popova, E. Manie, V. Boeva, A. Battistella, O. Goundiam, N.K. Smith, C.R. Mueller, V. Raynal, O. Mariani, X. Sastre-Garau, and M.-H. Stern. Cancer Research. 2016, 76(7):1882-91. PMID: 26787835

PI's publications before the official creation of the lab
  • Chimeric oncogene regulates the EGR2 sarcoma susceptibility gene via a GGAA-microsatellite. T.G.P. Grunewald, V. Bernard, P. Gilardi-Hebenstreit, V. Raynal, D. Surdez, M.-M. Aynaud, O. Mirabeau, F. Cidre-Aranaz, F. Tirode, S. Zaidi, G. Perot, A.H. Jonker, C. Lucchesi, M.-C. Le Deley, O. Oberlin, P. Marec-Berard, A.S. Veron, S. Reynaud, E. Lapouble, V. Boeva, T. Rio Frio, J. Alonso, S. Bhatia, G. Pierron, G. Cancel-Tassin, O. Cussenot, D.G. Cox, L.M. Morton, M.J. Machiela, S.J. Chanock, P. Charnay and O. Delattre. Nature Genetics. 2015 Sep;47(9):1073-8. doi: 10.1038/ng.3363. Epub 2015 Jul 27.PMID: 26214589
  • Changes in correlation between promoter methylation and gene expression in cancer. M. Moarii, V. Boeva, J.P. Vert, and F. Reyal. BMC Genomics. 2015, 16(1):873. PMID: 26510534.
  • Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. V. Boeva, T. Popova, M. Lienard, S. Toffoli, M. Kamal, C. Le Tourneau, D. Gentien, N. Servant, P. Gestraud, T. Rio Frio, P. Hupe., E. Barillot and J.-F. Laes. Bioinformatics, 2014, 30(24):3443-3450. PMID: 25016581.
  • Jarid2 is implicated in the initial Xist-induced targeting of PRC2 to the inactive X chromosome. S.T. da Rocha, V. Boeva, M. Escamilla-Del-Arenal, K. Ancelin, C. Granier, N. Reis Matias, S. Sanulli, J. Chow, E. Schulz, C. Picard, S. Kaneko, K. Helin, D. Reinberg, A. F. Stewart, A. Wutz, R. Margueron and E. Heard. Molecular Cell, 2014, 53 (2): 301-316. PMID: 24462204.
  • SegAnnDB: interactive web-based genomic segmentation. T.D. Hocking, V. Boeva, G. Rigaill, G. Schleiermacher, I. Janoueix-Lerosey, O. Delattre, W. Richer, F. Bourdeaut, M. Suguro, M. Seto, F. Bach, J.-P. Vert. Bioinformatics, 2014, 30(11):1539-1546. PMID: 24493034.
  • Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis. V. Boeva*, S. Jouannet*, R. Daveau, V. Combaret, C. Pierre-Eugene, A. Cazes, C. Louis-Brennetot, G. Schleiermacher, S. Ferrand, G. Pierron, A. Lermine, T. Rio Frio, V. Raynal, G. Vassal, E. Barillot, O. Delattre and I. Janoueix-Lerosey. PLoS ONE, 2013, 8(8): e72182. PMID: 23991058.
  • HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. H. Ashoor, A. Herault, A. Kamoun, F. Radvanyi, V.B. Bajic, E. Barillot and V. Boeva. Bioinformatics, 2013, 29 (23): 2979-2986. PMID: 24021381.
  • Learning smoothing models of copy number profiles using breakpoint annotations. T.D. Hocking, G. Schleiermacher, I. Janoueix-Lerosey, V. Boeva, J. Cappo, O. Delattre, F. Bach, J.P. Vert. BMC Bioinformatics. 2013 May 22;14(1):164. PMID: 23697330.
  • Characterization of rearrangements involving the ALK gene reveals a novel truncated form associated with tumor aggressiveness in neuroblastoma. A. Cazes, C. Louis-Brennetot, P. Mazot, F. Dingli, B. Lombard, V. Boeva, R. Daveau, J. Cappo, V. Combaret, G. Schleiermacher, S. Jouannet, S. Ferrand, G. Pierron, E. Barillot, D. Loew, M. Vigny, O. Delattre, I. Janoueix-Lerosey. Cancer Research, 2013, 73(1):195-204. PMID: 23139213.
  • Nebula -- a web-server for advanced ChIP-seq data analysis. V. Boeva, A. Lermine, C. Barette, C. Guillouf, E. Barillot. Bioinformatics, 2012, 28(19):2517-9. PMID: 22829625.
  • Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia. M. Ridinger-Saison*, V. Boeva*, P. Rimmele, I. Kulakovskiy, B. Levavasseur, I. Gallais, C. Paccard, P. Legoix-Ne, A. Nicolas, P. Hupe, E. Barillot, F. Moreau-Gachelin, and C. Guillouf. Nucleic Acids Research, 2012, 40(18):8927-41. PMID: 22790984.
  • Control-FREEC: a tool for assessing copy number and allelic content using next generation sequencing data. V. Boeva, T. Popova, K. Bleakley, P. Chiche, I. Janoueix-Lerosey, O. Delattre and E. Barillot. Bioinformatics, 2012, 28(3):423-5. PMID: 22155870.
  • Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. V. Boeva, A. Zinovyev, K. Bleakley, J.-P. Vert, I. Janoueix-Lerosey, O. Delattre and E. Barillot. Bioinformatics, 2011, 27(2):268-9. PMID: 21081509.
  • Deep and wide digging for binding motifs in ChIP-Seq data. I.V. Kulakovskiy, V. Boeva, A.V. Favorov and V.J. Makeev. Bioinformatics, 2010, 26(20):2622-3. PMID: 20736340.
  • De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. V. Boeva, D. Surdez, N. Guillon, F. Tirode, A.P. Fejes, O. Delattre, E. Barillot. Nucleic Acids Research, 2010, 38(11):e126. PMID: 20375099.
  • SVDetect - a bioinformatic tool to identify genomic structural variations from paired-end next-generation sequencing data. B. Zeitouni, V. Boeva, I. Janoueix-Lerosey, O. Delattre, A.Nicolas, E. Barillot. Bioinformatics, 2010, 26(15):1895-6. PMID: 20639544.
  • The oncogenic transcription factor EWS-FLI1 binds in vivo GGAA microsatellite sequences with potential transcriptional regulatory function. N. Guillon, F. Tirode, V. Boeva, O. Delattre. PLoS One, 2009, 4(3):e4932. PMID: 19305498.
  • Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. V. Boeva, J. Clement, M. Regnier, M.A. Roytberg, V.J. Makeev. Algorithms for Molecular Biology, 2007, 2:13. PMID: 17927813.
  • Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. V. Boeva, M. Regnier, D. Papatsenko, V. Makeev. Bioinformatics, 2006, 22(6), pp.676-684. PMID: 16403795.
  • Relationship between micro- and minisatellites in the human genome. V.A. Boeva, M.V. Fridman, V.J. Makeev. Biofizika, 2006, 51(4), pp.650-655. PMID: 16909842. [rus]

  Book chapters:
  • Analysis of somatic alterations in cancer genome: from SNP arrays to Next Generation Sequencing. T. Popova, V. Boeva, E. Manie, Y. Rozenholc, E. Barillot, M.-H. Stern. Genomics I - Humans, Animals and Plants. ISBN: 978-1-477554-913. iConcept Press. 2013.PDF