Assessing the Significance of Sets of Words. - Valentina Boeva; Julien Clément 001; Mireille Régnier; Mathias Vandenbogaert (CPM, 2005)

Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. - Valentina Boeva; Mireille Régnier; Dmitri A. Papatsenko; Vsevolod J. Makeev (Bioinform., 2006)

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. - Valentina Boeva; Julien Clément 001; Mireille Régnier; Mikhail A. Roytberg; Vsevolod J. Makeev (Algorithms Mol. Biol., 2007)

Deep and wide digging for binding motifs in ChIP-Seq data. - Ivan V. Kulakovskiy; Valentina Boeva; Alexander V. Favorov; Vsevolod J. Makeev (Bioinform., 2010)

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. - Bruno Zeitouni; Valentina Boeva; Isabelle Janoueix-Lerosey; Sophie Loeillet; Patricia Legoix-né; Alain Nicolas; Olivier Delattre; Emmanuel Barillot (Bioinform., 2010)

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. - Valentina Boeva; Andrei Yu. Zinovyev; Kevin Bleakley; Jean-Philippe Vert; Isabelle Janoueix-Lerosey; Olivier Delattre; Emmanuel Barillot (Bioinform., 2011)

Nebula - a web-server for advanced ChIP-seq data analysis. - Valentina Boeva; Alban Lermine; Camille Barette; Christel Guillouf; Emmanuel Barillot (Bioinform., 2012)

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. - Valentina Boeva; Tatiana G. Popova; Kevin Bleakley; Pierre Chiche; Julie Cappo; Gudrun Schleiermacher; Isabelle Janoueix-Lerosey; Olivier Delattre; Emmanuel Barillot (Bioinform., 2012)

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. - Haitham Ashoor; Aurélie Hérault; Aurélie Kamoun; François Radvanyi; Vladimir B. Bajic; Emmanuel Barillot; Valentina Boeva (Bioinform., 2013)

Learning smoothing models of copy number profiles using breakpoint annotations. - Toby Dylan Hocking; Gudrun Schleiermacher; Isabelle Janoueix-Lerosey; Valentina Boeva; Julie Cappo; Olivier Delattre; Francis R. Bach; Jean-Philippe Vert (BMC Bioinform., 2013)

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. - Valentina Boeva; Tatiana G. Popova; Maxime Lienard; Sebastien Toffoli; Maud Kamal; Christophe Le Tourneau; David Gentien; Nicolas Servant; Pierre Gestraud; Thomas Rio Frio; Philippe Hupé; Emmanuel Barillot; et al. (Bioinform., 2014)

SegAnnDB: interactive Web-based genomic segmentation. - Toby Dylan Hocking; Valentina Boeva; Guillem Rigaill; Gudrun Schleiermacher; Isabelle Janoueix-Lerosey; Olivier Delattre; Wilfrid Richer; Franck Bourdeaut; Miyuki Suguro; Masao Seto; Francis R. Bach; Jean-Philippe Vert (Bioinform., 2014)

RNF: a general framework to evaluate NGS read mappers. - Karel Brinda; Valentina Boeva; Gregory Kucherov (Bioinform., 2016)

SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. - Daria Iakovishina; Isabelle Janoueix-Lerosey; Emmanuel Barillot; Mireille Régnier; Valentina Boeva (Bioinform., 2016)

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages. - Paul Deveau; Emmanuel Barillot; Valentina Boeva; Andrei Yu. Zinovyev; Eric Bonnet (R J., 2016)

QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. - Paul Deveau; Leo Colmet Daage; Derek Oldridge; Virginie Bernard; Angela Bellini; Mathieu Chicard; Nathalie Clement; Eve Lapouble; Valerie Combaret; Anne Boland; Vincent Meyer; Jean-Francois Deleuze; et al. (Bioinform., 2018)

CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes. - Lélia Polit; Gwenneg Kerdivel; Sebastian Gregoricchio; Michela Esposito; Christel Guillouf; Valentina Boeva (BMC Bioinform., 2021)

Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. - Josephine Yates; Valentina Boeva (Briefings Bioinform., 2022)

Histopathological Image Classification with Cell Morphology Aware Deep Neural Networks. - Andrey Ignatov; Josephine Yates; Valentina Boeva (CVPR Workshops, 2024)

Feature Clock: High-Dimensional Effects in Two-Dimensional Plots. - Olga Ovcharenko; Rita Sevastjanova; Valentina Boeva (IEEE VIS, 2024)

scTree: Discovering Cellular Hierarchies in the Presence of Batch Effects in scRNA-seq Data. - Moritz Vandenhirtz; Florian Barkmann; Laura Manduchi; Julia E. Vogt; Valentina Boeva (CoRR, 2024)

UniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions. - Aayush Grover; Lin Zhang 031; Till Muser; Simeon Haefliger; Minjia Wang; Josephine Yates; Eliezer M. Van Allen; Fabian J. Theis; Ignacio Ibarra; Ekaterina A. Krymova; Valentina Boeva (Zenodo, 2025)

scSSL-Bench: Benchmarking Self-Supervised Learning for Single-Cell Data. - Olga Ovcharenko; Florian Barkmann; Philip Toma; Imant Daunhawer; Julia E. Vogt; Sebastian Schelter; Valentina Boeva (CoRR, 2025)

Generalized Linear Mode Connectivity for Transformers. - Alexander Theus; Alessandro Cabodi; Sotiris Anagnostidis; Antonio Orvieto; Sidak Pal Singh; Valentina Boeva (CoRR, 2025)