CV Thomas Walter

Maël Balluet, Florian Sizaire, Youssef El Habouz, Thomas Walter, Jérémy Pont, et al.. Neural network fast‐classifies biological images through features selecting to power automated microscopy. Journal of Microscopy, Wiley, 2022, 285 (1), pp.3-19. ⟨10.1111/jmi.13062⟩. ⟨hal-03408803⟩

Sandra Curras-Alonso, Juliette Soulier, Thomas Walter, Florian Mueller, Arturo Londoño-Vallejo, et al.. Spatial transcriptomics for respiratory research and medicine. European Respiratory Journal, European Respiratory Society, 2021, 58 (1), pp.2004314. ⟨10.1183/13993003.04314-2020⟩. ⟨hal-03633353⟩

Adham Safieddine, Emeline Coleno, Soha Salloum, Arthur Imbert, Abdel-Meneem Traboulsi, et al.. A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport. Nature Communications, Nature Publishing Group, 2021, 12 (1), pp.1352. ⟨10.1038/s41467-021-21585-7⟩. ⟨hal-03014936v2⟩

Racha Chouaib, Adham Safieddine, Xavier Pichon, Arthur Imbert, Oh Sung Kwon, et al.. A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting. Developmental Cell, Elsevier, 2020, 54 (6), pp.773 - 791.e5. ⟨10.1016/j.devcel.2020.07.010⟩. ⟨pasteur-02925687⟩

Joseph Boyd, Alice Pinheiro, Elaine Nery, Fabien Reyal, Thomas Walter. Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen. Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/btz774⟩. ⟨hal-02440603⟩

Mélanie Durand, Thomas Walter, Tiphène Pirnay, Thomas Naessens, Paul Guéguen, et al.. Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses. Journal of Experimental Medicine, Rockefeller University Press, 2019, 216 (7), pp.1561-1581. ⟨10.1084/jem.20181994⟩. ⟨hal-02440608⟩

Aline Derosiere, Vincent Nicolai, David Malka, Astrid Pozet, Julien Lazartigues, et al.. Prognosis and chemosensitivity of non-V600E BRAF mutations in metastatic colorectal carcinoma (mCRC): An AGEO French multicenter retrospective cohort.. Journal of clinical oncology, 2019, 37 (15, S), ⟨10.1200/JCO.2019.37.15\_suppl.3575⟩. ⟨hal-03606012⟩

Peter Naylor, Marick Lae, Fabien Reyal, Thomas Walter. Segmentation of Nuclei in Histopathology Images by deep regression of the distance map. IEEE Transactions on Medical Imaging, Institute of Electrical and Electronics Engineers, 2018, pp.1-12. ⟨hal-01984033⟩

Aubin Samacoits, Racha Chouaib, Adham Safieddine, Abdel-Meneem Traboulsi, Christophe Zimmer, et al.. A computational framework to study sub-cellular RNA localization. Nature Communications, Nature Publishing Group, 2018, 9 (1), pp.4584. ⟨10.1038/s41467-018-06868-w⟩. ⟨hal-01984014⟩

Elsa Bernard, Yunlong Jiao, Erwan Scornet, Véronique Stoven, Thomas Walter, et al.. Kernel Multitask Regression for Toxicogenetics. Molecular Informatics, Wiley-VCH, 2017, 36 (10), ⟨10.1002/minf.201700053⟩. ⟨hal-01679030⟩

Mayumi Isokane, Thomas Walter, Robert Mahen, Bianca Nijmeijer, Jean-Karim Hériché, et al.. ARHGEF17 is an essential spindle assembly checkpoint factor that targets Mps1 to kinetochores.. Journal of Cell Biology, Rockefeller University Press, 2016, 212 (6), pp.647-59. ⟨10.1083/jcb.201408089⟩. ⟨hal-01427937⟩

Nikolay Tsanov, Aubin Samacoits, Racha Chouaib, Abdel-Meneem Traboulsi, Thierry Gostan, et al.. smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability.. Nucleic Acids Research, Oxford University Press, 2016, ⟨10.1093/nar/gkw784⟩. ⟨pasteur-01375913⟩

Federica Eduati, Lara M Mangravite, Tao Wang, Hao Tang, J Christopher Bare, et al.. Prediction of human population responses to toxic compounds by a collaborative competition.. Nature Biotechnology, Nature Publishing Group, 2015, 33 (9), pp.933-40. ⟨10.1038/nbt.3299⟩. ⟨hal-01428019⟩

Mitko Veta, Paul J. Van Diest, Stefan M. Willems, Haibo Wang, Anant Madabhushi, et al.. Assessment of algorithms for mitosis detection in breast cancer histopathology images. Medical Image Analysis, Elsevier, 2015, 20 (1), pp.237-248. ⟨10.1016/j.media.2014.11.010⟩. ⟨hal-01246695⟩

Vaïa Machairas, Matthieu Faessel, David Cárdenas-Peña, Théodore Chabardes, Thomas Walter, et al.. Waterpixels. IEEE Transactions on Image Processing, Institute of Electrical and Electronics Engineers, 2015, 24 (11), pp.3707 - 3716. ⟨10.1109/TIP.2015.2451011⟩. ⟨hal-01212760⟩

Alice Schoenauer Sebag, Sandra Plancade, Céline Raulet-Tomkiewicz, Robert Barouki, Jean-Philippe Vert, et al.. A generic methodological framework for studying single cell motility in high-throughput time-lapse data. Bioinformatics, Oxford University Press (OUP), 2015, 31 (12), pp.i320-i328. ⟨10.1093/bioinformatics/btv225⟩. ⟨hal-01246689⟩

Veronika Graml, Xenia Studera, Jonathan L.D. Lawson, Anatole Chessel, Marco Geymonat, et al.. A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression. Developmental Cell, Elsevier, 2014, 31 (2), pp.227-239. ⟨10.1016/j.devcel.2014.09.005⟩. ⟨hal-01101880⟩

Justus Tegha-Dunghu, Elena Bausch, Beate Neumann, Annelie Wuensche, Thomas Walter, et al.. MAP1S controls microtubule stability throughout the cell cycle in human cells. Journal of Cell Science, Company of Biologists, 2014, 127, pp.5007-5013. ⟨10.1242/jcs.136457⟩. ⟨hal-01101879⟩

Jean-Karim Hériché, Jon G. Lees, Ian Morilla, Thomas Walter, Boryana Petrova, et al.. Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. Molecular Biology of the Cell, American Society for Cell Biology, 2014, 25 (16), pp.2522-2536. ⟨10.1091/mbc.E13-04-0221⟩. ⟨hal-01101877⟩

James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, et al.. A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology, Nature Publishing Group, 2014, 32, pp.1202-1212. ⟨10.1038/nbt.2877⟩. ⟨hal-01101874⟩

Gregoire Pau, Thomas Walter, Beate Neumann, Jean-Karim Hériché, Jan Ellenberg, et al.. Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay.. BMC Bioinformatics, BioMed Central, 2013, 14 (1), pp.308. ⟨10.1186/1471-2105-14-308⟩. ⟨inserm-00880889⟩

Moritz Mall, Thomas Walter, Mátyás Gorjánácz, Iain F Davidson, Thi Bach Nga Ly-Hartig, et al.. Mitotic lamin disassembly is triggered by lipid-mediated signaling.. Journal of Cell Biology, Rockefeller University Press, 2012, 198 (6), pp.981-90. ⟨hal-01428007⟩

Christian Conrad, Annelie Wünsche, Tze Heng Tan, Jutta Bulkescher, Frank Sieckmann, et al.. Micropilot: automation of fluorescence microscopy-based imaging for systems biology.. Nature Methods, Nature Publishing Group, 2011, 8 (3), pp.246-9. ⟨hal-01430280⟩

Michael Held, Michael Schmitz, Bernd Fischer, Thomas Walter, Beate Neumann, et al.. CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nature Methods, Nature Publishing Group, 2010, 7, pp.747 - 754. ⟨10.1038/nmeth.1486⟩. ⟨hal-01431427⟩

Bénédicte Dupas, Thomas Walter, Ali Erginay, Richard Ordonez, Nilanjana Deb-Joardar, et al.. Evaluation of automated fundus photograph analysis algorithms for detecting microaneurysms, haemorrhages and exudates, and of a computer-assisted diagnostic system for grading diabetic retinopathy. Diabetes and Metabolism, Elsevier Masson, 2010, 36 (3), pp.213-220. ⟨10.1016/j.diabet.2010.01.002⟩. ⟨hal-00836043⟩

Thomas Walter, Michael Held, Beate Neumann, Jean-Karim Hériché, Christian Conrad, et al.. Automatic identification and clustering of chromosome phenotypes in a genome wide RNAi screen by time-lapse imaging.. Journal of Structural Biology, Elsevier, 2010, 170 (1), pp.1-9. ⟨hal-01427996⟩

Beate Neumann, Thomas Walter, Jean-Karim Hériché, Jutta Bulkescher, Holger Erfle, et al.. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature, Nature Publishing Group, 2010, 464 (7289), pp.721. ⟨10.1038/nature08869⟩. ⟨hal-01144034⟩

J.-M. Lehn, G. Sihn, T. Walter, J.-C. Klein, I. Queguiner, et al.. Anti-angiogenic properties of myo-inositol trispyrophosphate in ovo and growth reduction of implanted glioma. FEBS Letters, Wiley, 2007, pp.962-966. ⟨10.1016/j.febslet.2007.01.079⟩. ⟨hal-00166409⟩

Joseph Boyd, Zelia Gouveia, Franck Perez, Thomas Walter. EXPERIMENTALLY-GENERATED GROUND TRUTH FOR DETECTING CELL TYPES IN AN IMAGE-BASED IMMUNOTHERAPY SCREEN. 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), Apr 2020, Iowa City, United States. pp.886-890, ⟨10.1109/ISBI45749.2020.9098696⟩. ⟨hal-02976141⟩

Peter Naylor, Joseph Boyd, Marick Lae, Fabien Reyal, Thomas Walter. Predicting Residual Cancer Burden in a triple negative breast cancer cohort. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2019, Venice, Italy. pp.933-937, ⟨10.1109/ISBI.2019.8759205⟩. ⟨hal-02440647⟩

Rémy Dubois, Arthur Imbert, Aubin Samacoits, Marion Peter, Edouard Bertrand, et al.. A Deep Learning Approach To Identify MRNA Localization Patterns. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2019, Venice, France. pp.1386-1390, ⟨10.1109/ISBI.2019.8759235⟩. ⟨hal-02343547⟩

Joseph Boyd, Alice Pinhiero, Elaine Nery, Fabien Reyal, Thomas Walter. ANALYSING DOUBLE-STRAND BREAKS IN CULTURED CELLS FOR DRUG SCREENING APPLICATIONS BY CAUSAL INFERENCE. IEEE International Symposium on Biomedical Imaging, Apr 2018, Washington, United States. ⟨hal-01984323⟩

Peter Naylor, Marik Laé, Fabien Reyal, Thomas Walter. Nuclei segmentation in histopathology images using deep neural networks. 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017, Melbourne, Australia. ⟨hal-01683969⟩

V Machairas, T Baldeweck, T Walter, Etienne Decencière. NEW GENERAL FEATURES BASED ON SUPERPIXELS FOR IMAGE SEGMENTATION LEARNING. International Symposium on Biomedical Imaging, Apr 2016, Prague, Czech Republic. ⟨hal-01276132⟩

Vaïa Machairas, Etienne Decencière, Thomas Walter. Spatial Repulsion Between Markers Improves Watershed Performance. 12th International Symposium, ISMM 2015, Reykjavik, Iceland, May 27-29, 2015, May 2015, Reykjavik, Iceland. pp.194-202, ⟨10.1007/978-3-319-18720-4_17⟩. ⟨hal-01246692⟩

Vaïa Machairas, Etienne Decencière, Thomas Walter. Waterpixels: Superpixels based on the watershed transformation. IEEE International Conference On Image Processing, Oct 2014, Paris, France. ⟨10.1109/ICIP.2014.7025882⟩. ⟨hal-01139797⟩

Tristan Lazard, Guillaume Bataillon, Peter Naylor, Tatiana Popova, François-Clément Bidard, et al.. Deep Learning identifies new morphological patterns of Homologous Recombination Deficiency in luminal breast cancers from whole slide images. 2022. ⟨hal-03633351⟩

Peter Naylor, Tristan Lazard, Guillaume Bataillon, Marick Lae, Anne Vincent-Salomon, et al.. Neural network for the prediction of treatment response in Triple Negative Breast Cancer *. 2022. ⟨hal-03633354⟩

Melanie Lubrano Di Scandalea, Tristan Lazard, Guillaume Balezo, Yaëlle Bellahsen-Harrar, Cécile Badoual, et al.. Automatic grading of cervical biopsies by combining full and self-supervision. 2022. ⟨hal-03533712⟩

Mélanie Lubran Di Scandalea, Tristan Lazard, Guillaume Balezo, Yaëlle Bellahsen-Harrar, Cécile Badoual, et al.. Automatic grading of cervical biopsies by combining full and self-supervision. 2022. ⟨hal-03633350⟩

Xavier Pichon, Konstadinos Moissoglu, Emeline Coleno, Tianhong Wang, Arthur Imbert, et al.. The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions. 2021. ⟨hal-03116720⟩

Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, et al.. FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. 2021. ⟨hal-03533689⟩

Tristan Lazard, Guillaume Bataillon, Peter Naylor, Tatiana Popova, François-Clément Bidard, et al.. Deep Learning identifies new morphological patterns of Homologous Recombination Deficiency in luminal breast cancers from whole slide images. 2021. ⟨hal-03533688⟩

Maël Balluet, Florian Sizaire, Thomas Walter, Jérémy Pont, Baptiste Giroux, et al.. Neural network fast-classifies biological images using features selected after their random-forests-importance to power smart microscopy. 2020. ⟨hal-03065051⟩

Racha Chouaib, Adham Safieddine, Xavier Pichon, Arthur Imbert, Oh Sung Kwon, et al.. A localization screen reveals translation factories and widespread co-translational RNA targeting. 2020. ⟨pasteur-02873144⟩

Thomas Walter. Bioimage Informatics for Phenomics. Bioinformatics [q-bio.QM]. Sorbonne Université, 2020. ⟨tel-02981391⟩