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Thomas Walter



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HT-smFISH: a cost effective and flexible workflow for high-throughput single molecule RNA imaging

Adham Safieddine , Emeline Coleno , Frederic Lionneton , Abdel-Meneem Traboulsi , Soha Salloum
Nature Protocols, 2023, 18, pp.157-187. ⟨10.1038/s41596-022-00750-2⟩
Journal articles hal-03834928v1
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FISH-quant v2: a scalable and modular tool for smFISH image analysis

Arthur Imbert , Wei Ouyang , Adham Safieddine , Emeline Coleno , Christophe Zimmer
RNA, 2022, 28 (6), pp.786-795. ⟨10.1261/rna.079073.121⟩
Journal articles hal-03942851v2

Deep learning identifies morphological patterns of homologous recombination deficiency in luminal breast cancers from whole slide images

Tristan Lazard , Guillaume Bataillon , Peter Naylor , Tatiana Popova , François-Clément Bidard
Cell Reports Medicine, 2022, 3 (12), pp.100872. ⟨10.1016/j.xcrm.2022.100872⟩
Journal articles hal-03936608v1
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Prediction of Treatment Response in Triple Negative Breast Cancer From Whole Slide Images

Peter Naylor , Tristan Lazard , Guillaume Bataillon , Marick Laé , Anne Vincent-Salomon
Frontiers in Signal Processing, 2022, 2, ⟨10.3389/frsip.2022.851809⟩
Journal articles hal-03942865v1

Second-Line Treatment and Prognostic Factors in Neuroendocrine Carcinoma.

Julien Hadoux , Thomas Walter , Christina Kanaan , Segolene Hescot , Vincent Hautefeuille
Endocrine-Related Cancer, 2022, pp.ERC-22-0102. ⟨10.1530/ERC-22-0102⟩
Journal articles hal-03746086v1
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Neural network fast‐classifies biological images through features selecting to power automated microscopy

Maël Balluet , Florian Sizaire , Youssef El Habouz , Thomas Walter , Jérémy Pont
Journal of Microscopy, 2022, 285 (1), pp.3-19. ⟨10.1111/jmi.13062⟩
Journal articles hal-03408803v1
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A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport

Adham Safieddine , Emeline Coleno , Soha Salloum , Arthur Imbert , Abdel-Meneem Traboulsi
Nature Communications, 2021, 12 (1), pp.1352. ⟨10.1038/s41467-021-21585-7⟩
Journal articles hal-03014936v2

Spatial transcriptomics for respiratory research and medicine

Sandra Curras-Alonso , Juliette Soulier , Thomas Walter , Florian Mueller , Arturo Londoño-Vallejo
European Respiratory Journal, 2021, 58 (1), pp.2004314. ⟨10.1183/13993003.04314-2020⟩
Journal articles hal-03633353v1
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A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting

Racha Chouaib , Adham Safieddine , Xavier Pichon , Arthur Imbert , Oh Sung Kwon
Developmental Cell, 2020, 54 (6), pp.773 - 791.e5. ⟨10.1016/j.devcel.2020.07.010⟩
Journal articles pasteur-02925687v1
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Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses

Mélanie Durand , Thomas Walter , Tiphène Pirnay , Thomas Naessens , Paul Guéguen
Journal of Experimental Medicine, 2019, 216 (7), pp.1561-1581. ⟨10.1084/jem.20181994⟩
Journal articles hal-02440608v1
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Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen

Joseph Boyd , Alice Pinheiro , Elaine Del Nery , Fabien Reyal , Thomas Walter
Journal articles hal-02440603v1

Prognosis and chemosensitivity of non-V600E BRAF mutations in metastatic colorectal carcinoma (mCRC): An AGEO French multicenter retrospective cohort.

Aline Derosiere , Vincent Nicolai , David Malka , Astrid Pozet , Julien Lazartigues
Journal of Clinical Oncology, 2019, 37 (15, S), ⟨10.1200/JCO.2019.37.15\_suppl.3575⟩
Journal articles hal-03606012v1
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A computational framework to study sub-cellular RNA localization

Aubin Samacoits , Racha Chouaib , Adham Safieddine , Abdel-Meneem Traboulsi , Christophe Zimmer
Nature Communications, 2018, 9 (1), pp.4584. ⟨10.1038/s41467-018-06868-w⟩
Journal articles hal-01984014v1

Segmentation of Nuclei in Histopathology Images by deep regression of the distance map

Peter Naylor , Marick Lae , Fabien Reyal , Thomas Walter
IEEE Transactions on Medical Imaging, 2018, pp.1-12
Journal articles hal-01984033v1

Kernel Multitask Regression for Toxicogenetics

Elsa Bernard , Yunlong Jiao , Erwan Scornet , Véronique Stoven , Thomas Walter
Molecular Informatics, 2017, 36 (10), ⟨10.1002/minf.201700053⟩
Journal articles hal-01679030v1

ARHGEF17 is an essential spindle assembly checkpoint factor that targets Mps1 to kinetochores.

Mayumi Isokane , Thomas Walter , Robert Mahen , Bianca Nijmeijer , Jean-Karim Hériché
Journal of Cell Biology, 2016, 212 (6), pp.647-59. ⟨10.1083/jcb.201408089⟩
Journal articles hal-01427937v1
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smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability.

Nikolay Tsanov , Aubin Samacoits , Racha Chouaib , Abdel-Meneem Traboulsi , Thierry Gostan
Nucleic Acids Research, 2016, ⟨10.1093/nar/gkw784⟩
Journal articles pasteur-01375913v1
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Vaïa Machairas , Matthieu Faessel , David Cárdenas-Peña , Théodore Chabardes , Thomas Walter
IEEE Transactions on Image Processing, 2015, 24 (11), pp.3707 - 3716. ⟨10.1109/TIP.2015.2451011⟩
Journal articles hal-01212760v1

Assessment of algorithms for mitosis detection in breast cancer histopathology images

Mitko Veta , Paul J. Van Diest , Stefan M. Willems , Haibo Wang , Anant Madabhushi
Medical Image Analysis, 2015, 20 (1), pp.237-248. ⟨10.1016/⟩
Journal articles hal-01246695v1

Prediction of human population responses to toxic compounds by a collaborative competition.

Federica Eduati , Lara M Mangravite , Tao Wang , Hao Tang , J Christopher Bare
Nature Biotechnology, 2015, 33 (9), pp.933-40. ⟨10.1038/nbt.3299⟩
Journal articles hal-01428019v1

A generic methodological framework for studying single cell motility in high-throughput time-lapse data

Alice Schoenauer Sebag , Sandra Plancade , Céline Raulet-Tomkiewicz , Robert Barouki , Jean-Philippe Vert
Bioinformatics, 2015, 31 (12), pp.i320-i328. ⟨10.1093/bioinformatics/btv225⟩
Journal articles hal-01246689v1

MAP1S controls microtubule stability throughout the cell cycle in human cells

Justus Tegha-Dunghu , Elena Bausch , Beate Neumann , Annelie Wuensche , Thomas Walter
Journal of Cell Science, 2014, 127, pp.5007-5013. ⟨10.1242/jcs.136457⟩
Journal articles hal-01101879v1

A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression

Veronika Graml , Xenia Studera , Jonathan L.D. Lawson , Anatole Chessel , Marco Geymonat
Developmental Cell, 2014, 31 (2), pp.227-239. ⟨10.1016/j.devcel.2014.09.005⟩
Journal articles hal-01101880v1

Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation

Jean-Karim Hériché , Jon G. Lees , Ian Morilla , Thomas Walter , Boryana Petrova
Molecular Biology of the Cell, 2014, 25 (16), pp.2522-2536. ⟨10.1091/mbc.E13-04-0221⟩
Journal articles hal-01101877v1

A community effort to assess and improve drug sensitivity prediction algorithms

James C Costello , Laura M Heiser , Elisabeth Georgii , Mehmet Gönen , Michael P Menden
Nature Biotechnology, 2014, 32, pp.1202-1212. ⟨10.1038/nbt.2877⟩
Journal articles hal-01101874v1
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Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay.

Gregoire Pau , Thomas Walter , Beate Neumann , Jean-Karim Hériché , Jan Ellenberg
BMC Bioinformatics, 2013, 14 (1), pp.308. ⟨10.1186/1471-2105-14-308⟩
Journal articles inserm-00880889v1

Mitotic lamin disassembly is triggered by lipid-mediated signaling.

Moritz Mall , Thomas Walter , Mátyás Gorjánácz , Iain F Davidson , Thi Bach Nga Ly-Hartig
Journal of Cell Biology, 2012, 198 (6), pp.981-90
Journal articles hal-01428007v1

Micropilot: automation of fluorescence microscopy-based imaging for systems biology.

Christian Conrad , Annelie Wünsche , Tze Heng Tan , Jutta Bulkescher , Frank Sieckmann
Nature Methods, 2011, 8 (3), pp.246-9
Journal articles hal-01430280v1
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CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging

Michael W Held , Michael W Schmitz , Bernd H Fischer , Thomas Walter , Beate H Neumann
Nature Methods, 2010, 7, pp.747 - 754. ⟨10.1038/nmeth.1486⟩
Journal articles hal-01431427v1

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

Beate Neumann , Thomas Walter , Jean-Karim Hériché , Jutta Bulkescher , Holger Erfle
Nature, 2010, 464 (7289), pp.721. ⟨10.1038/nature08869⟩
Journal articles hal-01144034v1

Evaluation of automated fundus photograph analysis algorithms for detecting microaneurysms, haemorrhages and exudates, and of a computer-assisted diagnostic system for grading diabetic retinopathy

Bénédicte Dupas , Thomas R. Walter , Ali Erginay , Richard Ordonez , Nilanjana Deb-Joardar
Diabetes & Metabolism, 2010, 36 (3), pp.213-220. ⟨10.1016/j.diabet.2010.01.002⟩
Journal articles hal-00836043v1

Automatic identification and clustering of chromosome phenotypes in a genome wide RNAi screen by time-lapse imaging.

Thomas Walter , Michael Held , Beate Neumann , Jean-Karim Hériché , Christian Conrad
Journal of Structural Biology, 2010, 170 (1), pp.1-9
Journal articles hal-01427996v1

Anti-angiogenic properties of myo-inositol trispyrophosphate in ovo and growth reduction of implanted glioma

J.-M. Lehn , G. Sihn , T. Walter , J.-C. Klein , I. Queguiner
FEBS Letters, 2007, 581, pp.962-966. ⟨10.1016/j.febslet.2007.01.079⟩
Journal articles hal-00166409v1
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Joseph Boyd , Zelia Gouveia , Franck Perez , Thomas Walter
2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), Apr 2020, Iowa City, United States. pp.886-890, ⟨10.1109/ISBI45749.2020.9098696⟩
Conference papers hal-02976141v1
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Predicting Residual Cancer Burden in a triple negative breast cancer cohort

Peter Naylor , Joseph Boyd , Marick Lae , Fabien Reyal , Thomas Walter
2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2019, Venice, Italy. pp.933-937, ⟨10.1109/ISBI.2019.8759205⟩
Conference papers hal-02440647v1

A Deep Learning Approach To Identify MRNA Localization Patterns

Rémy Dubois , Arthur Imbert , Aubin Samacoits , Marion Peter , Edouard Bertrand
2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2019, Venice, France. pp.1386-1390, ⟨10.1109/ISBI.2019.8759235⟩
Conference papers hal-02343547v1


Joseph Boyd , Alice Pinhiero , Elaine Del Nery , Fabien Reyal , Thomas Walter
IEEE International Symposium on Biomedical Imaging, Apr 2018, Washington, United States
Conference papers hal-01984323v1

Nuclei segmentation in histopathology images using deep neural networks

Peter Naylor , Marik Laé , Fabien Reyal , Thomas Walter
2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017, Melbourne, Australia
Conference papers hal-01683969v1
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V Machairas , T Baldeweck , T Walter , Etienne Decencière
International Symposium on Biomedical Imaging, Apr 2016, Prague, Czech Republic
Conference papers hal-01276132v1

Spatial Repulsion Between Markers Improves Watershed Performance

Vaïa Machairas , Etienne Decencière , Thomas Walter
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⟩
Conference papers hal-01246692v1
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Waterpixels: Superpixels based on the watershed transformation

Vaïa Machairas , Etienne Decencière , Thomas Walter
IEEE International Conference On Image Processing, Oct 2014, Paris, France. ⟨10.1109/ICIP.2014.7025882⟩
Conference papers hal-01139797v1
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Simple and Efficient Confidence Score for Grading Whole Slide Images

Mélanie Lubrano , Yaëlle Bellahsen-Harrar , Rutger Fick , Cécile Badoual , Thomas Walter
Preprints, Working Papers, ... hal-04030031v1
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PointFISH -- learning point cloud representations for RNA localization patterns

Arthur Imbert , Florian Mueller , Thomas Walter
Preprints, Working Papers, ... hal-04029994v1
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Giga-SSL: Self-Supervised Learning for Gigapixel Images

Tristan Lazard , Marvin Lerousseau , Etienne Decencière , Thomas Walter
Preprints, Working Papers, ... hal-04030020v1
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Diagnosis with Confidence: Deep Learning for Reliable Classification of Squamous Lesions of the Upper Aerodigestive Tract

Mélanie Lubrano , Yaëlle Bellahsen-Harrar , Sylvain Berlemont , Thomas Walter , Cécile Badoual
Preprints, Working Papers, ... hal-03942781v1

Neural network for the prediction of treatment response in Triple Negative Breast Cancer *

Peter Naylor , Tristan Lazard , Guillaume Bataillon , Marick Lae , Anne Vincent-Salomon
Preprints, Working Papers, ... hal-03633354v1
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Automatic grading of cervical biopsies by combining full and self-supervision

Melanie Lubrano Di Scandalea , Tristan Lazard , Guillaume Balezo , Yaëlle Bellahsen-Harrar , Cécile Badoual
Preprints, Working Papers, ... hal-03533712v1
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Deep Learning identifies new morphological patterns of Homologous Recombination Deficiency in luminal breast cancers from whole slide images

Tristan Lazard , Guillaume Bataillon , Peter Naylor , Tatiana Popova , François-Clément Bidard
Preprints, Working Papers, ... hal-03533688v1

The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions

Xavier Pichon , Konstadinos Moissoglu , Emeline Coleno , Tianhong Wang , Arthur Imbert
Preprints, Working Papers, ... hal-03116720v1
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A localization screen reveals translation factories and widespread co-translational RNA targeting

Racha Chouaib , Adham Safieddine , Xavier Pichon , Arthur Imbert , Oh Sung Kwon
Preprints, Working Papers, ... pasteur-02873144v1

Neural network fast-classifies biological images using features selected after their random-forests-importance to power smart microscopy

Maël Balluet , Florian Sizaire , Thomas Walter , Jérémy Pont , Baptiste Giroux
Preprints, Working Papers, ... hal-03065051v1
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Bioimage Informatics for Phenomics

Thomas Walter
Bioinformatics [q-bio.QM]. Sorbonne Université, 2020
Habilitation à diriger des recherches tel-02981391v1