@article{Hocking2026finite,
  title={{Finite Sample Complexity Analysis of Binary Segmentation}},
  author={Toby Dylan Hocking},
  journal={Algorithms},
  volume={19},
  number={9},
  ARTICLE-NUMBER = {754},
  doi={10.3390/a19090754},
  year={2026}
}

@article{Jorge2026hicream,
  title={{hicream: a flexible framework to identify significantly different regions in Hi-C data}},
  journal={Bioinformatics},
  author={Elise Jorge and Toby Dylan Hocking and Pierre Neuvial and Nathalie Vialaneix and Sylvain Foissac},
  issn = {1367-4811},
  doi = {10.1093/bioinformatics/btag631},
  volume = {btag631},
  month = {08},
  year={2026}
}

@article{Sutherland2026autism,
  title={{Pediatric Autism Identification in Primary Care from 2013 to 2023}},
  author={Vincent Sutherland and Toby Dylan Hocking and David C Folch and Underwood Carrasco, Veronica I and Katharine E Zuckerman and Olivia J Lindly},
  poster_authors={Sutherland, V and Hocking, TD and Underwood Carrasco, VI and Gillis, Margaret and Woods, Adrienne and Folch, DC and Zuckerman, KE and Lindly, OJ},
  journal={Academic Pediatrics},
  volume={26},
  number={6},
  year={2026}
}

@book{Hocking2026visualisation,
  title={Visualisation interactive de données dans R avec animint2},
  author={Toby Dylan Hocking},
  year={2026},
  publisher={Université de Sherbrooke, fabriqueREL, license CC BY-SA},
  url={https://animint-manual-fr.netlify.app},
  doi={10.71892/11143/1448}
}

@article{Amoakohene2026atime,
  title={Asymptotic benchmarking using the atime package},
  author={Amoakohene, D and Chetia, A and Steinmacher, I and Hocking, TD},
  journal={R Journal},
  volume={18},
  number={1},
  pages={169--187},
  year={2026}
}

@article{Hocking2026soak,
  title={{SOAK: Same/Other/All K-fold cross-validation for estimating similarity of patterns in data subsets}},
  author={Toby Dylan Hocking and Gabrielle Thibault and Cameron Scott Bodine and Paul Nelson Arellano and Alexander F Shenkin and Olivia Lindly},
  journal={Statistical Analysis and Data Mining},
  volume={19},
  number={1},
  year={2026}
}
 
@inproceedings{Oliveira2025governance,
  title={{Governance Matters: Lessons from Restructuring the data.table OSS Project}},
  author={Oliveira, P and Amoakohene, D and Hocking, TD and Gerosa, M and Steinmacher, I},
  booktitle={2025 IEEE International Conference on Software Maintenance and Evolution (ICSME)},
  volume={},
  number={},
  pages={1-12},
  year={2025},
  keywords={Surveys;Software maintenance;Reviews;Scalability;Throughput;Data mining;Sustainable development;Open source software;Software engineering;Recruitment;Open Source Software;Governance Model;Sustainability},
  doi={10.1109/ICSME64153.2025.00067}
}

@article{Nguyen2025mlp,
  title={{Penalty Learning for Optimal Partitioning using Multilayer Perceptron}},
  author={Nguyen, TL and Hocking, TD},
  journal={Statistics and Computing},
  volume={35},
  article={153},
  year={2025}
}

@article{Agyapong2025cv,
  title={Cross-Validation for Training and Testing Co-occurrence Network Inference Algorithms},
  author={Agyapong, Daniel and Propster, Jeff R and Marks, Jane and Hocking, Toby Dylan},
  journal={BMC Bioinformatics},
  volume={26},
  number={74}
  year={2025}
}

@article{Gurney2024power,
  doi = {10.1088/1748-9326/ad8364},
  url = {https://dx.doi.org/10.1088/1748-9326/ad8364},
  month = {oct},
  publisher = {IOP Publishing},
  volume = {19},
  number = {11},
  pages = {114062},
  author = {Kevin R Gurney and Bilal Aslam and Pawlok Dass and Lech Gawuc and Toby Dylan Hocking and Jarrett J Barber and Anna Kato},
  title = {Assessment of the Climate Trace global powerplant CO2 emissions},
  journal = {Environmental Research Letters},
  year={2024}
}

@article{Bodine2024mapping,
author = {Bodine, C. S. and Buscombe, D. and Hocking, T. D.},
title = {Automated River Substrate Mapping From Sonar Imagery With Machine Learning},
journal = {Journal of Geophysical Research: Machine Learning and Computation},
volume = {1},
number = {3},
keywords = {side-scan sonar, substrate mapping, aquatic habitat, acoustic remote sensing, deep learning, semantic segmentation},
doi = {10.1029/2024JH000135},
note = {e2024JH000135},
year = {2024}
}

@article{Tao2024reply,
  title={Reply to: Model uncertainty obscures major driver of soil carbon},
  author={Tao, Feng and Houlton, Benjamin Z and Frey, Serita D and Lehmann, Johannes and Manzoni, Stefano and Huang, Yuanyuan and Jiang, Lifen and Mishra, Umakant and Hungate, Bruce A and Schmidt, Michael WI and Markus Reichstein and Nuno Carvalhais and Philippe Ciais and Ying-Ping Wang and Bernhard Ahrens and Gustaf Hugelius and Toby D. Hocking and Xingjie Lu and Zheng Shi and Kostiantyn Viatkin and Ronald Vargas and Yusuf Yigini and Christian Omuto and Ashish A. Malik and Guillermo Peralta and Rosa Cuevas-Corona and Luciano E. Di Paolo and Isabel Luotto and Cuijuan Liao and Yi-Shuang Liang and Vinisa S. Saynes and Xiaomeng Huang and Yiqi Luo},
  journal={Nature},
  volume={627},
  number={8002},
  pages={E4--E6},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

@article{Kaufman2024functional,
  title={{Functional Labeled Optimal Partitioning}},
  author={Kaufman, Jacob M and Stenberg, Alyssa J and Hocking, Toby D},
  journal={Journal of Computational and Graphical Statistics},
  pages={1131--1138},
  year={2024},
  volume={33},
  number={4}
}

@article{Harshe2023exoskeleton,
  author={Harshe, Karl and Williams, Jack R. and Hocking, Toby D. and Lerner, Zachary F.},
  journal={IEEE Robotics and Automation Letters}, 
  publisher={IEEE},
  title={Predicting Neuromuscular Engagement to Improve Gait Training With a Robotic Ankle Exoskeleton}, 
  year={2023},
  volume={8},
  number={8},
  pages={5055-5060},
  keywords={Recruitment;Legged locomotion;Immune system;Training;Exoskeletons;Biological control systems;Robots;Exoskeletons;deep learning methods;physical human-robot interaction;wearable robotics},
  doi={10.1109/LRA.2023.3291919}}

@article{Tao2023nature,
author = {Feng Tao and Yuanyuan Huang and Bruce A. Hungate and Stefano Manzoni and Serita D. Frey and Michael W. I. Schmidt and Markus Reichstein and Nuno Carvalhais and Philippe Ciais and Lifen Jiang and Johannes Lehmann and Umakant Mishra and Gustaf Hugelius and Toby D. Hocking and Xingjie Lu and Zheng Shi and Kostiantyn Viatkin and Ronald Vargas and Yusuf Yigini and Christian Omuto and Ashish A. Malik and Guillermo Perualta and Rosa Cuevas-Corona and Luciano E. Di Paolo and Isabel Luotto and Cuijuan Liao and Yi-Shuang Liang and Vinisa S. Saynes and Xiaomeng Huang and Yiqi Luo},
title = {Microbial carbon use efficiency promotes global soil carbon storage},
note = {DOI:10.1038/s41586-023-06042-3},
journal = {Nature},
volume = 618,
pages = {981–985},
year = 2023
}

@article{Hillman2023jmlr,
  author  = {Jonathan Hillman and Toby Dylan Hocking},
  title   = {Optimizing {ROC} Curves with a Sort-Based Surrogate Loss for Binary Classification and Changepoint Detection},
  journal = {Journal of Machine Learning Research},
  year    = {2023},
  volume  = {24},
  number  = {70},
  pages   = {1--24},
  url     = {http://jmlr.org/papers/v24/21-0751.html}
}

@INPROCEEDINGS{Sweeney2023insect,
  author={Sweeney, Nathaniel and Xu, Caroline and Shaw, Joseph A. and Hocking, Toby D. and Whitaker, Bradley M.},
  booktitle={2023 Intermountain Engineering, Technology and Computing (IETC)}, 
  title={Insect Identification in Pulsed Lidar Images Using Changepoint Detection Algorithms}, 
  year={2023},
  pages={93-97},
  links={[Publisher](https://ieeexplore.ieee.org/abstract/document/10152205)},
  doi={10.1109/IETC57902.2023.10152205}}

@article{Runge2023jss,
 title={gfpop: An R Package for Univariate Graph-Constrained Change-Point Detection},
 volume={106},
 url={https://www.jstatsoft.org/index.php/jss/article/view/v106i06},
 doi={10.18637/jss.v106.i06},
 number={6},
 journal={Journal of Statistical Software},
 author={Runge, Vincent and Hocking, Toby Dylan and Romano, Gaetano and Afghah, Fatemeh and Fearnhead, Paul and Rigaill, Guillem},
 year={2023},
 links={[Publisher](https://www.jstatsoft.org/article/view/v106i06), [Preprint](https://arxiv.org/abs/2002.03646), [Software](https://github.com/vrunge/gfpop), [GUI](https://github.com/julianstanley/gfpopgui), [Reproducible](https://github.com/vrunge/gfpop/blob/master/vignettes/applications.Rmd)},
 pages={1–39}
}

@article{Hocking2023lopart,
year = {2023}, 
title = {{Labeled optimal partitioning}}, 
author = {Hocking, Toby Dylan and Srivastava, Anuraag}, 
journal = {Computational Statistics}, 
issn = {0943-4062}, 
doi = {10.1007/s00180-022-01238-z}, 
pages = {461--480},
volume = {38}
}

@inproceedings{Barr2022classifying,
  title={Classifying Imbalanced Data with {AUM} Loss},
  author={Barr, Joseph R and Hocking, Toby D and Morton, Garinn and Thatcher, Tyler and Shaw, Peter},
  booktitle={2022 Fourth International Conference on Transdisciplinary AI (TransAI)},
  pages={135--141},
  year={2022},
  organization={IEEE}
}

@inproceedings{Hocking2022interpretable,
  title={Interpretable linear models for predicting security vulnerabilities in source code},
  author={Hocking, Toby D and Barr, Joseph R and Thatcher, Tyler},
  booktitle={2022 Fourth International Conference on Transdisciplinary AI (TransAI)},
  pages={149--155},
  year={2022},
  organization={IEEE}
}

@inproceedings{Barr2022graph,
  title={Graph embedding: A methodological survey},
  author={Barr, Joseph R and Shaw, Peter and Abu-Khzam, Faisal N and Thatcher, Tyler and Hocking, Toby Dylan},
  booktitle={2022 fourth international conference on transdisciplinary AI (TransAI)},
  pages={142--148},
  year={2022},
  organization={IEEE}
}

@article{Mihaljevic2022sparsemodr,
  title={SPARSEMODr: Rapidly simulate spatially explicit and stochastic models of COVID-19 and other infectious diseases},
  author={Mihaljevic, Joseph R and Borkovec, Seth and Ratnavale, Saikanth and Hocking, Toby D and Banister, Kelsey E and Eppinger, Joseph E and Hepp, Crystal and Doerry, Eck},
  journal={Biology Methods and Protocols},
  volume={7},
  number={1},
  pages={bpac022},
  year={2022},
  publisher={Oxford University Press}
}

@InCollection{Hocking2022intro,
  author =    {Toby Dylan Hocking},
  editor = {Yiqi Luo},
  booktitle = {Land Carbon Cycle Modeling: Matrix Approach, Data Assimilation, and Ecological Forecasting},
  title =        {Introduction to machine learning and neural networks},
  publisher =    {CRC Press},
  isbn={9780429155659},
  doi={10.1201/9780429155659},
  chapter = {36},
  year = {2022}
  }

@article{Barnwal2022jcgs,
author = {Avinash Barnwal and Hyunsu Cho and Toby Hocking},
title = {Survival Regression with Accelerated Failure Time Model in XGBoost},
journal = {Journal of Computational and Graphical Statistics},
volume = {31},
number = {4},
pages = {1292--1302},
year = {2022},
publisher = {ASA Website},
doi = {10.1080/10618600.2022.2067548}
}

@article{Chaves2022chatbot,
author = {Chaves, Ana Paula and Egbert, Jesse and Hocking, Toby and Doerry, Eck and Gerosa, Marco Aurelio},
title = {Chatbots Language Design: The Influence of Language Variation on User Experience with Tourist Assistant Chatbots},
year = {2022},
issue_date = {April 2022},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {29},
number = {2},
issn = {1073-0516},
doi = {10.1145/3487193},
journal = {ACM Trans. Comput.-Hum. Interact.},
month = {jan},
articleno = {13},
numpages = {38},
keywords = {Chatbots, language design, conversational agents, user perceptions, register}
}

@article{Hocking2022jss,
 title={Generalized Functional Pruning Optimal Partitioning (GFPOP) for Constrained Changepoint Detection in Genomic Data},
 volume={101},
 url={https://www.jstatsoft.org/index.php/jss/article/view/v101i10},
 doi={10.18637/jss.v101.i10},
 number={10},
 journal={Journal of Statistical Software},
 author={Hocking, Toby Dylan and Rigaill, Guillem and Fearnhead, Paul and Bourque, Guillaume},
 year={2022},
 pages={1–31}
}

@article{Vargovich2022breakpoints,
author = {Joseph Vargovich and Toby Dylan Hocking},
title = {Linear time dynamic programming for computing breakpoints in the regularization path of models selected from a finite set},
journal = {Journal of Computational and Graphical Statistics},
volume = {31},
number = {2},
pages = {313--323},
year  = {2022},
publisher = {Taylor & Francis},
doi = {10.1080/10618600.2021.2000422}
}

@INPROCEEDINGS{Kolla2021fuzz,
  author={Kolla, Akhila Chowdary and Groce, Alex and Hocking, Toby Dylan},
  booktitle={2021 IEEE 32nd International Symposium on Software Reliability Engineering (ISSRE)}, 
  title={Fuzz Testing the Compiled Code in R Packages}, 
  year={2021},
  pages={300-308},
  doi={10.1109/ISSRE52982.2021.00040}}

@article{Hocking2021reshaping,
  author = {Toby Dylan Hocking},
  title = {{Wide-to-tall Data Reshaping Using Regular Expressions and the nc Package}},
  year = {2021},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2021-029},
  pages = {69--82},
  volume = {13},
  number = {1}
}

@article{Liehrmann2021chipseq,
  title={Increased peak detection accuracy in over-dispersed {ChIP-seq} data with supervised segmentation models},
  author={Liehrmann, Arnaud and Rigaill, Guillem and Hocking, Toby Dylan},
  journal={BMC Bioinformatics},
  volume={22},
  number={323},
  year={2021}
}

@article{Fotoohinasab2021greedy,
title = {A greedy graph search algorithm based on changepoint analysis for automatic QRS complex detection},
journal = {Computers in Biology and Medicine},
volume = {130},
pages = {104208},
year = {2021},
issn = {0010-4825},
doi = {10.1016/j.compbiomed.2021.104208},
url = {https://www.sciencedirect.com/science/article/pii/S0010482521000020},
author = {Atiyeh Fotoohinasab and Toby Hocking and Fatemeh Afghah},
keywords = {ECG segmentation, R-peak detection, Changepoint detection, Graph learning}
}

@article{Abraham2021gut,
author = {Abraham, Andrew J. and Prys-Jones, Tomos O. and De Cuyper, Annelies and Ridenour, Chase and Hempson, Gareth P. and Hocking, Toby and Clauss, Marcus and Doughty, Christopher E.},
title = {Improved estimation of gut passage time considerably affects trait-based dispersal models},
journal = {Functional Ecology},
volume = {35},
number = {4},
pages = {860-869},
keywords = {allometry, birds, diffusion capacity, dispersal, ecosystem service, functional traits, mammals, passage time},
doi = {10.1111/1365-2435.13726},
year = {2021}
}

@INPROCEEDINGS{Fotoohinasab2020automaticQRSdetectionAsilomar,
  author={Fotoohinasab, Atiyeh and Hocking, Toby and Afghah, Fatemeh},
  booktitle={2020 54th Asilomar Conference on Signals, Systems, and Computers}, 
  title={A Graph-Constrained Changepoint Learning Approach for Automatic QRS-Complex Detection}, 
  year={2020},
  pages={950-954},
  doi={10.1109/IEEECONF51394.2020.9443307}}

@INPROCEEDINGS{Fotoohinasab2020segmentationEMBC,
  author={Fotoohinasab, Atiyeh and Hocking, Toby and Afghah, Fatemeh},
  booktitle={2020 42nd Annual International Conference of the IEEE Engineering in Medicine Biology Society (EMBC)}, 
  title={A Graph-constrained Changepoint Detection Approach for ECG Segmentation}, 
  year={2020},
  pages={332-336},
  doi={10.1109/EMBC44109.2020.9175333}}

@article{Hocking2020jmlr,
  author  = {Toby Dylan Hocking and Guillem Rigaill and Paul Fearnhead and Guillaume Bourque},
  title   = {{Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection in Genomic Data}},
  journal = {Journal of Machine Learning Research},
  year    = {2020},
  volume  = {21},
  number  = {87},
  pages   = {1--40},
  url     = {http://jmlr.org/papers/v21/18-843.html}
}

@inproceedings{Hocking2020psb,
  title={{Machine Learning Algorithms for Simultaneous Supervised Detection of Peaks in Multiple Samples and Cell Types}},
  author={Toby Dylan Hocking and Guillaume Bourque},
  booktitle={Proc. Pacific Symposium on Biocomputing},
  volume = 25,
  pages = {367--378},
  year={2020}
}

@article{Hocking2019regex,
  author = {Toby Dylan Hocking},
  title = {{Comparing namedCapture with other R packages for regular expressions}},
  year = {2019},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2019-050},
  pages = {328--346},
  volume = {11},
  number = {2}
}

@article{Jewell2019biostatistics,
    author = {Jewell, Sean W and Hocking, Toby Dylan and Fearnhead, Paul and Witten, Daniela M},
    title = "{Fast nonconvex deconvolution of calcium imaging data}",
    journal = {Biostatistics},
    volume = {21},
    number = {4},
    pages = {709-726},
    year = {2019},
    month = {02},
    issn = {1465-4644},
    doi = {10.1093/biostatistics/kxy083},
    eprint = {https://academic.oup.com/biostatistics/article-pdf/21/4/709/33893963/kxy083.pdf}
}

@article{Sievert2019jcgs,
author = {Carson Sievert and Susan VanderPlas and Jun Cai and Kevin Ferris and Faizan Uddin Fahad Khan and Toby Dylan Hocking},
title = {Extending ggplot2 for Linked and Animated Web Graphics},
journal = {Journal of Computational and Graphical Statistics},
volume = {28},
number = {2},
pages = {299-308},
year  = {2019},
publisher = {Taylor & Francis}
}

@article{Depuydt2018meta,
  title={Meta-mining of copy number profiles of high-risk neuroblastoma tumors},
  author={Depuydt, Pauline and Koster, Jan and Boeva, Valentina and Hocking, Toby D and Speleman, Frank and Schleiermacher, Gudrun and De Preter, Katleen},
  journal={Scientific data},
  volume={5},
  number={1},
  pages={1--9},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{Alirezaie2018clinpred,
title = {ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants},
journal = {The American Journal of Human Genetics},
volume = {103},
number = {4},
pages = {474-483},
year = {2018},
issn = {0002-9297},
doi = {10.1016/j.ajhg.2018.08.005},
url = {https://www.sciencedirect.com/science/article/pii/S0002929718302714},
author = {Najmeh Alirezaie and Kristin D. Kernohan and Taila Hartley and Jacek Majewski and Toby Dylan Hocking},
keywords = {pathogenicity prediction, whole-exome sequencing, rare disease, cancer, diagnostic, computational biology, machine learning, variant interpretation, predictive modeling}
}

@article{Depuydt2018genomic,
  title={Genomic amplifications and distal 6q loss: novel markers for poor survival in high-risk neuroblastoma patients},
  author={Depuydt, Pauline and Boeva, Valentina and Hocking, Toby D and Cannoodt, Robrecht and Ambros, Inge M and Ambros, Peter F and Asgharzadeh, Shahab and Attiyeh, Edward F and Combaret, Valérie and Defferrari, Raffaella and Matthias Fischer and Barbara Hero and Michael D Hogarty and Meredith S Irwin and Jan Koster and Susan Kreissman and Ruth Ladenstein and Eve Lapouble and Geneviève Laureys and Wendy B London and Katia Mazzocco and Akira Nakagawara and Rosa Noguera and Miki Ohira and Julie R Park and Ulrike Pötschger and Jessica Theissen and Gian Paolo Tonini and Dominique Valteau-Couanet and Luigi Varesio and Rogier Versteeg and Frank Speleman and John M Maris and Gudrun Schleiermacher and Katleen De Preter},
  journal={JNCI: Journal of the National Cancer Institute},
  volume={110},
  number={10},
  pages={1084--1093},
  year={2018},
  publisher={Oxford University Press}
}

@inproceedings{Drouin2017mmit,
title = {Maximum Margin Interval Trees},
author = {Drouin, Alexandre and Hocking, Toby and Laviolette, Francois},
booktitle = {Advances in Neural Information Processing Systems 30},
editor = {I. Guyon and U. V. Luxburg and S. Bengio and H. Wallach and R. Fergus and S. Vishwanathan and R. Garnett},
pages = {4947--4956},
year = {2017},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/7080-maximum-margin-interval-trees.pdf}
}

@article{Hocking2017bioinfo,
    author = {Hocking, Toby Dylan and Goerner-Potvin, Patricia and Morin, Andreanne and Shao, Xiaojian and Pastinen, Tomi and Bourque, Guillaume},
    title = "{Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning}",
    journal = {Bioinformatics},
    volume = {33},
    number = {4},
    pages = {491--499},
    year = {2017},
    month = {11},
    issn = {1367-4803}
}

@Article{Maidstone2017optimal,
 author="Maidstone, Robert and Hocking, Toby and Rigaill, Guillem and Fearnhead, Paul",
 title="On optimal multiple changepoint algorithms for large data",
 journal="Statistics and Computing",
 volume=27,
 year="2017",
 pages="519--533",
 issn="1573-1375",
 doi={10.1007/s11222-016-9636-3}
}

@Article{Shimada2016leukemia,
   Author="Shimada, K.  and Shimada, S.  and Sugimoto, K.  and Nakatochi, M.  and Suguro, M.  and Hirakawa, A.  and Hocking, T. D.  and Takeuchi, I.  and Tokunaga, T.  and Takagi, Y.  and Sakamoto, A.  and Aoki, T.  and Naoe, T.  and Nakamura, S.  and Hayakawa, F.  and Seto, M.  and Tomita, A.  and Kiyoi, H. ",
   Title="{{D}evelopment and analysis of patient-derived xenograft mouse models in intravascular large {B}-cell lymphoma}",
   Journal="Leukemia",
   Year="2016",
   Volume="30",
   Number="7",
   Pages="1568--1579",
   Month="07"
}

@article{Chicard2016cancer,
    author = {Chicard, Mathieu and Boyault, Sandrine and Colmet Daage, Leo and Richer, Wilfrid and Gentien, David and Pierron, Gaelle and Lapouble, Eve and Bellini, Angela and Clement, Nathalie and Iacono, Isabelle and Bréjon, Stéphanie and Carrere, Marjorie and Reyes, Cécile and Hocking, Toby and Bernard, Virginie and Peuchmaur, Michel and Corradini, Nadège and Faure-Conter, Cécile and Coze, Carole and Plantaz, Dominique and Defachelles, Anne Sophie and Thebaud, Estelle and Gambart, Marion and Millot, Frédéric and Valteau-Couanet, Dominique and Michon, Jean and Puisieux, Alain and Delattre, Olivier and Combaret, Valérie and Schleiermacher, Gudrun},
    title = "{Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma}",
    journal = {Clinical Cancer Research},
    volume = {22},
    number = {22},
    pages = {5564-5573},
    year = {2016},
    month = {11},
    issn = {1078-0432},
    url = {https://aacrjournals.org/clincancerres/article-pdf/22/22/5564/2035258/5564.pdf},
    doi = {10.1158/1078-0432.CCR-16-0500}
}

@inproceedings{Hocking2015icml,
  title={{PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data}},
  author={Toby Dylan Hocking and Guillem Rigaill and Guillaume Bourque},
  booktitle={Proc. 32nd ICML},
  pages = {324--332},
  year={2015}
}

@Article{Suguro2014cancer,
   Author="Suguro, M.  and Yoshida, N.  and Umino, A.  and Kato, H.  and Tagawa, H.  and Nakagawa, M.  and Fukuhara, N.  and Karnan, S.  and Takeuchi, I.  and Hocking, T. D.  and Arita, K.  and Karube, K.  and Tsuzuki, S.  and Nakamura, S.  and Kinoshita, T.  and Seto, M. ",
   Title="{{C}lonal heterogeneity of lymphoid malignancies correlates with poor prognosis}",
   Journal="Cancer Sci",
   Year="2014",
   Volume="105",
   Number="7",
   Pages="897--904",
   Month="Jul"
}

@Article{Hocking2014bioinformatics,
  author = 	 {Hocking, TD and Boeva, V and Rigaill, G and Schleiermacher, G and Janoueix-Lerosey, I and Delattre, O and Richer, W and Bourdeaut, F and Suguro, M and Seto, M and Bach, F and Vert, JP},
  title = 	 {{SegAnnDB}: interactive Web-based genomic segmentation},
  journal = 	 {Bioinformatics},
  year = 	 2014,
  volume = 	 30,
  number = 	 11,
  pages = 	 {1539--46}}

@article{Hocking2013sustainable,
  title={Sustainable, Extensible Documentation Generation using inlinedocs},
  author={Hocking, Toby Dylan and Wutzler, Thomas and Ponting, Keith and Grosjean, Philippe},
  journal={Journal of Statistical Software},
  volume={54},
  pages={1--20},
  year={2013}
}

@Article{Hocking2013bioinformatics,
  author = 	 {Toby Dylan Hocking and Gudrun Schleiermacher and Isabelle Janoueix-Lerosey and Valentina Boeva and Julie Cappo and Oliver Delattre and Francis Bach and Jean-Philippe Vert},
  title = 	 {Learning smoothing models of copy number profiles using breakpoint annotations},
  journal = 	 {BMC Bioinformatics},
  year = 	 2013,
  volume = 	 14,
  number = 	 164,
  month = 	 {May}}

@inproceedings{Hocking2013icml,
  title={Learning sparse penalties for change-point detection using max margin interval regression},
  author={ Rigaill, Guillem and Hocking, Toby and Vert, Jean-Philippe and Bach, Francis},
  booktitle={Proc. 30th ICML},
  pages={172--180},
  year={2013}
}

@phdthesis{Hocking2012phd,
  title={Learning algorithms and statistical software, with applications to bioinformatics},
  author={Hocking, Toby Dylan},
  year={2012},
  school={Ecole normale supérieure de Cachan}
}

@inproceedings{Hocking2011clusterpath,
  title={Clusterpath an algorithm for clustering using convex fusion penalties},
  author={Hocking, Toby Dylan and Joulin, Armand and Bach, Francis and Vert, Jean-Philippe},
  booktitle={28th international conference on machine learning},
  pages={1},
  year={2011}
}

@article{Gautier2010bayesian,
  title={A Bayesian outlier criterion to detect SNPs under selection in large data sets},
  author={Gautier, Mathieu and Hocking, Toby Dylan and Foulley, Jean-Louis},
  journal={PLoS one},
  volume={5},
  number={8},
  pages={e11913},
  year={2010},
  publisher={Public Library of Science San Francisco, USA}
}

@article{Doyon2008heritable,
  title={Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases},
  author={Doyon, Yannick and McCammon, Jasmine M and Miller, Jeffrey C and Faraji, Farhoud and Ngo, Catherine and Katibah, George E and Amora, Rainier and Hocking, Toby D and Zhang, Lei and Rebar, Edward J and Gregory, Philip D and Urnov, Fyodor D and Amacher, Sharon L},
  journal={Nature biotechnology},
  volume={26},
  number={6},
  pages={702--708},
  year={2008},
  publisher={Nature Publishing Group US New York}
}