• My page on Google Scholar.
  • Peer review notice: in addition to peer-reviewed journals, I publish papers at machine learning conferences such as ICML and NIPS, which have double-blind peer reviews, and only accept about 20% of submitted papers.
  • Reproducible Research notice: a “Reproducible” link for each paper below provides source code and data that I used to perform the analysis and make the figures/tables.
  • Software notice: a “Software” link for each paper below provides a software package with a reference implementation of the algorithms described in our paper.

In progress

  • Sievert C, Cai J, VanderPlas S, Khan F, Hocking TD. Extending ggplot2’s grammar of graphics implementation for linked and dynamic graphics on the web. Software, Reproducible
  • Hocking TD, Rigaill G, Fearnhead P, Bourque G. A log-linear segmentation algorithm for peak detection in genomic data. Preprint arXiv:1703.03352. Under review at Annals of Applied Statistics. Software, Reproducible
  • Hocking TD, Khare A. Learning penalty functions for changepoint detection using elastic-net regularized accelerated failure time models. Software, Reproducible
  • Jewell S, Hocking TD, Fearnhead P, Witten D. Fast Nonconvex Deconvolution of Calcium Imaging Data. Preprint arXiv:1802.07380. Under review at PLOS Comp Bio.
  • Narahara M, Hocking TD, Bourque G, Yamada R, Setoh K, Matsuda F, Lathrop M. Transcriptomic analysis of antibody responses to seasonal influenza vaccine reveals predictive gene signatures and potential key transcription factors.
  • Alirezaie N, Majewski J, Hocking TD. A supervised machine learning method for predicting pathogenicity of genetic variants.
  • Venuto D, Hocking TD. Support vector machines for predicting outcomes of chess games.

2018

  • Depuydt P, Boeva V, Hocking TD, Cannoodt R, Ambros IM, Ambros PF, Asgharzadeh S, Attiyeh EF, Combaret V, Defferrari R, Fischer M, Hero B, Hogarty MD, Irwin MS, Koster J, Kreissman S, Ladenstein R, Lapouble E, Laureys G, London WB, Mazzocco K, Nakagawara A, Noguera R, Ohira M, Park JR, Pötschger U, Theissen J, Tonini GP, Valteau-Couanet D, Varesio L, Versteeg R, Speleman F, Maris JM, Schleiermacher G, De Preter K. Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients. Journal of the National Cancer Institute 2008. DOI:10.1093/jnci/djy022. JNCI

2017

  • Drouin A, Hocking TD, Laviolette F. Maximum margin interval trees. Neural Information Processing Systems (NIPS) 2017. Software, Reproducible, arXiv, NIPS, video
  • Hocking TD, Goerner-Potvin P, Morin A, Shao X, Pastinen T, Bourque G. Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. Bioinformatics (2017) 33 (4): 491-499. pubmed, Software, Reproducible

2016

  • Shimada K, Shimada S, Sugimoto K, Nakatochi M, Suguro M, Hirakawa A, Hocking TD, Takeuchi I, Tokunaga T, Takagi Y, Sakamoto A, Aoki T, Naoe T, Nakamura S, Hayakawa F, Seto M, Tomita A, Kiyoi H. Development and analysis of patient-derived xenograft mouse models in intravascular large B-cell lymphoma. Leukemia 2016. pubmed
  • Chicard M, Boyault S, Colmet-Daage L, Richer W, Gentien D, Pierron G, Lapouble E, Bellini A, Clement N, Iacono I, Bréjon S, Carrere M, Reyes C, Hocking TD, Bernard V, Peuchmaur M, Corradini N, Faure-Conter C, Coze C, Plantaz D, Defachelles A-S, Thebaud E, Gambart M, Millot F, Valteau-Couanet D, Michon J, Puisieux A, Delattre O, Combaret V, Schleiermacher G. Genomic copy number profiling using circulating free tumor DNA highlights heterogeneity in neuroblastoma. Clinical Cancer Research 2016. journal
  • Maidstone R, Hocking TD, Rigaill G, Fearnhead P. On optimal multiple changepoint algorithms for large data. Statistics and Computing (2016). doi:10.1007/s11222-016-9636-3 journal, Software, Reproducible

2015

2014

  • Suguro M, Yoshida N, Umino A, Kato H, Tagawa H, Nakagawa M, Fukuhara N, Karnan S, Takeuchi I, Hocking TD, Arita K, Karube K, Tsuzuki S, Nakamura S, Kinoshita T, Seto M. Clonal heterogeneity of lymphoid malignancies correlates with poor prognosis. Cancer Sci. 2014 Jul;105(7):897-904. pubmed
  • Hocking TD, Boeva V, Rigaill G, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Richer W, Bourdeaut F, Suguro M, Seto M, Bach F, Vert J-P. SegAnnDB: interactive Web-based genomic segmentation. Bioinformatics (2014) 30 (11): 1539-1546. DOI:10.1093/bioinformatics/btu072 pubmed, Software, Reproducible
  • Spanurattana S, Sugiyama M, Hocking TD. Support vector comparison machines. Preprint arXiv:1401.8008. Software, Reproducible

2013

  • Hocking TD, Wutzler T, Ponting K and Grosjean P. Sustainable, extensible documentation generation using inlinedocs. Journal of Statistical Software (2013), 54(6), 1-20. DOI:10.18637/jss.v054.i06 journal, Software, Reproducible
  • Hocking TD, Schleiermacher G, Janoueix-Lerosey I, Boeva V, Cappo J, Delattre O, Bach F, Vert J-P. Learning smoothing models of copy number profiles using breakpoint annotations. BMC Bioinfo. 2013, 14:164. DOI:10.1186/1471-2105-14-164 journal, Software, Reproducible
  • Hocking TD, Rigaill G, Bach F, Vert J-P. Learning sparse penalties for change-point detection using max-margin interval regression. International Conference on Machine Learning (ICML), 2013. PMLR, video Software, Reproducible

2012

  • Hocking TD, Rigaill G. SegAnnot: an R package for fast segmentation of annotated piecewise constant signals, Preprint hal-00759129. Software, Reproducible
  • Hocking TD. Learning algorithms and statistical software, with applications to bioinformatics. PhD thesis, Ecole Normale Superieure de Cachan, France. tel-00906029, Reproducible

2011

  • Hocking TD, Joulin A, Bach F, Vert J-P. Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties. International Conference on Machine Learning (ICML), 2011. pdf, video Software, Reproducible

2010

  • Gautier M, Hocking TD, Foulley JL. A Bayesian outlier criterion to detect SNPs under selection in large data sets. PloS ONE 5 (8), e11913 (2010). journal

2008

  • Doyon Y, McCammon JM, Miller JC, Faraji F, Ngo C, Katibah GE, Amora R, Hocking TD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Amacher SL. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nature biotechnology 26 (6), 702-70 (2008). pubmed