Neil Lawrence's Publications

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2017

Technical Reports

2016

Journal Papers

Conference Papers

Technical Reports

2015

Journal Papers

    Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

    Antti Honkela University of Helsinki, Jaakko Peltonen Aalto University, Hande Topa Aalto University, Iryna Charapitsa Institute for Molecular Biology, Mainz, Filomena Matarese Radboud University, Korbinian Grote Genomatix Software, Hendrik G. Stunnenberg Radboud University, George Reid Institute for Molecular Biology, Mainz, Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester in Proc. Natl. Acad. Sci. USA 112 (42), pp 13115-13120

    A reverse-engineering approach to dissect post-translational modulators of transcription factor’s activity from transcriptional data

    Gennaro Gambardella, Ivana Peluso, Sandro Montefusco, Mukesh Bansal, Diego L. Medina, Neil D. Lawrence University of Sheffield, Diego Bernardo in BMC Bioinformatics 16 (279)

Conference Papers

    Semi-described and semi-supervised learning with Gaussian processes

    Andreas Damianou University of Sheffield, Neil D. Lawrence University of Sheffield in 31st Conference on Uncertainty in Artificial Intelligence (UAI)

2014

Journal Papers

    Consistent mapping of government malaria records across a changing territory delimitation

    Ricardo Andrade-Pacheco UCSF Global Health Science, Martin Mubangizi United Nations Global Pulse, John Quinn United Nations Global Pulse and Makerere University, Neil D. Lawrence University of Sheffield in Malaria Journal 13 (Suppl 1)

    Time-frequency Analysis as Probabilistic Inference

    Richard E. Turner, Maneesh Sahani in IEEE Transactions on Signal Processing 62 (23), pp 6171-6181

    Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data

    Ciira Maina Dedan Kimathi University of Technology, Antti Honkela University of Helsinki, Filomena Matarese, Korbinian Grote, Hendrik G. Stunnenberg, George Reid, Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester in PLoS Computat Biol 10 (5), pp 0-0

    Fast nonparametric clustering of structured time-series

    James Hensman University of Lancaster, Magnus Rattray University of Manchester, Neil D. Lawrence University of Sheffield in IEEE Transactions on Pattern Analysis and Machine Intelligence

    Warped linear mixed models for the genetic analysis of transformed phenotypes

    Nicoló Fusi Microsoft Research, New England, Christoph Lippert Human Longevity, Inc, Neil D. Lawrence University of Sheffield, Oliver Stegle European Bioinformatics Institute in Nature Communications 5 (4890)

    Variational Inference for Uncertainty on the Inputs of Gaussian Process Models

    Andreas Damianou University of Sheffield, Michalis K. Titsias University of Athens, Neil D. Lawrence University of Sheffield in ar{X}iv preprint ar{X}iv:1409.2287

Conference Papers

Technical Reports

Miscellaneous

2013

Journal Papers

    Linear Latent Force Models Using Gaussian Processes

    Mauricio A. Álvarez Universidad Tecnológica de Pereira, Colombia, David Luengo Universidad Politécnica de Madrid, Neil D. Lawrence University of Sheffield in IEEE Transactions on Pattern Analysis and Machine Intelligence 35 (11), pp 2693-2705

    Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters

    James Hensman University of Lancaster, Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester in BMC Bioinformatics 14 (252)

    Detecting Regulatory Gene-Environment Interactions with Unmeasured Environmental Factors

    Nicoló Fusi Microsoft Research, New England, Christoph Lippert Human Longevity, Inc, Karsten Borgwardt ETH Zurich, Neil D. Lawrence University of Sheffield, Oliver Stegle European Bioinformatics Institute in Bioinformatics 29 (11), pp 1382-1389

    Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased susceptibility to excitotoxicity

    Alice Brockington, Ke Ning, Paul R. Heath, Elizabeth Wood, Janine Kirby, Nicoló Fusi Microsoft Research, New England, Neil D. Lawrence University of Sheffield, Stephen B. Wharton, Paul G. Ince, Pamela J. Shaw in Acta Neuropathologica 125 (1)

Conference Papers

Book Chapters

    Mining Regulatory Network Connections by Ranking Transcription Factor Target Genes Using Time Series Expression Data

    Antti Honkela University of Helsinki, Magnus Rattray University of Manchester, Neil D. Lawrence University of Sheffield in Data Mining for Systems Biology (, , eds)

2012

Journal Papers

    Identifying Targets of Multiple Co-regulated Transcription Factors from Expression Time-series by Bayesian Model Comparison

    Michalis K. Titsias University of Athens, Antti Honkela University of Helsinki, Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester in BMC Systems Biology 6 (53)

    Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of Telomere Clustering and Chromosome Rigidity to Homologue Juxtaposition

    Christopher A. Penfold University of Cambridge, Paul E. Brown, Neil D. Lawrence University of Sheffield, Alastair S. H. Goldman in PLoS Computat Biol 8 (5), pp 0-0

    Improved linear mixed models for genome-wide association studies

    Jennifer Listgarten, Christoph Lippert Human Longevity, Inc, Carl M. Kadie, Robert I. Davidson, Eleazar Eskin, David Heckerman in Nature Methods 9, pp 525-526

    A Unifying Probabilistic Perspective for Spectral Dimensionality Reduction: Insights and New Models

    Neil D. Lawrence University of Sheffield in Journal of Machine Learning Research 13

    Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

    Nicoló Fusi Microsoft Research, New England, Oliver Stegle European Bioinformatics Institute, Neil D. Lawrence University of Sheffield in PLoS Computat Biol 8, pp 0-0

    Genome-wide occupancy links Hoxa2 to Wnt-$\beta$-catenin signaling in mouse embryonic development

    Ian J. Donaldson, Shilu Amin, James Hensman University of Lancaster, Eva Kutejova, Magnus Rattray University of Manchester, Neil D. Lawrence University of Sheffield, Andrew Hayes, Christopher M. Ward, Nicoletta Bobola in Nucleaic Acids Research 40 (9), pp 3390-4001

    Kernels for Vector-Valued Functions: A Review

    Mauricio A. Álvarez Universidad Tecnológica de Pereira, Colombia, Lorenzo Rosasco University of Genoa, Neil D. Lawrence University of Sheffield in Foundations and Trends in Machine Learning 4 (3), pp 195-266

Conference Papers

Technical Reports

2011

Journal Papers

    Computationally Efficient Convolved Multiple Output Gaussian Processes

    Mauricio A. Álvarez Universidad Tecnológica de Pereira, Colombia, Neil D. Lawrence University of Sheffield in Journal of Machine Learning Research 12, pp 1425-1466

    Demodulation as Probabilistic Inference

    Richard E. Turner, Maneesh Sahani in IEEE Transactions on Audio, Speech, and Language Processing 19 (), pp 2398-2411

    Overlapping Mixtures of Gaussian Processes for the Data Association Problem

    Miguel Lázaro Gredilla, Steven Van Vaerenbergh, Neil D. Lawrence University of Sheffield in Pattern Recognition 10 (4)

    A Simple Approach to Ranking Differentially Expressed Gene Expression Time Courses through Gaussian Process Regression

    Alfredo A. Kalaitzis Microsoft, Neil D. Lawrence University of Sheffield in BMC Bioinformatics 12 (180)

    tigre: Transcription factor inference through Gaussian process reconstruction of expression for Bioconductor

    Antti Honkela University of Helsinki, Pei Gao Peking University, Jonatan Ropponen, Magnus Rattray University of Manchester, Neil D. Lawrence University of Sheffield in Bioinformatics 27, pp 1026-1027

Conference Papers

Book Chapters

Technical Reports

2010

Journal Papers

    Model-based Method for Transcription Factor Target Identification with Limited Data

    Antti Honkela University of Helsinki, Charles Girardot, E. Hilary Gustafson, Ya-Hsin Liu, Eileen E. M. Furlong, Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester in Proc. Natl. Acad. Sci. USA 107 (17), pp 7793-7798

    Elementary properties of CaV1.3 Ca2+ channels expressed in mouse cochlear inner hair cells

    Valeria Zampini, Stuart Leigh Johnson, Christoph Franz, Neil D. Lawrence University of Sheffield, Stefan Muenkner Jutta Engel, Marlies Knipper, Jacopo Magistretti, Sergio Masetto, Walter Marcotti in The Journal of Physiology 588, pp 187-189

    TFInfer: a tool for probabilistic inference of transcription factor activities

    H. M. Shahzad Asif, Matthew D. Rolfe, Jeff Green, Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester, Guido Sanguinetti University of Edinburgh in Bioinformatics 26, pp 2635-2636

Conference Papers

Book Chapters

    Introduction to Learning and Inference in Computational Systems Biology

    Neil D. Lawrence University of Sheffield in Chapter 1 of Learning and Inference in Computational Systems Biology (, , , eds)

    Gaussian Processes for Missing Species in Biochemical Systems

    Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester, Pei Gao Peking University, Michalis K. Titsias University of Athens in Chapter 9 of Learning and Inference in Computational Systems Biology (, , , eds)

    A Brief Introduction to Bayesian Inference

    Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester in Chapter 5 of Learning and Inference in Computational Systems Biology (, , , eds)

Technical Reports

2009

Journal Papers

    puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis

    Richard D. Pearson, Xuejun Liu Nanjing University of Aeronautics and Astronautics, Guido Sanguinetti University of Edinburgh, Marta Milo University of Sheffield, Neil D. Lawrence University of Sheffield, Magnus Rattray University of Manchester in BMC Bioinformatics 10 (211)

    The variational Gaussian approximation revisited

    Manfred Opper, Cedric Archambeau in Neural Computation 21 (3), pp 786-792

Conference Papers

Technical Reports

2008

Journal Papers

    Probabilistic approach to detecting dependencies between data sets

    Aarto Klami, Sami Kaski in Neurocomputing 72, pp 39-46

    Gaussian Process Modelling of Latent Chemical Species: Applications to Inferring Transcription Factor Activities

    Pei Gao Peking University, Antti Honkela University of Helsinki, Magnus Rattray University of Manchester, Neil D. Lawrence University of Sheffield in Bioinformatics 24, pp 0-0

Conference Papers

2007

Conference Papers

    Model-driven detection of Clean Speech Patches in Noise

    Jonathan Laidler Plusnet, Sheffield, Martin Cooke University of the Basque Country, Neil D. Lawrence University of Sheffield in Proceedings of Interspeech 2007

    Modelling transcriptional regulation using Gaussian Processes

    Neil D. Lawrence University of Sheffield, Guido Sanguinetti University of Edinburgh, Magnus Rattray University of Manchester in Advances in Neural Information Processing Systems (, , eds), pp 785-792

    Learning for Larger Datasets with the Gaussian Process Latent Variable Model

    Neil D. Lawrence University of Sheffield in Proceedings of the Eleventh International Workshop on Artificial Intelligence and Statistics (, eds), pp 243-250

    Hierarchical Gaussian Process Latent Variable Models

    Neil D. Lawrence University of Sheffield, Andrew J. Moore in Proceedings of the International Conference in Machine Learning ( ed.), pp 481-488

    WiFi-SLAM Using Gaussian Process Latent Variable Models

    Brian D. Ferris, Dieter Fox, Neil D. Lawrence University of Sheffield in Proceedings of the 20th International Joint Conference on Artificial Intelligence (IJCAI 2007) ( ed.), pp 2480-2485

    Gaussian Process Latent Variable Models for Fault Detection

    Luka Eciolaza, M. Alkarouri, Neil D. Lawrence University of Sheffield, Visakan Kadirkamanathan, Peter J. Fleming in Computational Intelligence and Data Mining, pp 287-292

Miscellaneous

2006

Journal Papers

Conference Papers

Book Chapters

Technical Reports

2005

Journal Papers

Conference Papers

Book Chapters

Technical Reports

Miscellaneous

2004

Journal Papers

Conference Papers

    Learning to Learn with the Informative Vector Machine

    Neil D. Lawrence University of Sheffield, John C. Platt Google in Proceedings of the International Conference in Machine Learning (, eds), pp 512-519

    Gaussian Process Models for Visualisation of High Dimensional Data

    Neil D. Lawrence University of Sheffield in Advances in Neural Information Processing Systems (, , eds), pp 329-336

    Acoustic Space Dimensionality Selection and Combination using the Maximum Entropy Principle

    Yasser H. Abdel-Haleem, Steve Renals University of Edinburgh, Neil D. Lawrence University of Sheffield in International Conference on Acoustics, Speech and Signal Processing

Technical Reports

2003

Journal Papers

    A Probabilistic Model for the Extraction of Expression Levels from Oligonucleotide Arrays

    Marta Milo University of Sheffield, Alireza Fazeli, Mahesan Niranjan University of Southampton, Neil D. Lawrence University of Sheffield in Biochemical Transations 31 (6), pp 1510-1512

Conference Papers

    Variational Inference for Visual Tracking

    Jaco Vermaak, Neil D. Lawrence University of Sheffield, Patrick Pérez in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp 773-780

    A Variational Approach to Robust Bayesian Interpolation

    Michael E. Tipping, Neil D. Lawrence University of Sheffield in Neural Networks for Signal Processing XIII (, , , , , eds), pp 229-238

    Fast Forward Selection to Speed Up Sparse Gaussian Process Regression

    Matthias Seeger Amazon, Christopher K. I. Williams, Neil D. Lawrence University of Sheffield in Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics (, eds)

    Bayesian Processing of Microarray Images

    Neil D. Lawrence University of Sheffield, Marta Milo University of Sheffield, Mahesan Niranjan University of Southampton, Penny Rashbass, Stephan Soullier in Neural Networks for Signal Processing XIII (, , , , , eds), pp 71-80

    Fast Sparse Gaussian Process Methods: The Informative Vector Machine

    Neil D. Lawrence University of Sheffield, Matthias Seeger Amazon, Ralf Herbrich Amazon in Advances in Neural Information Processing Systems (, , eds), pp 625-632

Technical Reports

2002

Conference Papers

    Optimising Synchronisation Times for Mobile Devices

    Neil D. Lawrence University of Sheffield, Anthony I. T. Rowstron, Christopher M. Bishop Microsoft Research, Cambridge, Michael J. Taylor in Advances in Neural Information Processing Systems (, , eds), pp 1401-1408

Technical Reports

2001

Journal Papers

    A Comparison of State-of-the-Art Classification Techniques with Application to Cytogenetics

    Boaz Lerner Ben Gurion University, Neil D. Lawrence University of Sheffield in Neural Computing and Applications 10 (1), pp 39-47

Conference Papers

Technical Reports

Miscellaneous

2000

Technical Reports

1999

Technical Reports

1998

Conference Papers

Technical Reports

0001

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