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@article{angermueller2016deep,
title={Deep Learning for Computational Biology},
author={Angermueller, Christof, Tanel Pärnamaa, Leopold Parts, and Oliver Stegle},
journal={Molecular Systems Biology},
volume = {12},
number = {7},
pages = {878},
year={2016}
}
@article{penfold2017nonparametric,
title={Nonparametric Bayesian inference of transcriptional branching and recombination identifies regulators of early human germ cell development},
author={Penfold, Christopher Andrew and Sybirna, Anastasiya and Reid, John and Huang, Yun and Wernisch, Lorenz and Ghahramani, Zoubin and Grant, Murray and Surani, M Azim},
journal={bioRxiv},
pages={167684},
year={2017},
publisher={Cold Spring Harbor Labs Journals}
}
@article {Breeze873,
author = {Breeze, Emily and Harrison, Elizabeth and McHattie, Stuart and Hughes, Linda and Hickman, Richard and Hill, Claire and Kiddle, Steven and Kim, Youn-sung and Penfold, Christopher A. and Jenkins, Dafyd and Zhang, Cunjin and Morris, Karl and Jenner, Carol and Jackson, Stephen and Thomas, Brian and Tabrett, Alexandra and Legaie, Roxane and Moore, Jonathan D. and Wild, David L. and Ott, Sascha and Rand, David and Beynon, Jim and Denby, Katherine and Mead, Andrew and Buchanan-Wollaston, Vicky},
title = {High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation},
volume = {23},
number = {3},
pages = {873--894},
year = {2011},
doi = {10.1105/tpc.111.083345},
publisher = {American Society of Plant Biologists},
issn = {1040-4651},
URL = {http://www.plantcell.org/content/23/3/873},
eprint = {http://www.plantcell.org/content/23/3/873.full.pdf},
journal = {The Plant Cell Online}
}
@article{Huang2017stella,
title={Stella controls transcriptional and endogenous retrovirus programmes during maternal-to-zygotic transition},
author={Huang, Yun and Kim, Jong, Kyoung and Do, Dang V and Lee, Caroline and Penfold, Christopher A. and Zylicz, Jan J and Marioni, John C. and Hackett, Jamie A. and Surani, M. Azim},
journal={eLife},
volume={1},
number={1},
pages={1},
year={2017},
publisher={eLife}
}
@article{payer2003stella,
title={Stella is a maternal effect gene required for normal early development in mice},
author={Payer, Bernhard and Saitou, Mitinori and Barton, Sheila C and Thresher, Rosemary and Dixon, John PC and Zahn, Dirk and Colledge, William H and Carlton, Mark BL and Nakano, Toru and Surani, M Azim},
journal={Current Biology},
volume={13},
number={23},
pages={2110--2117},
year={2003},
publisher={Elsevier}
}
@article{bortvin2004dppa3,
title={Dppa3/Pgc7/stella is a maternal factor and is not required for germ cell specification in mice},
author={Bortvin, Alex and Goodheart, Mary and Liao, Michelle and Page, David C},
journal={BMC developmental biology},
volume={4},
number={1},
pages={2},
year={2004},
publisher={BioMed Central}
}
@article{panula2016over,
title={Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells},
author={Panula, Sarita and Reda, Ahmed and Stukenborg, Jan-Bernd and Ramathal, Cyril and Sukhwani, Meena and Albalushi, Halima and Edsg{\"a}rd, Daniel and Nakamura, Michiko and S{\"o}der, Olle and Orwig, Kyle E and others},
journal={PloS one},
volume={11},
number={10},
pages={e0165268},
year={2016},
publisher={Public Library of Science}
}
@article{kobayashi2017principles,
title={Principles of early human development and germ cell program from conserved model systems},
author={Kobayashi, Toshihiro and Zhang, Haixin and Tang, Walfred WC and Irie, Naoko and Withey, Sarah and Klisch, Doris and Sybirna, Anastasiya and Dietmann, Sabine and Contreras, David A and Webb, Robert and others},
journal={Nature},
volume={546},
number={7658},
pages={416--420},
year={2017},
publisher={Nature Research}
}
@article{van2012visualizing,
title={Visualizing non-metric similarities in multiple maps},
author={Van der Maaten, Laurens and Hinton, Geoffrey},
journal={Machine learning},
volume={87},
number={1},
pages={33--55},
year={2012},
publisher={Springer}
}
@article{van2009learning,
title={Learning a parametric embedding by preserving local structure},
author={van der Maaten, Laurens},
journal={RBM},
volume={500},
number={500},
pages={26},
year={2009}
}
@article{maaten2008visualizing,
title={Visualizing data using t-SNE},
author={Maaten, Laurens van der and Hinton, Geoffrey},
journal={Journal of Machine Learning Research},
volume={9},
number={Nov},
pages={2579--2605},
year={2008}
}
@article{reich2008principal,
title={Principal component analysis of genetic data},
author={Reich, David and Price, Alkes L and Patterson, Nick},
journal={Nature genetics},
volume={40},
number={5},
pages={491--492},
year={2008},
publisher={Nature Publishing Group}
}
@article{guo2015transcriptome,
title={The transcriptome and {DNA} methylome landscapes of human primordial germ cells},
author={Guo, Fan and Yan, Liying and Guo, Hongshan and Li, Lin and Hu, Boqiang and Zhao, Yangyu and Yong, Jun and Hu, Yuqiong and Wang, Xiaoye and Wei, Yuan and others},
journal={Cell},
volume={161},
number={6},
pages={1437--1452},
year={2015},
publisher={Elsevier}
}
@article{yan2013single,
title={Single-cell {RNA}-Seq profiling of human preimplantation embryos and embryonic stem cells},
author={Yan, Liying and Yang, Mingyu and Guo, Hongshan and Yang, Lu and Wu, Jun and Li, Rong and Liu, Ping and Lian, Ying and Zheng, Xiaoying and Yan, Jie and others},
journal={Nature structural \& molecular biology},
volume={20},
number={9},
pages={1131--1139},
year={2013},
publisher={Nature Publishing Group}
}
@article{novembre2008interpreting,
title={Interpreting principal component analyses of spatial population genetic variation},
author={Novembre, John and Stephens, Matthew},
journal={Nature genetics},
volume={40},
number={5},
pages={646--649},
year={2008},
publisher={Nature Publishing Group}
}
@article{saal2007poor,
title={Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity},
author={Saal, Lao H and Johansson, Peter and Holm, Karolina and Gruvberger-Saal, Sofia K and She, Qing-Bai and Maurer, Matthew and Koujak, Susan and Ferrando, Adolfo A and Malmstr{\"o}m, Per and Memeo, Lorenzo and others},
journal={Proceedings of the National Academy of Sciences},
volume={104},
number={18},
pages={7564--7569},
year={2007},
publisher={National Acad Sciences}
}
@article{ringner2008principal,
title={What is principal component analysis?},
author={Ringn{\'e}r, Markus},
journal={Nature biotechnology},
volume={26},
number={3},
pages={303--304},
year={2008},
publisher={Nature Publishing Group}
}
@article{craig1997developmental,
title={Developmental expression of morphoregulatory genes in the mouse embryo: an analytical approach using a novel technology},
author={Craig, JC and Eberwine, JH and Calvin, JA and Wlodarczyk, B and Bennett, GD and Finnell, RH},
journal={Biochemical and molecular medicine},
volume={60},
number={2},
pages={81--91},
year={1997},
publisher={Elsevier}
}
@article{hilsenbeck1999statistical,
title={Statistical analysis of array expression data as applied to the problem of tamoxifen resistance},
author={Hilsenbeck, Susan G and Friedrichs, William E and Schiff, Rachel and O'connell, Peter and Hansen, Rhonda K and Osborne, C Kent and Fuqua, Suzanne AW},
journal={Journal of the National Cancer Institute},
volume={91},
number={5},
pages={453--459},
year={1999},
publisher={Oxford University Press}
}
@article{vohradsky1997identification,
title={Identification of procaryotic developmental stages by statistical analyses of two-dimensional gel patterns},
author={Vohradsky, Ji{\v{r}}{\'\i} and Li, Xin-Ming and Thompson, Charles J},
journal={Electrophoresis},
volume={18},
number={8},
pages={1418--1428},
year={1997},
publisher={Wiley Online Library}
}
@article{sforza1964analysis,
title={Analysis of human evolution},
author={Sforza, Cavalli LL and Edwards, Anthony William Fairbank},
journal={Genet. Today},
volume={3},
pages={923--933},
year={1964}
}
@article{hotelling1933analysis,
title={Analysis of a complex of statistical variables into principal components.},
author={Hotelling, Harold},
journal={Journal of educational psychology},
volume={24},
number={6},
pages={417},
year={1933},
publisher={Warwick \& York}
}
@article{pearson1901liii,
title={LIII. On lines and planes of closest fit to systems of points in space},
author={Pearson, Karl},
journal={The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science},
volume={2},
number={11},
pages={559--572},
year={1901},
publisher={Taylor \& Francis}
}
@article{tang2009mrna,
title={mRNA-Seq whole-transcriptome analysis of a single cell},
author={Tang, Fuchou and Barbacioru, Catalin and Wang, Yangzhou and Nordman, Ellen and Lee, Clarence and Xu, Nanlan and Wang, Xiaohui and Bodeau, John and Tuch, Brian B and Siddiqui, Asim and others},
journal={Nature methods},
volume={6},
number={5},
pages={377--382},
year={2009},
publisher={Nature Publishing Group}
}
@article{svensson2017moore,
title={Moore's Law in Single Cell Transcriptomics},
author={Svensson, Valentine and Vento-Tormo, Roser and Teichmann, Sarah A},
journal={arXiv preprint arXiv:1704.01379},
year={2017}
}
@article{tang2015unique,
title={A unique gene regulatory network resets the human germline epigenome for development},
author={Tang, Walfred WC and Dietmann, Sabine and Irie, Naoko and Leitch, Harry G and Floros, Vasileios I and Bradshaw, Charles R and Hackett, Jamie A and Chinnery, Patrick F and Surani, M Azim},
journal={Cell},
volume={161},
number={6},
pages={1453--1467},
year={2015},
publisher={Elsevier}
}
@article{irie2015sox17,
title={{SOX}17 is a critical specifier of human primordial germ cell fate},
author={Irie, Naoko and Weinberger, Leehee and Tang, Walfred WC and Kobayashi, Toshihiro and Viukov, Sergey and Manor, Yair S and Dietmann, Sabine and Hanna, Jacob H and Surani, M Azim},
journal={Cell},
volume={160},
number={1},
pages={253--268},
year={2015},
publisher={Elsevier}
}
@article {Bechtold,
author = {Bechtold, Ulrike and Penfold, Christopher A and Jenkins, Dafyd J and Legaie, Roxane and Moore, Jonathan D and Lawson, Tracy and Matthews, Jack SA and Vialet-Chabrand, Silvere RM and Baxter, Laura and Subramaniam, Sunitha and Hickman, Richard and Florance, Hannah and Sambles, Christine and Salmon, Deborah L and Feil, Regina and Bowden, Laura and Hill, Claire and Baker, Neil R. and Lunn, John E. and Finkenstadt, Barbel and Mead, Andrew and Buchanan-Wollaston, Vicky and Beynon, Jim L. and Rand, David A and Wild, David L and Denby, Katherine J. and Ott, Sascha and Smirnoff, Nicholas and Mullineaux, Philip Mark},
title = {Time-series transcriptomics reveals that AGAMOUS-LIKE22 links primary metabolism to developmental processes in drought-stressed Arabidopsis},
year = {2016},
doi = {10.1105/tpc.15.00910},
publisher = {American Society of Plant Biologists},
issn = {1040-4651},
URL = {http://www.plantcell.org/content/early/2016/02/03/tpc.15.00910},
eprint = {http://www.plantcell.org/content/early/2016/02/03/tpc.15.00910.full.pdf},
journal = {The Plant Cell Online}
}
@article{Lewis15,
title={Transcriptional Dynamics Driving {MAMP}-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in {A}rabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000},
author={Lewis, Laura A and Polanski, Krzysztof and de Torres-Zabala, Marta and Jayaraman, Siddharth and Bowden, Laura and Moore, Jonathan and
, Christopher A and Jenkins, Dafyd J and Hill, Claire and Baxter, Laura and others},
journal={The Plant Cell},
volume={27},
number={11},
pages={3038--3064},
year={2015},
publisher={Am Soc Plant Biol}
}
@article{windram2012arabidopsis,
title={Arabidopsis defense against {B}otrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis},
author={Windram, Oliver and Madhou, Priyadharshini and McHattie, Stuart and Hill, Claire and Hickman, Richard and Cooke, Emma and Jenkins, Dafyd J and Penfold, Christopher A and Baxter, Laura and Breeze, Emily and others},
journal={The Plant Cell},
volume={24},
number={9},
pages={3530--3557},
year={2012},
publisher={Am Soc Plant Biol}
}
@Book{xie2015,
title = {Dynamic Documents with {R} and knitr},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2015},
edition = {2nd},
note = {ISBN 978-1498716963},
url = {http://yihui.name/knitr/},
}
@Book{James2013,
title = {An Introduction to Statistical Learning with Applications in R},
author = {Gareth James and Daniella Witten and Trevor Hastie and Robert Tibshirani},
publisher = {Springer-Verlag},
address = {New York},
year = {2013},
note = {ISBN 978-1-4614-7137-0},
url = {http://www-bcf.usc.edu/~gareth/ISL/},
doi = {10.1007/978-1-4614-7138-7}
}
@Book{Manly1994,
title = {Multivariate Statistical Methods: A Primer},
author = {Bryan F.J. Manly},
publisher = {Chapman and Hall},
address = {London},
year = {1994},
edition = {2nd},
note = {ISBN 0 412 60300 4},
}
@Book{Kuhn2013,
title = {Applied Predictive Modeling},
author={Max Kuhn and Kjell Johnson},
publisher = {Springer},
address = {New York},
year={2013},
}
@Article{Hill2007,
author="Hill, Andrew A.
and LaPan, Peter
and Li, Yizheng
and Haney, Steve",
title="Impact of image segmentation on high-content screening data quality for SK-BR-3 cells",
journal="BMC Bioinformatics",
year="2007",
month="Sep",
day="14",
volume="8",
number="1",
pages="340",
abstract="High content screening (HCS) is a powerful method for the exploration of cellular signalling and morphology that is rapidly being adopted in cancer research. HCS uses automated microscopy to collect images of cultured cells. The images are subjected to segmentation algorithms to identify cellular structures and quantitate their morphology, for hundreds to millions of individual cells. However, image analysis may be imperfect, especially for ``HCS-unfriendly'' cell lines whose morphology is not well handled by current image segmentation algorithms. We asked if segmentation errors were common for a clinically relevant cell line, if such errors had measurable effects on the data, and if HCS data could be improved by automated identification of well-segmented cells.",
issn="1471-2105",
doi="10.1186/1471-2105-8-340",
url="https://doi.org/10.1186/1471-2105-8-340"
}
@Article{Harris2008,
Author="Harris, L. W. and Wayland, M. and Lan, M. and Ryan, M. and Giger, T. and Lockstone, H. and Wuethrich, I. and Mimmack, M. and Wang, L. and Kotter, M. and Craddock, R. and Bahn, S. ",
Title="{{T}he cerebral microvasculature in schizophrenia: a laser capture microdissection study}",
Journal="PLoS ONE",
Year="2008",
Volume="3",
Number="12",
Pages="e3964"
}
@Article{Petalidis2008,
Author="Petalidis, L. P. and Oulas, A. and Backlund, M. and Wayland, M. T. and Liu, L. and Plant, K. and Happerfield, L. and Freeman, T. C. and Poirazi, P. and Collins, V. P. ",
Title="{{I}mproved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data}",
Journal="Mol. Cancer Ther.",
Year="2008",
Volume="7",
Number="5",
Pages="1013--1024",
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year = {2011},
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publisher = {American Society of Plant Biologists},
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publisher={Elsevier}
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