Commit 603cb492 authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros

Updated bibliography.

parent 23153b89
......@@ -28,8 +28,8 @@ SRC := $(basename $(shell grep -l '\\begin{document}' *.tex))
DIA_PIC := $(basename $(shell ls *.dia))
FIG_PIC := $(basename $(shell ls *.fig))
GNP := $(basename $(shell ls *.gnp))
PIC_EXT := dot gif jpg png ppm svg xcf bmp
PIC := $(foreach I, $(PIC_EXT), $(basename $(shell ls *.$I)))
PIC_EXT := .dot .gif .jpg .png .ppm .svg .xcf .bmp
PIC := $(foreach I, $(PIC_EXT), $(basename $(shell ls *$I)))
# Output.
PDF := $(addsuffix .pdf, $(SRC))
......@@ -37,7 +37,7 @@ RTF := $(addsuffix .rtf, $(SRC))
DOC := $(addsuffix .docx, $(SRC))
# Temporary files.
TMP := blg log nav out snm toc dvi aux idx vrb ps glg glo ist -blx.bib run.xml
TMP := .blg .log .nav .out .snm .toc .dvi .aux .idx .vrb .ps .glg .glo .ist -blx.bib .run.xml
PNG := $(addsuffix .png, $(DIA_PIC))
TNP := $(addsuffix .tnp, $(GNP))
......@@ -46,7 +46,7 @@ BIB := $(addsuffix .bbl, $(SRC))
GLS := $(addsuffix .gls, $(GLS))
EPS := $(addsuffix .eps, $(DIA_PIC) $(FIG_PIC) $(GNP) $(PIC))
TEX_T_EXT := pstex pstex_t
TEX_T := $(foreach I, $(TEX_T_EXT), $(addsuffix .$I, $(FIG_PIC)))
TEX_T := $(foreach I, $(TEX_T_EXT), $(addsuffix $I, $(FIG_PIC)))
# Do not delete the semi-permanent files automatically.
.PRECIOUS: $(BIB) $(GLS) $(EPS) $(TEX_T)
......@@ -67,7 +67,7 @@ rtf: $(RTF)
doc: $(DOC)
clean:
rm -f $(foreach I, $(TMP), $(addsuffix .$I, $(SRC))) $(PNG) $(TNP)
rm -f $(foreach I, $(TMP), $(addsuffix $I, $(SRC))) $(PNG) $(TNP)
distclean: clean
rm -f $(PDF) $(RTF) $(DOC) $(BIB) $(EPS) $(TEX_T)
......@@ -147,7 +147,7 @@ release: all clean
%.aux: %.tex $(EPS) $(TEX_T)
$(TEX) $< ;\
if (grep -s "LaTeX Warning: Citation" $*.log); then \
if (grep -s "Package biblatex Warning: Please (re)run BibTeX" $*.log); then \
$(MAKE) $*.bbl ;\
$(TEX) $< ;\
fi ;\
......
......@@ -653,3 +653,152 @@ year={2013},
month={Jan},
pages={e55734}
}
@article{Vis_2015,
keywords = {jlaros},
title={An efficient algorithm for the extraction of HGVS variant descriptions from sequences.},
author={Vis, J.K. and Vermaat, M and Taschner, P.E.M. and Kok, J.N. and Laros, J.F.J.},
journal={Bioinformatics},
year={2015},
month={Jul}
}
@article{van_Leeuwen_2015,
keywords={consortium},
title={Population-specific genotype imputations using minimac or IMPUTE2}, volume={10}, ISSN={1750-2799}, url={http://dx.doi.org/10.1038/nprot.2015.077}, DOI={10.1038/nprot.2015.077}, number={9}, journal={Nature Protocols}, publisher={Nature Publishing Group}, author={van Leeuwen, Elisabeth M and Kanterakis, Alexandros and Deelen, Patrick and Kattenberg, Mathijs V and Abdellaoui, Abdel and Hofman, Albert and Schönhuth, Alexander and Kanterakis, Alexandros and Menelaou, Androniki and de Craen, Anton J M and et al.}, year={2015}, month={Jul}, pages={1285–1296}}
@article{Kloosterman_2015,
keywords={consortium},
title={Characteristics of de novo structural changes in the human genome}, volume={25}, ISSN={1549-5469}, url={http://dx.doi.org/10.1101/gr.185041.114}, DOI={10.1101/gr.185041.114}, number={6}, journal={Genome Res.}, publisher={Cold Spring Harbor Laboratory Press}, author={Kloosterman, Wigard P. and Francioli, Laurent C. and Hormozdiari, Fereydoun and Marschall, Tobias and Hehir-Kwa, Jayne Y. and Abdellaoui, Abdel and Lameijer, Eric-Wubbo and Moed, Matthijs H. and Koval, Vyacheslav and Renkens, Ivo and et al.}, year={2015}, month={Apr}, pages={792–801}}
@article{Yoshihara_2015,
keywords={consortium},
title={Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body}, volume={10}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0117581}, DOI={10.1371/journal.pone.0117581}, number={3}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Yoshihara, Masahito and Ohmiya, Hiroko and Hara, Susumu and Kawasaki, Satoshi and Hayashizaki, Yoshihide and Itoh, Masayoshi and Kawaji, Hideya and Tsujikawa, Motokazu and Nishida, Kohji}, editor={Kerkis, IrinaEditor}, year={2015}, month={Mar}, pages={e0117581}}
@article{Pulyakhina_2015,
keywords = {jlaros},
title={SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing}, volume={43}, ISSN={1362-4962}, url={http://dx.doi.org/10.1093/nar/gkv242}, DOI={10.1093/nar/gkv242}, number={12}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Pulyakhina, Irina and Gazzoli, Isabella and ’t Hoen, Peter A.C. and Verwey, Nisha and den Dunnen, Johan and Aartsma-Rus, Annemieke and Laros, Jeroen F.J.}, year={2015}, month={Mar}, pages={e80–e80}}
@article{van_Leeuwen_2015,
keywords={consortium},
title={Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels}, volume={6}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/ncomms7065}, DOI={10.1038/ncomms7065}, journal={Nat Comms}, publisher={Nature Publishing Group}, author={van Leeuwen, Elisabeth M. and Karssen, Lennart C. and Deelen, Joris and Isaacs, Aaron and Medina-Gomez, Carolina and Mbarek, Hamdi and Kanterakis, Alexandros and Trompet, Stella and Postmus, Iris and Verweij, Niek and et al.}, year={2015}, month={Mar}, pages={6065}}
@misc{backtranslate,
keywords={software},
title={BackTranslate: Functions for reverse translation.},
author={J.F.J. Laros},
url={https://pypi.python.org/pypi/backtranslate},
year={2015}
}
@misc{barcode,
keywords={software},
title={barcode: Design NGS barcodes.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/barcode},
year={2013}
}
@misc{binparser,
keywords={software},
title={BinParser: General binary file parser.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/bin-parser},
year={2015}
}
@misc{famparser,
keywords={software},
title={FamParser: FAM file parser.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/fam-parser},
year={2015}
}
@misc{fastools,
keywords={software},
title={Fastools: FASTA/FASTQ analysis and manipulation toolkit.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/fastools},
year={2014}
}
@misc{kpal,
keywords={software},
title={kPal: k-mer analysis toolkit and programming library.},
author={Vermaat, M. and Laros, J.F.J.},
url={https://pypi.python.org/pypi/kPAL},
year={2014}
}
@misc{memoise,
keywords={software},
title={Memoise decorator.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/memoise},
year={2013}
}
@misc{onlinearray,
keywords={software},
title={An array-like object that calls a function.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/online-array},
year={2014}
}
@misc{piletools,
keywords={software},
title={Piletools: Mpileup analysis toolkit.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/piletools},
year={2015}
}
@misc{simreads,
keywords={software},
title={Generate simulated reads.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/sim-reads},
year={2015}
}
@misc{tracwiki,
keywords={software},
title={TracWiki: Checkout and commit trac wiki pages.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/tracwiki},
year={2012}
}
@misc{tssv,
keywords={software},
title={TSSV: Targeted characterisation of short structural variation.},
author={Laros, J.F.J.},
url={https://pypi.python.org/pypi/tssv},
year={2014}
}
@misc{mutalyzer,
keywords={software},
title={Mutalyzer: Sequence variant nomenclature checking according to the
guidelines of the Human Genome Variation Society.},
author={Vermaat, M. and Vis, J.K. and Schaafsma, G.C.P. and Stouten, G.R. and Laros, J.F.J.},
url={},
year={2015}
}
@misc{extractor,
keywords={software},
title={HGVS variant description extractor.},
author={Vis, J.K. and Vermaat, M. and Laros, J.F.J.},
url={https://github.com/mutalyzer/description-extractor},
year={2015}
}
@misc{snp,
keywords={software},
title={Finding non-binary SNP candidates.},
author={Laros, J.F.J.},
url={https://github.com/jfjlaros/snp},
year={2015}
}
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