remove some fluffy citations and reorganize acknowledgements

bib/references.bib

@@ -1600,7 +1600,7 @@ @article{chakraborty2018hidden
 }
 
 @article{zhou2017antcaller,
-  title={AntCaller: an accurate variant caller incorporating ancient {DNA} damage},
+  title={{AntCaller}: an accurate variant caller incorporating ancient {DNA} damage},
   author={Zhou, Boyan and Wen, Shaoqing and Wang, Lingxiang and Jin, Li and Li, Hui and Zhang, Hong},
   journal={Molecular Genetics and Genomics},
   volume={292},
@@ -1896,7 +1896,7 @@ @article{earl2014alignathon
 }
 
 @article{Iqbal_2012,
-  title={De novo assembly and genotyping of variants using colored de Bruijn graphs},
+  title={De novo assembly and genotyping of variants using colored de {B}ruijn graphs},
   volume={44},
   ISSN={1546-1718},
   url={http://dx.doi.org/10.1038/ng.1028},
@@ -1934,7 +1934,7 @@ @article{Laing_2010
 }
 
 @article{Zhao_2011,
-  title={PGAP: pan-genomes analysis pipeline},
+  title={{PGAP}: pan-genomes analysis pipeline},
   volume={28},
   ISSN={1367-4803},
   url={http://dx.doi.org/10.1093/bioinformatics/btr655},
@@ -1965,7 +1965,7 @@ @article{Li_2018
 }
 
 @article{Jandrasits_2018,
-  title={seq-seq-pan: Building a computational pan-genome data structure on whole genome alignment},
+  title={seq-seq-pan: {B}uilding a computational pan-genome data structure on whole genome alignment},
   author={Jandrasits, Christine and Dabrowski, Piotr W and Fuchs, Stephan and Renard, Bernhard Y},
   journal={BMC Genomics},
   volume={19},
@@ -2148,7 +2148,7 @@ @ARTICLE{Church2015-vt
 }
 
 @article{Leggett_2013,
-	title={Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de Bruijn graphs},
+	title={Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de {B}ruijn graphs},
 	author={Leggett, Richard M and Ramirez-Gonzalez, Ricardo H and Verweij, Walter and Kawashima, Cintia G and Iqbal, Zamin and Jones, Jonathan DG and Caccamo, Mario and MacLean, Daniel},
 	journal={PLoS One},
 	volume={8},

sections/applications.tex

@@ -271,7 +271,7 @@ \subsubsection{Transcriptomics}
 A mapping bias in favor of one of the alleles can therefore create illusory differences in expression between the alleles.
 Using variation information during mapping can help ameliorate this and improve estimates of ASE \cite{Castel2015-ef,Miao2018-ps}.
 
-The simplest approach to using variation data in mapping involves creating a personalized diploid genome or transcriptome, which is then used as the reference for a standard linear mapping method \cite{Rozowsky_2011,Raghupathy2018-sd}.
+The simplest approach to using variation data in mapping involves creating a personalized diploid genome or transcriptome, which is then used as the reference for a standard linear mapping method \cite{Raghupathy2018-sd}.
 %Methods using this approach have been shown to reduce reference bias and improve estimation of ASE, relative to traditional single reference genome methods, but they are generally limited by requiring phased haplotypes of either the whole genome or the individual genes for the individuals under study.
 Methods using this approach have been shown to reduce reference bias, but they require diploid reconstruction of the genome in question.
 Variant-aware mappers like \textsc{GSNAP} \cite{Wu2010-hv}, \textsc{iMapSplice} \cite{Liu_2018}, \textsc{ASElux} \cite{Miao2018-ps}, and \textsc{HISAT2} \cite{Kim_2019} remove this necessity, and have been shown to reduce reference bias at known SNVs during mapping \cite{Castel2015-ef,Liu_2018}.

sections/endmatter.tex

@@ -6,4 +6,11 @@ \section*{DISCLOSURE STATEMENT}
 
 % Acknowledgements
 \section*{ACKNOWLEDGMENTS}
-Research reported in this publication was supported the National Institutes of Health under Award Numbers U54HG007990, U01HL137183 and 2U41HG007234. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of National Institute of Health. The research was also made possible by the generous financial support of the W.M. Keck Foundation (DT06172015). T.M.\ acknowledges funding from the German Federal Ministry for Research and Education (BMBF 031L0184). The work of J.A.S. was supported by the Carlsberg Foundation. We would also like to thank all the attendees of the joint NCBI/UCSC Pangenomics Hackathon which took place at UCSC in the spring of 2019 and which spurred many conversations that contributed to this review. SH acknowledges funding from the central innovation programme (ZIM) for SMEs of the Federal Ministry for Economic Affairs and Energy of Germany. JDS thanks BBSRC for funding BB/S004661/1.
+Research reported in this publication was supported the National Institutes of Health under Award Numbers U54HG007990, U01HL137183 and 2U41HG007234.
+Its contents are solely the responsibility of the authors and do not necessarily represent the official views of National Institute of Health.
+The research was also made possible by the generous financial support of the W.M. Keck Foundation (DT06172015).
+T.M.\ acknowledges funding from the German Federal Ministry for Research and Education (BMBF 031L0184).
+The work of J.A.S. was supported by the Carlsberg Foundation.
+S.H. acknowledges funding from the central innovation programme (ZIM) for SMEs of the Federal Ministry for Economic Affairs and Energy of Germany.
+J.D.S. thanks BBSRC for funding BB/S004661/1.
+We would also like to thank all the attendees of the joint NCBI/UCSC Pangenomics Hackathon which took place at UCSC in the spring of 2019 and which spurred many conversations that contributed to this review.

sections/intro.tex

@@ -72,7 +72,7 @@ \subsection{Resequencing implies reference bias}
 \subsection{Human pangenomics}
 
 Estimates based on short read sequencing data have placed the human pangenome at between 1\% \cite{li2010building} and 10\% \cite{sherman2019assembly} larger than the GRCh38 human reference assembly.
-Others have demonstrated up to several Mbp of sequence are present in each new individual and not in the reference \cite{Hehir-Kwa2016-hb,Steinberg_2016,Audano_2019}.
+Others have demonstrated up to several Mbp of sequence are present in each new individual and not in the reference \cite{Hehir-Kwa2016-hb,Audano_2019}.
 %Although these estimates vary based on the author's definition of what constitutes novel sequence or allelic variation, we should expect them to rise as we consider larger cohorts of humans and improve our ability to ascertain variants in repeat-rich genomic regions.
 %We expect to gain greater insight into the extent, placement and significance of novel sequences when they are discovered in
 We expect that whole genome telomere-to-telomere assemblies constructed from long single-molecule sequencing data will provide greater insight into the extent, placement, and significance of these novel sequences \cite{miga2019telomere,Langley_2019}.