4641904citation.bib

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@misc{pedersen_fast_2019,
	Author = {Pedersen, Brent},
	Copyright = {MIT},
	Date-Added = {2019-07-31 18:53:57 +0000},
	Date-Modified = {2019-07-31 18:53:57 +0000},
	Month = jul,
	Note = {original-date: 2013-12-02T21:17:07Z},
	Title = {fast and accurate alignment of {BS}-{Seq} reads. {Contribute} to brentp/bwa-meth development by creating an account on {GitHub}},
	Url = {https://github.com/brentp/bwa-meth},
	Urldate = {2019-07-31},
	Year = {2019},
	Bdsk-Url-1 = {https://github.com/brentp/bwa-meth}}

@misc{ben_fast_2019,
	Author = {Ben},
	Copyright = {GPL-3.0},
	Date-Added = {2019-07-31 18:52:25 +0000},
	Date-Modified = {2019-07-31 18:52:25 +0000},
	Month = jul,
	Note = {original-date: 2012-12-20T19:25:11Z},
	Title = {A fast and sensitive gapped read aligner. {Contribute} to {BenLangmead}/bowtie2 development by creating an account on {GitHub}},
	Url = {https://github.com/BenLangmead/bowtie2},
	Urldate = {2019-07-31},
	Year = {2019},
	Bdsk-Url-1 = {https://github.com/BenLangmead/bowtie2}}

@article{krueger_bismark:_2011,
	Author = {Krueger, Felix and Andrews, Simon R.},
	Date-Added = {2019-07-31 18:52:25 +0000},
	Date-Modified = {2019-07-31 18:52:25 +0000},
	Doi = {10.1093/bioinformatics/btr167},
	File = {Full Text PDF:/Users/ckumar/Zotero/storage/WEI34X6T/Krueger and Andrews - 2011 - Bismark a flexible aligner and methylation caller.pdf:application/pdf;Snapshot:/Users/ckumar/Zotero/storage/VST243K8/216956.html:text/html},
	Issn = {1367-4803},
	Journal = {Bioinformatics},
	Language = {en},
	Month = jun,
	Number = {11},
	Pages = {1571--1572},
	Shorttitle = {Bismark},
	Title = {Bismark: a flexible aligner and methylation caller for {Bisulfite}-{Seq} applications},
	Url = {https://academic.oup.com/bioinformatics/article/27/11/1571/216956},
	Urldate = {2019-07-31},
	Volume = {27},
	Year = {2011},
	Bdsk-Url-1 = {https://academic.oup.com/bioinformatics/article/27/11/1571/216956},
	Bdsk-Url-2 = {https://doi.org/10.1093/bioinformatics/btr167}}

@article{pedersen_fast_2014,
	Author = {Pedersen, Brent S. and Eyring, Kenneth and De, Subhajyoti and Yang, Ivana V. and Schwartz, David A.},
	Date-Added = {2019-07-31 18:52:25 +0000},
	Date-Modified = {2019-07-31 18:52:25 +0000},
	File = {arXiv\:1401.1129 PDF:/Users/ckumar/Zotero/storage/X9EPFYQN/Pedersen et al. - 2014 - Fast and accurate alignment of long bisulfite-seq .pdf:application/pdf;arXiv.org Snapshot:/Users/ckumar/Zotero/storage/WK2HX8IE/1401.html:text/html},
	Journal = {arXiv:1401.1129 [q-bio]},
	Keywords = {Quantitative Biology - Genomics},
	Month = jan,
	Note = {arXiv: 1401.1129},
	Title = {Fast and accurate alignment of long bisulfite-seq reads},
	Url = {http://arxiv.org/abs/1401.1129},
	Urldate = {2019-07-31},
	Year = {2014},
	Bdsk-Url-1 = {http://arxiv.org/abs/1401.1129}}

@article{li_fast_2010,
	Author = {Li, Heng and Durbin, Richard},
	Date-Added = {2019-07-31 18:52:25 +0000},
	Date-Modified = {2019-07-31 18:52:25 +0000},
	Doi = {10.1093/bioinformatics/btp698},
	File = {Full Text PDF:/Users/ckumar/Zotero/storage/NRPFS8GW/Li and Durbin - 2010 - Fast and accurate long-read alignment with Burrows.pdf:application/pdf;Snapshot:/Users/ckumar/Zotero/storage/LBPX3U95/211735.html:text/html},
	Issn = {1367-4803},
	Journal = {Bioinformatics},
	Language = {en},
	Month = mar,
	Number = {5},
	Pages = {589--595},
	Title = {Fast and accurate long-read alignment with {Burrows}--{Wheeler} transform},
	Url = {https://academic.oup.com/bioinformatics/article/26/5/589/211735},
	Urldate = {2019-07-31},
	Volume = {26},
	Year = {2010},
	Bdsk-Url-1 = {https://academic.oup.com/bioinformatics/article/26/5/589/211735},
	Bdsk-Url-2 = {https://doi.org/10.1093/bioinformatics/btp698}}

@article{langmead_scaling_2019,
	Author = {Langmead, Ben and Wilks, Christopher and Antonescu, Valentin and Charles, Rone},
	Date-Added = {2019-07-31 18:39:56 +0000},
	Date-Modified = {2019-07-31 18:39:56 +0000},
	Doi = {10.1093/bioinformatics/bty648},
	File = {Full Text PDF:/Users/ckumar/Zotero/storage/GXSVGY4H/Langmead et al. - 2019 - Scaling read aligners to hundreds of threads on ge.pdf:application/pdf;Snapshot:/Users/ckumar/Zotero/storage/9XFN6A5B/5055585.html:text/html},
	Issn = {1367-4803},
	Journal = {Bioinformatics},
	Language = {en},
	Month = feb,
	Number = {3},
	Pages = {421--432},
	Title = {Scaling read aligners to hundreds of threads on general-purpose processors},
	Url = {https://academic.oup.com/bioinformatics/article/35/3/421/5055585},
	Urldate = {2019-07-31},
	Volume = {35},
	Year = {2019},
	Bdsk-Url-1 = {https://academic.oup.com/bioinformatics/article/35/3/421/5055585},
	Bdsk-Url-2 = {https://doi.org/10.1093/bioinformatics/bty648}}

@webpage{novaseq-6000,
	Author = {Illumina},
	Date-Added = {2018-08-15 11:53:12 -0400},
	Date-Modified = {2018-08-15 11:55:09 -0400},
	Note = {https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html},
	Title = {Novaseq 6000}}

@article{church_modernizing_2011,
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	Date-Modified = {2018-08-15 11:32:04 -0400},
	Doi = {10.1371/journal.pbio.1001091},
	Issn = {1545-7885},
	Journal = {PLoS biology},
	Keywords = {Databases, Genetic, Genome, Human, GRCh37, Humans, International Cooperation},
	Language = {eng},
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	Pmcid = {PMC3130012},
	Pmid = {21750661},
	Title = {Modernizing reference genome assemblies},
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	Date-Modified = {2018-08-15 11:07:38 -0400},
	Eprint = {/oup/backfile/content_public/journal/nar/46/d1/10.1093_nar_gkx1153/2/gkx1153.pdf},
	Journal = {Nucleic Acids Research},
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	Title = {ClinVar: improving access to variant interpretations and supporting evidence},
	Volume = {46},
	Year = {2018},
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@misc{ryan_methyldackel_nodate,
	Author = {Ryan, Devon},
	Language = {English},
	Note = {https://github.com/dpryan79/MethylDackel},
	Shorttitle = {{MethylDackel}},
	Title = {{MethylDackel}},
	Urldate = {2018-08-09}}

@article{doi:10.1093/bioinformatics/btr167,
	Author = {Krueger, Felix and Andrews, Simon R.},
	Date-Modified = {2018-08-15 11:07:38 -0400},
	Eprint = {/oup/backfile/content_public/journal/bioinformatics/27/11/10.1093_bioinformatics_btr167/1/btr167.pdf},
	Journal = {Bioinformatics},
	Number = {11},
	Pages = {1571-1572},
	Title = {Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications},
	Volume = {27},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btr167}}

@article{2014arXiv1401.1129P,
	Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
	Adsurl = {http://adsabs.harvard.edu/abs/2014arXiv1401.1129P},
	Archiveprefix = {arXiv},
	Author = {{Pedersen}, B.~S. and {Eyring}, K. and {De}, S. and {Yang}, I.~V. and {Schwartz}, D.~A.},
	Eprint = {1401.1129},
	Journal = {ArXiv e-prints},
	Keywords = {Quantitative Biology - Genomics},
	Month = jan,
	Primaryclass = {q-bio.GN},
	Title = {{Fast and accurate alignment of long bisulfite-seq reads}},
	Year = 2014}

@article{karimzadeh2018,
	Author = {Karimzadeh, Mehran and Ernst, Carl and Kundaje, Anshul and Hoffman, Michael M.},
	Journal = {Nucleic Acids Research},
	Title = {Umap and Bismap: quantifying genome and methylome mappability},
	Year = {2018}}

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	Eprint = {/oup/backfile/content_public/journal/bioinformatics/28/14/10.1093_bioinformatics_bts277/2/bts277.pdf},
	Journal = {Bioinformatics},
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	Date-Modified = {2018-08-15 11:07:38 -0400},
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	Date-Modified = {2018-08-15 11:07:38 -0400},
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	Publisher = {MyJove Corporation},
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	Year = {2015},
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	Date-Modified = {2018-08-15 11:07:38 -0400},
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@misc{the_sam/bam_format_specification_working_group_sequence_2018,
	Author = {The SAM/BAM Format Specification Working Group},
	Language = {English},
	Month = may,
	Note = {https://samtools.github.io/hts-specs/SAMv1.pdf},
	Shorttitle = {{SAM} {Format} {Specification}},
	Title = {Sequence {Alignment}/{Map} {Format} {Specification}},
	Urldate = {2018-08-09},
	Year = {2018}}

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	Eprint = {/oup/backfile/content_public/journal/bioinformatics/26/17/10.1093_bioinformatics_btq351/2/btq351.pdf},
	Journal = {Bioinformatics},
	Note = {http://genome.ucsc.edu/},
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	Pages = {2204-2207},
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	Date-Modified = {2018-08-15 11:07:38 -0400},
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@misc{johnurbangenome_biofinysics_2014,
	title = {Biofinysics: {How} does bowtie2 assign {MAPQ} scores?},
	shorttitle = {Biofinysics},
	url = {http://biofinysics.blogspot.com/2014/05/how-does-bowtie2-assign-mapq-scores.html},
	urldate = {2021-06-18},
	journal = {Biofinysics},
	author = {Johnurbangenome},
	month = may,
	year = {2014},
}

@misc{noauthor_qc_nodate,
	title = {{QC} {Fail} {Sequencing} : {MAPQ} values are really useful but their implementation is a mess},
	url = {https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/},
	language = {en},
	urldate = {2021-06-18},
}


@article{zhao_crossmap_2014,
	title = {{CrossMap}: a versatile tool for coordinate conversion between genome assemblies},
	volume = {30},
	issn = {1367-4811},
	url = {https://pubmed.ncbi.nlm.nih.gov/24351709},
	doi = {10.1093/bioinformatics/btt730},
	language = {eng},
	number = {7},
	journal = {Bioinformatics (Oxford, England)},
	author = {Zhao, Hao and Sun, Zhifu and Wang, Jing and Huang, Haojie and Kocher, Jean-Pierre and Wang, Liguo},
	month = apr,
	year = {2014},
	note = {Edition: 2013/12/18
Publisher: Oxford University Press},
	keywords = {Animals, Mice, Humans, *Genome, *Software, Base Sequence, Genomics/*methods, High-Throughput Nucleotide Sequencing/*methods, Sequence Alignment},
	pages = {1006--1007},
}


@article{doi:10.1093/bioinformatics/btv098,
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  title = {Sambamba: fast processing of NGS alignment formats},
  journal = {Bioinformatics},
  volume = {31},
  number = {12},
  pages = {2032-2034},
  year = {2015},
  doi = {10.1093/bioinformatics/btv098},
  URL = { + http://dx.doi.org/10.1093/bioinformatics/btv098}
  }


@misc{alavi_burgshrimpsliftover_t2t_2021,
	title = {burgshrimps/liftover\_T2T},
	url = {https://github.com/burgshrimps/liftover_T2T},
	abstract = {Chain files and scripts for coordinate conversions between hg38 and CHM13 (T2T assembly).},
	urldate = {2021-07-07},
	author = {Alavi, Nico},
	month = may,
	year = {2021},
	note = {original-date: 2020-11-03T21:50:35Z},
}

@misc{noauthor_marblchm13_2021,
	title = {marbl/{CHM13}},
	url = {https://github.com/marbl/CHM13},
	abstract = {The complete sequence of a human genome},
	urldate = {2021-07-07},
	publisher = {MarBL},
	month = jul,
	year = {2021},
	note = {original-date: 2019-02-28T16:00:16Z},
}

@article{nurk_complete_2021,
	title = {The complete sequence of a human genome},
	copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2021.05.26.445798v1},
	doi = {10.1101/2021.05.26.445798},
	language = {en},
	urldate = {2021-07-07},
	journal = {bioRxiv},
	author = {Nurk, Sergey and Koren, Sergey and Rhie, Arang and Rautiainen, Mikko and Bzikadze, Andrey V. and Mikheenko, Alla and Vollger, Mitchell R. and Altemose, Nicolas and Uralsky, Lev and Gershman, Ariel and Aganezov, Sergey and Hoyt, Savannah J. and Diekhans, Mark and Logsdon, Glennis A. and Alonge, Michael and Antonarakis, Stylianos E. and Borchers, Matthew and Bouffard, Gerard G. and Brooks, Shelise Y. and Caldas, Gina V. and Cheng, Haoyu and Chin, Chen-Shan and Chow, William and Lima, Leonardo G. de and Dishuck, Philip C. and Durbin, Richard and Dvorkina, Tatiana and Fiddes, Ian T. and Formenti, Giulio and Fulton, Robert S. and Fungtammasan, Arkarachai and Garrison, Erik and Grady, Patrick G. S. and Graves-Lindsay, Tina A. and Hall, Ira M. and Hansen, Nancy F. and Hartley, Gabrielle A. and Haukness, Marina and Howe, Kerstin and Hunkapiller, Michael W. and Jain, Chirag and Jain, Miten and Jarvis, Erich D. and Kerpedjiev, Peter and Kirsche, Melanie and Kolmogorov, Mikhail and Korlach, Jonas and Kremitzki, Milinn and Li, Heng and Maduro, Valerie V. and Marschall, Tobias and McCartney, Ann M. and McDaniel, Jennifer and Miller, Danny E. and Mullikin, James C. and Myers, Eugene W. and Olson, Nathan D. and Paten, Benedict and Peluso, Paul and Pevzner, Pavel A. and Porubsky, David and Potapova, Tamara and Rogaev, Evgeny I. and Rosenfeld, Jeffrey A. and Salzberg, Steven L. and Schneider, Valerie A. and Sedlazeck, Fritz J. and Shafin, Kishwar and Shew, Colin J. and Shumate, Alaina and Sims, Yumi and Smit, Arian F. A. and Soto, Daniela C. and Sović, Ivan and Storer, Jessica M. and Streets, Aaron and Sullivan, Beth A. and Thibaud-Nissen, Françoise and Torrance, James and Wagner, Justin and Walenz, Brian P. and Wenger, Aaron and Wood, Jonathan M. D. and Xiao, Chunlin and Yan, Stephanie M. and Young, Alice C. and Zarate, Samantha and Surti, Urvashi and McCoy, Rajiv C. and Dennis, Megan Y. and Alexandrov, Ivan A. and Gerton, Jennifer L. and O'Neill, Rachel J. and Timp, Winston and Zook, Justin M. and Schatz, Michael C. and Eichler, Evan E. and Miga, Karen H. and Phillippy, Adam M.},
	month = may,
	year = {2021},
	note = {Publisher: Cold Spring Harbor Laboratory
Section: New Results},
	pages = {2021.05.26.445798},
}


@misc{noauthor_miniconda_2021,
	title = {Miniconda},
	url = {https://docs.conda.io/en/latest/},
	publisher = {Anaconda},
	month = apr,
	year = {2021},
}


@article{di_tommaso_nextflow_2017,
	title = {Nextflow enables reproducible computational workflows},
	volume = {35},
	copyright = {2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/nbt.3820},
	doi = {10.1038/nbt.3820},
	language = {en},
	number = {4},
	urldate = {2021-07-12},
	journal = {Nature Biotechnology},
	author = {Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W. and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
	month = apr,
	year = {2017},
	pages = {316--319},
}


@misc{krueger_felixkruegerbismark_2021,
	title = {{FelixKrueger}/{Bismark}},
	copyright = {GPL-3.0},
	url = {https://github.com/FelixKrueger/Bismark},
	abstract = {A tool to map bisulfite converted sequence reads and determine cytosine methylation states},
	urldate = {2021-07-13},
	author = {Krueger, Felix},
	month = jul,
	year = {2021},
	note = {original-date: 2015-11-07T18:14:13Z},
}


@article{vaisvila_enzymatic_2021,
	title = {Enzymatic methyl sequencing detects {DNA} methylation at single-base resolution from picograms of {DNA}},
	issn = {1088-9051, 1549-5469},
	url = {https://genome.cshlp.org/content/early/2021/06/17/gr.266551.120},
	doi = {10.1101/gr.266551.120},
	language = {en},
	urldate = {2021-07-13},
	journal = {Genome Research},
	author = {Vaisvila, Romualdas and Ponnaluri, V. K. Chaithanya and Sun, Zhiyi and Langhorst, Bradley W. and Saleh, Lana and Guan, Shengxi and Dai, Nan and Campbell, Matthew A. and Sexton, Brittany S. and Marks, Katherine and Samaranayake, Mala and Samuelson, James C. and Church, Heidi E. and Tamanaha, Esta and Corrêa, Ivan R. and Pradhan, Sriharsa and Dimalanta, Eileen T. and Evans, Thomas C. and Williams, Louise and Davis, Theodore B.},
	month = jun,
	year = {2021},
	pmid = {34140313},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press
Publisher: Cold Spring Harbor Lab},
}


@incollection{lee_detection_2021,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Detection of {Modified} {Bases} in {Bacteriophage} {Genomic} {DNA}},
	isbn = {978-1-07-160876-0},
	url = {https://doi.org/10.1007/978-1-0716-0876-0_5},
	language = {en},
	urldate = {2021-07-13},
	booktitle = {{DNA} {Modifications}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Lee, Yan-Jiun and Weigele, Peter R.},
	editor = {Ruzov, Alexey and Gering, Martin},
	year = {2021},
	doi = {10.1007/978-1-0716-0876-0_5},
	keywords = {Bacteriophages, DNA modifications, HPLC, Mass spectrometry},
	pages = {53--66},
}


@article{kuo_5-methylcytosine_1968,
	title = {5-{Methylcytosine} replacing cytosine in the deoxyribonucleic acid of a bacteriophage for {Xanthomonas} oryzae},
	volume = {34},
	issn = {0022-2836},
	url = {https://www.sciencedirect.com/science/article/pii/0022283668902635},
	doi = {10.1016/0022-2836(68)90263-5},
	language = {en},
	number = {2},
	urldate = {2021-07-30},
	journal = {Journal of Molecular Biology},
	author = {Kuo, Tsong-teh and Huang, Tan-chi and Teng, Mei-hui},
	month = jun,
	year = {1968},
	pages = {373--375},
}


@article{robinson_integrative_2011,
	title = {Integrative genomics viewer},
	volume = {29},
	copyright = {2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/nbt.1754},
	doi = {10.1038/nbt.1754},
	language = {en},
	number = {1},
	urldate = {2021-08-09},
	journal = {Nature Biotechnology},
	author = {Robinson, James T. and Thorvaldsdóttir, Helga and Winckler, Wendy and Guttman, Mitchell and Lander, Eric S. and Getz, Gad and Mesirov, Jill P.},
	month = jan,
	year = {2011},
	pages = {24--26},
}


@article{gel_karyoploter_2017,
	title = {{karyoploteR}: an {R}/{Bioconductor} package to plot customizable genomes displaying arbitrary data},
	volume = {33},
	issn = {1367-4803},
	shorttitle = {{karyoploteR}},
	url = {https://doi.org/10.1093/bioinformatics/btx346},
	doi = {10.1093/bioinformatics/btx346},
	number = {19},
	urldate = {2021-08-12},
	journal = {Bioinformatics},
	author = {Gel, Bernat and Serra, Eduard},
	month = oct,
	year = {2017},
	pages = {3088--3090},
}

@article{perez_structural_1997,
        title = {Structural and biochemical similarities reveal a family of proteins related to the {MAL} proteolipid, a component of detergent-insoluble membrane microdomains},
        volume = {232},
        issn = {0006-291X},
        doi = {10.1006/bbrc.1997.6338},
        abstract = {The MAL gene encodes a proteolipid protein displaying a cell type-specific pattern of expression, including T lymphocytes, myelin-forming cells, and epithelial renal MDCK cells, which has been recently identified as a component of detergent-insoluble membranes known to be enriched in glycolipids and cholesterol. Sequence alignment revealed a high degree of conservation of the MAL protein across species and evidenced the existence of a significant level of overall identity between MAL and two other proteins, BENE and the plasmolipin proteolipid. Moreover, using subcellular fractionation of transiently transfected COS-7 cells, both MAL and BENE were identified in detergent-resistant membranes. These results suggest the existence of a novel family of MAL-related proteins (including MAL, BENE, and plasmolipin) with primary structure homologies and with the distinctive features of having unusual biochemical properties such as lipid-like behaviour and/or the ability to reside in glycolipid-enriched membrane microdomains.},
        language = {eng},
        number = {3},
        journal = {Biochemical and Biophysical Research Communications},
        author = {Pérez, P. and Puertollano, R. and Alonso, M. A.},
        month = mar,
        year = {1997},
        pmid = {9126323},
        keywords = {Amino Acid Sequence, Animals, Base Sequence, COS Cells, DNA Primers, Dogs, Humans, Membrane Proteins, Membrane Transport Proteins, Mice, Molecular Sequence Data, Molecular Structure, Myelin and Lymphocyte-Associated Proteolipid Proteins, Myelin Proteins, Proteolipids, Rats, Sequence Homology, Amino Acid},
        pages = {618--621},
}

@article{hildebrandt_novel_1997,
        title = {A novel gene encoding an {SH3} domain protein is mutated in nephronophthisis type 1},
        volume = {17},
        issn = {1061-4036},
        doi = {10.1038/ng1097-149},
        abstract = {Juvenile nephronophthisis (NPH), an autosomal recessive cystic kidney disease, is the primary genetic cause of chronic renal failure in children. About two thirds of patients with NPH carry a large homozygous deletion at the gene locus NPH1 on 2q13. We here identify a novel gene. NPHP1, which extends over most of this common deletion. The 4.5-kb transcript encodes a protein with an SH3 domain, which is highly conserved throughout evolution. The 11-kb interval between the 3' end of NPHP1 and an inverted repeat containing the distal deletion breakpoint was found to contain the first exon of a second gene, MALL. In patients with a hemizygous deletion of the NPH1 region, additional point mutations were found in NPHP1 but not in MALL.},
        language = {eng},
        number = {2},
        journal = {Nature Genetics},
        author = {Hildebrandt, F. and Otto, E. and Rensing, C. and Nothwang, H. G. and Vollmer, M. and Adolphs, J. and Hanusch, H. and Brandis, M.},
        month = oct,
        year = {1997},
        pmid = {9326933},
        keywords = {Adaptor Proteins, Signal Transducing, Amino Acid Sequence, Base Sequence, Child, Cytoskeletal Proteins, DNA Mutational Analysis, DNA Primers, DNA, Complementary, Exons, Gene Expression, Humans, Kidney Diseases, Cystic, Membrane Proteins, Molecular Sequence Data, Mutation, Polymerase Chain Reaction, Polymorphism, Single-Stranded Conformational, Proteins, Sequence Deletion, Sequence Homology, Amino Acid, Sequence Tagged Sites, src Homology Domains},
        pages = {149--153},
}

@article{seki_characterization_1997,
        title = {Characterization of {cDNA} clones in size-fractionated {cDNA} libraries from human brain},
        volume = {4},
        issn = {1340-2838},
        doi = {10.1093/dnares/4.5.345},
        abstract = {To evaluate the size-fractionated cDNA libraries of human brain previously constructed (O. O'hara et al. DNA Research, 4, 53-59, 1997), the occurrence of chimeric clones and the content of clones with coding potentiality were analyzed using the randomly sampled clones with insert sizes of 5 to 7 kb. When the chromosomal location of 30 clones was determined by the radiation-hybrid mapping method, the map positions assigned from the 3'- and 5'-end sequences separately were coincident for 29 clones, suggesting that the occurrence of chimeric clones is at most 1/30. Using 91 clones mapped to chromosome 1, the content of clones that have the potentiality coding for proteins larger than 100 amino acid residues was estimated to be approximately 50\% (46 out of 91 clones) on the basis of nucleotide sequence analysis and coding potentiality assay in vitro. No significant open reading frames were detected in the remaining clones. Although the clones coding for short peptides may not have been included in the above estimation, the libraries constructed from the whole brain mRNA fraction appear to contain a considerable amount of clones corresponding to the 5'-truncated transcripts in an unprocessed form and/or those with long 3'-untranslated regions.},
        language = {eng},
        number = {5},
        journal = {DNA research: an international journal for rapid publication of reports on genes and genomes},
        author = {Seki, N. and Ohira, M. and Nagase, T. and Ishikawa, K. and Miyajima, N. and Nakajima, D. and Nomura, N. and Ohara, O.},
        month = oct,
        year = {1997},
        pmid = {9455484},
        keywords = {Animals, Brain Chemistry, Chimera, Chromosome Mapping, Chromosomes, Human, Pair 1, Cloning, Molecular, DNA, Complementary, Electrophoresis, Polyacrylamide Gel, Gene Library, HSP40 Heat-Shock Proteins, Humans, Open Reading Frames, Polymerase Chain Reaction, Repetitive Sequences, Nucleic Acid, RNA, Messenger, Sequence Homology, Nucleic Acid, Sequence Tagged Sites, Transcription, Genetic},
        pages = {345--349},
        file = {Full Text:/Users/langhorst/Zotero/storage/BP9YZ459/Seki et al. - 1997 - Characterization of cDNA clones in size-fractionat.pdf:application/pdf},
}

@article{potashkin_bioinformatic_2020,
        title = {Bioinformatic {Analysis} {Reveals} {Phosphodiesterase} {4D}-{Interacting} {Protein} as a {Key} {Frontal} {Cortex} {Dementia} {Switch} {Gene}},
        volume = {21},
        issn = {1422-0067},
        doi = {10.3390/ijms21113787},
        abstract = {: The mechanisms that initiate dementia are poorly understood and there are currently no treatments that can slow their progression. The identification of key genes and molecular pathways that may trigger dementia should help reveal potential therapeutic reagents. In this study, SWItch Miner software was used to identify phosphodiesterase 4D-interacting protein as a key factor that may lead to the development of Alzheimer's disease, vascular dementia, and frontotemporal dementia. Inflammation, PI3K-AKT, and ubiquitin-mediated proteolysis were identified as the main pathways that are dysregulated in these dementias. All of these dementias are regulated by 12 shared transcription factors. Protein-chemical interaction network analysis of dementia switch genes revealed that valproic acid may be neuroprotective for these dementias. Collectively, we identified shared and unique dysregulated gene expression, pathways and regulatory factors among dementias. New key mechanisms that lead to the development of dementia were revealed and it is expected that these data will advance personalized medicine for patients.},
        language = {eng},
        number = {11},
        journal = {International Journal of Molecular Sciences},
        author = {Potashkin, Judith A. and Bottero, Virginie and Santiago, Jose A. and Quinn, James P.},
        month = may,
        year = {2020},
        pmid = {32471155},
        pmcid = {PMC7313474},
        keywords = {Adaptor Proteins, Signal Transducing, Alzheimer Disease, Alzheimer’s disease, bioinformatic analysis, Brain, cardiomyopathy-associated protein 2, Computational Biology, Cytoskeletal Proteins, Data Mining, Databases, Genetic, Dementia, Dementia, Vascular, Frontal Lobe, frontotemporal dementia, Frontotemporal Dementia, gene expression, Gene Expression Regulation, Genes, Switch, Humans, inflammation, myomegalin, personalized medicine, phosphodiesterase 4D-interacting protein, PI3K-AKT pathway, Signal Transduction, Software, switch genes, Transcription Factors, Transcriptome, ubiquitin mediated protein, valproic acid, vascular dementia},
        pages = {E3787},
        file = {Full Text:/Users/langhorst/Zotero/storage/7489Z33Z/Potashkin et al. - 2020 - Bioinformatic Analysis Reveals Phosphodiesterase 4.pdf:application/pdf},
}

@article{fragoza_extensive_2019,
        title = {Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations},
        volume = {10},
        issn = {2041-1723},
        doi = {10.1038/s41467-019-11959-3},
        abstract = {Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their influence remains largely unexplored. To address this gap, we leverage the ExAC database of 60,706 human exomes to investigate experimentally the impact of 2009 missense single nucleotide variants (SNVs) across 2185 protein-protein interactions, generating interaction profiles for 4797 SNV-interaction pairs, of which 421 SNVs segregate at {\textgreater} 1\% allele frequency in human populations. We find that interaction-disruptive SNVs are prevalent at both rare and common allele frequencies. Furthermore, these results suggest that 10.5\% of missense variants carried per individual are disruptive, a higher proportion than previously reported; this indicates that each individual's genetic makeup may be significantly more complex than expected. Finally, we demonstrate that candidate disease-associated mutations can be identified through shared interaction perturbations between variants of interest and known disease mutations.},
        language = {eng},
        number = {1},
        journal = {Nature Communications},
        author = {Fragoza, Robert and Das, Jishnu and Wierbowski, Shayne D. and Liang, Jin and Tran, Tina N. and Liang, Siqi and Beltran, Juan F. and Rivera-Erick, Christen A. and Ye, Kaixiong and Wang, Ting-Yi and Yao, Li and Mort, Matthew and Stenson, Peter D. and Cooper, David N. and Wei, Xiaomu and Keinan, Alon and Schimenti, John C. and Clark, Andrew G. and Yu, Haiyuan},
        month = sep,
        year = {2019},
        pmid = {31515488},
        pmcid = {PMC6742646},
        keywords = {Alleles, Animals, Base Sequence, Disease, Gene Frequency, Genetic Predisposition to Disease, Genetic Variation, Genetics, Population, Genome, Human, HEK293 Cells, Humans, Mice, Mutation, Missense, Phenotype, Polymorphism, Single Nucleotide, Protein Binding},
        pages = {4141},
        file = {Full Text:/Users/langhorst/Zotero/storage/JDC8NRYY/Fragoza et al. - 2019 - Extensive disruption of protein interactions by ge.pdf:application/pdf},
}

@article{camargo_disrupted_2007,
        title = {Disrupted in {Schizophrenia} 1 {Interactome}: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia},
        volume = {12},
        issn = {1359-4184},
        shorttitle = {Disrupted in {Schizophrenia} 1 {Interactome}},
        doi = {10.1038/sj.mp.4001880},
        abstract = {Disrupted in Schizophrenia 1 (DISC1) is a schizophrenia risk gene associated with cognitive deficits in both schizophrenics and the normal ageing population. In this study, we have generated a network of protein-protein interactions (PPIs) around DISC1. This has been achieved by utilising iterative yeast-two hybrid (Y2H) screens, combined with detailed pathway and functional analysis. This so-called 'DISC1 interactome' contains many novel PPIs and provides a molecular framework to explore the function of DISC1. The network implicates DISC1 in processes of cytoskeletal stability and organisation, intracellular transport and cell-cycle/division. In particular, DISC1 looks to have a PPI profile consistent with that of an essential synaptic protein, which fits well with the underlying molecular pathology observed at the synaptic level and the cognitive deficits seen behaviourally in schizophrenics. Utilising a similar approach with dysbindin (DTNBP1), a second schizophrenia risk gene, we show that dysbindin and DISC1 share common PPIs suggesting they may affect common biological processes and that the function of schizophrenia risk genes may converge.},
        language = {eng},
        number = {1},
        journal = {Molecular Psychiatry},
        author = {Camargo, L. M. and Collura, V. and Rain, J.-C. and Mizuguchi, K. and Hermjakob, H. and Kerrien, S. and Bonnert, T. P. and Whiting, P. J. and Brandon, N. J.},
        month = jan,
        year = {2007},
        pmid = {17043677},
        keywords = {Biological Transport, Carrier Proteins, Cell Division, Cognition, Cytoskeleton, Dysbindin, Dystrophin-Associated Proteins, Humans, Nerve Tissue Proteins, Risk Factors, Schizophrenia, Synapses, Two-Hybrid System Techniques},
        pages = {74--86},
        file = {Full Text:/Users/langhorst/Zotero/storage/XQCY2XFW/Camargo et al. - 2007 - Disrupted in Schizophrenia 1 Interactome evidence.pdf:application/pdf},
}

@article{snuderl_recurrent_2018,
        title = {Recurrent homozygous deletion of {DROSHA} and microduplication of {PDE4DIP} in pineoblastoma},
        volume = {9},
        issn = {2041-1723},
        doi = {10.1038/s41467-018-05029-3},
        abstract = {Pineoblastoma is a rare and highly aggressive brain cancer of childhood, histologically belonging to the spectrum of primitive neuroectodermal tumors. Patients with germline mutations in DICER1, a ribonuclease involved in microRNA processing, have increased risk of pineoblastoma, but genetic drivers of sporadic pineoblastoma remain unknown. Here, we analyzed pediatric and adult pineoblastoma samples (n = 23) using a combination of genome-wide DNA methylation profiling and whole-exome sequencing or whole-genome sequencing. Pediatric and adult pineoblastomas showed distinct methylation profiles, the latter clustering with lower-grade pineal tumors and normal pineal gland. Recurrent variants were found in genes involved in PKA- and NF-κB signaling, as well as in chromatin remodeling genes. We identified recurrent homozygous deletions of DROSHA, acting upstream of DICER1 in microRNA processing, and a novel microduplication involving chromosomal region 1q21 containing PDE4DIP (myomegalin), comprising the ancient DUF1220 protein domain. Expresion of PDE4DIP and DUF1220 proteins was present exclusively in pineoblastoma with PDE4DIP gain.},
        language = {eng},
        number = {1},
        journal = {Nature Communications},
        author = {Snuderl, Matija and Kannan, Kasthuri and Pfaff, Elke and Wang, Shiyang and Stafford, James M. and Serrano, Jonathan and Heguy, Adriana and Ray, Karina and Faustin, Arline and Aminova, Olga and Dolgalev, Igor and Stapleton, Stacie L. and Zagzag, David and Chiriboga, Luis and Gardner, Sharon L. and Wisoff, Jeffrey H. and Golfinos, John G. and Capper, David and Hovestadt, Volker and Rosenblum, Marc K. and Placantonakis, Dimitris G. and LeBoeuf, Sarah E. and Papagiannakopoulos, Thales Y. and Chavez, Lukas and Ahsan, Sama and Eberhart, Charles G. and Pfister, Stefan M. and Jones, David T. W. and Karajannis, Matthias A.},
        month = jul,
        year = {2018},
        pmid = {30030436},
        pmcid = {PMC6054684},
        keywords = {Adaptor Proteins, Signal Transducing, Adult, Aged, Brain Neoplasms, Child, Cytoskeletal Proteins, DEAD-box RNA Helicases, DNA Methylation, Exome, Gene Deletion, Gene Duplication, Genome, Human, Homozygote, Humans, Middle Aged, Muscle Proteins, Nuclear Proteins, Pineal Gland, Pinealoma, Protein Domains, Ribonuclease III, Transcriptome},
        pages = {2868},
        file = {Full Text:/Users/langhorst/Zotero/storage/KSIZBD9X/Snuderl et al. - 2018 - Recurrent homozygous deletion of DROSHA and microd.pdf:application/pdf},
}

@article{kang_atypical_2015,
        title = {Atypical retinopathy in patients with nephronophthisis type 1: an uncommon ophthalmological finding},
        volume = {43},
        issn = {1442-9071},
        shorttitle = {Atypical retinopathy in patients with nephronophthisis type 1},
        doi = {10.1111/ceo.12469},
        abstract = {BACKGROUND: Progressive retinal degeneration without retinal pigmentation has been repeatedly observed in Korean nephronophthisis (NPHP) type 1 patients with a total homozygous deletion of NPHP1.
DESIGN: Retrospective case series.
PARTICIPANTS: Patients with clinical diagnosis of NPHP and genetic diagnosis of total deletion of NPHP1 (n = 5) were included in this study.
METHODS: Patients with clinical diagnosis of NPHP (n = 57) were screened for total deletion of NPHP1 by polymerase chain reaction (PCR) for the 20 exons of NPHP1. The clinical and ophthalmological findings of NPHP type 1 patients were reviewed. Additionally, four exons of MALL, a gene adjacent to NPHP1, were amplified using PCR, and amplification failure was considered a homozygous deletion encompassing the corresponding exons.
MAIN OUTCOME MEASURE: Ophthalmological findings in NPHP type 1 patients.
RESULTS: Five of 57 patients with clinical diagnosis of NPHP were diagnosed as having NPHP type 1 by genetic analysis. Chronic renal failure was diagnosed in these five patients at 7.9-15.4 years of age. All the patients with NPHP type 1 had progressive decline in visual acuity with various ages of onset (2-17 years). Ophthalmological examinations revealed unexpected findings of retinopathy with large or small flecks, which was compatible with Stargardt-like retinopathy or albipunctatus retinopathy in majority of them (four of five). The genetic study revealed an additional deletion of exon 1 of the adjacent gene MALL.
CONCLUSIONS: We report the unexpectedly common retinal involvement of NPHP type 1 with an additional MALL deletion in a Korean cohort.},
        language = {eng},
        number = {5},
        journal = {Clinical \& Experimental Ophthalmology},
        author = {Kang, Hee Gyung and Ahn, Yo Han and Kim, Jeong Hun and Ha, Il-Soo and Yu, Young Suk and Park, Yong-Hoon and Cheong, Hae Il},
        month = jul,
        year = {2015},
        pmid = {25401970},
        keywords = {Adaptor Proteins, Signal Transducing, Adolescent, Age of Onset, Child, Cytoskeletal Proteins, Electroretinography, Exons, Female, Fluorescein Angiography, Gene Amplification, Humans, Kidney Diseases, Cystic, Male, MALL, Membrane Proteins, Myelin and Lymphocyte-Associated Proteolipid Proteins, nephronophthisis, NPHP1, Ophthalmoscopy, Polymerase Chain Reaction, Retinal Degeneration, retinopathy, Retrospective Studies, Sequence Deletion, Tomography, Optical Coherence, Vision Disorders, Visual Acuity},
        pages = {437--442},
}

@article{overlack_direct_2011,
        title = {Direct interaction of the {Usher} syndrome {1G} protein {SANS} and myomegalin in the retina},
        volume = {1813},
        issn = {0006-3002},
        doi = {10.1016/j.bbamcr.2011.05.015},
        abstract = {The human Usher syndrome (USH) is the most frequent cause of combined hereditary deaf-blindness. USH is genetically heterogeneous with at least 11 chromosomal loci assigned to 3 clinical types, USH1-3. We have previously demonstrated that all USH1 and 2 proteins in the eye and the inner ear are organized into protein networks by scaffold proteins. This has contributed essentially to our current understanding of the function of USH proteins and explains why defects in proteins of different families cause very similar phenotypes. We have previously shown that the USH1G protein SANS (scaffold protein containing ankyrin repeats and SAM domain) contributes to the periciliary protein network in retinal photoreceptor cells. This study aimed to further elucidate the role of SANS by identifying novel interaction partners. In yeast two-hybrid screens of retinal cDNA libraries we identified 30 novel putative interacting proteins binding to the central domain of SANS (CENT). We confirmed the direct binding of the phosphodiesterase 4D interacting protein (PDE4DIP), a Golgi associated protein synonymously named myomegalin, to the CENT domain of SANS by independent assays. Correlative immunohistochemical and electron microscopic analyses showed a co-localization of SANS and myomegalin in mammalian photoreceptor cells in close association with microtubules. Based on the present results we propose a role of the SANS-myomegalin complex in microtubule-dependent inner segment cargo transport towards the ciliary base of photoreceptor cells.},
        language = {eng},
        number = {10},
        journal = {Biochimica Et Biophysica Acta},
        author = {Overlack, Nora and Kilic, Dilek and Bauss, Katharina and Märker, Tina and Kremer, Hannie and van Wijk, Erwin and Wolfrum, Uwe},
        month = oct,
        year = {2011},
        pmid = {21767579},
        keywords = {Adaptor Proteins, Signal Transducing, Animals, Cattle, Cells, Cultured, Chlorocebus aethiops, COS Cells, Cytoskeletal Proteins, Humans, Macaca mulatta, Mice, Mice, Inbred C57BL, Models, Biological, Muscle Proteins, Nerve Tissue Proteins, Nuclear Proteins, PDE4DIP, Photoreceptor Cells, Vertebrate, Protein Binding, Retina, Yeasts},
        pages = {1883--1892},
        file = {Full Text:/Users/langhorst/Zotero/storage/GTNMCYA4/Overlack et al. - 2011 - Direct interaction of the Usher syndrome 1G protei.pdf:application/pdf},
}

@article{auer_rare_2015,
        title = {Rare and {Coding} {Region} {Genetic} {Variants} {Associated} {With} {Risk} of {Ischemic} {Stroke}: {The} {NHLBI} {Exome} {Sequence} {Project}},
        volume = {72},
        issn = {2168-6157},
        shorttitle = {Rare and {Coding} {Region} {Genetic} {Variants} {Associated} {With} {Risk} of {Ischemic} {Stroke}},
        doi = {10.1001/jamaneurol.2015.0582},
        abstract = {IMPORTANCE: Stroke is the second leading cause of death and the third leading cause of years of life lost. Genetic factors contribute to stroke prevalence, and candidate gene and genome-wide association studies (GWAS) have identified variants associated with ischemic stroke risk. These variants often have small effects without obvious biological significance. Exome sequencing may discover predicted protein-altering variants with a potentially large effect on ischemic stroke risk.
OBJECTIVE: To investigate the contribution of rare and common genetic variants to ischemic stroke risk by targeting the protein-coding regions of the human genome.
DESIGN, SETTING, AND PARTICIPANTS: The National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP) analyzed approximately 6000 participants from numerous cohorts of European and African ancestry. For discovery, 365 cases of ischemic stroke (small-vessel and large-vessel subtypes) and 809 European ancestry controls were sequenced; for replication, 47 affected sibpairs concordant for stroke subtype and an African American case-control series were sequenced, with 1672 cases and 4509 European ancestry controls genotyped. The ESP's exome sequencing and genotyping started on January 1, 2010, and continued through June 30, 2012. Analyses were conducted on the full data set between July 12, 2012, and July 13, 2013.
MAIN OUTCOMES AND MEASURES: Discovery of new variants or genes contributing to ischemic stroke risk and subtype (primary analysis) and determination of support for protein-coding variants contributing to risk in previously published candidate genes (secondary analysis).
RESULTS: We identified 2 novel genes associated with an increased risk of ischemic stroke: a protein-coding variant in PDE4DIP (rs1778155; odds ratio, 2.15; P = 2.63 × 10(-8)) with an intracellular signal transduction mechanism and in ACOT4 (rs35724886; odds ratio, 2.04; P = 1.24 × 10(-7)) with a fatty acid metabolism; confirmation of PDE4DIP was observed in affected sibpair families with large-vessel stroke subtype and in African Americans. Replication of protein-coding variants in candidate genes was observed for 2 previously reported GWAS associations: ZFHX3 (cardioembolic stroke) and ABCA1 (large-vessel stroke).
CONCLUSIONS AND RELEVANCE: Exome sequencing discovered 2 novel genes and mechanisms, PDE4DIP and ACOT4, associated with increased risk for ischemic stroke. In addition, ZFHX3 and ABCA1 were discovered to have protein-coding variants associated with ischemic stroke. These results suggest that genetic variation in novel pathways contributes to ischemic stroke risk and serves as a target for prediction, prevention, and therapy.},
        language = {eng},
        number = {7},
        journal = {JAMA neurology},
        author = {Auer, Paul L. and Nalls, Mike and Meschia, James F. and Worrall, Bradford B. and Longstreth, W. T. and Seshadri, Sudha and Kooperberg, Charles and Burger, Kathleen M. and Carlson, Christopher S. and Carty, Cara L. and Chen, Wei-Min and Cupples, L. Adrienne and DeStefano, Anita L. and Fornage, Myriam and Hardy, John and Hsu, Li and Jackson, Rebecca D. and Jarvik, Gail P. and Kim, Daniel S. and Lakshminarayan, Kamakshi and Lange, Leslie A. and Manichaikul, Ani and Quinlan, Aaron R. and Singleton, Andrew B. and Thornton, Timothy A. and Nickerson, Deborah A. and Peters, Ulrike and Rich, Stephen S. and {National Heart, Lung, and Blood Institute Exome Sequencing Project}},
        month = jul,
        year = {2015},
        pmid = {25961151},
        pmcid = {PMC4673986},
        keywords = {Adaptor Proteins, Signal Transducing, Aged, Brain Ischemia, Cytoskeletal Proteins, Exome, Female, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Humans, Male, Middle Aged, Muscle Proteins, National Heart, Lung, and Blood Institute (U.S.), Nuclear Proteins, Open Reading Frames, Palmitoyl-CoA Hydrolase, PDE4DIP, Stroke, United States},
        pages = {781--788},
        file = {Full Text:/Users/langhorst/Zotero/storage/B2A8TW98/Auer et al. - 2015 - Rare and Coding Region Genetic Variants Associated.pdf:application/pdf},
}