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@article{lupski2009genomic,
title={Genomic disorders ten years on},
author={Lupski, James R},
journal={Genome medicine},
volume={1},
pages={1--11},
year={2009},
publisher={Springer}
}
@article{zhang2015non,
title={Non-coding genetic variants in human disease},
author={Zhang, Feng and Lupski, James R},
journal={Human molecular genetics},
volume={24},
number={R1},
pages={R102--R110},
year={2015},
publisher={Oxford University Press}
}
@article{sahu2011identification,
title={Identification of protein-coding regions in DNA sequences using a time-frequency filtering approach},
author={Sahu, Sitanshu Sekhar and Panda, Ganapati},
journal={Genomics, Proteomics and Bioinformatics},
volume={9},
number={1-2},
pages={45--55},
year={2011},
publisher={Oxford University Press}
}
@article{khurana2016role,
title={Role of non-coding sequence variants in cancer},
author={Khurana, Ekta and Fu, Yao and Chakravarty, Dimple and Demichelis, Francesca and Rubin, Mark A and Gerstein, Mark},
journal={Nature Reviews Genetics},
volume={17},
number={2},
pages={93--108},
year={2016},
publisher={Nature Publishing Group UK London}
}
@article{french2020role,
title={The role of noncoding variants in heritable disease},
author={French, JD and Edwards, SL},
journal={Trends in Genetics},
volume={36},
number={11},
pages={880--891},
year={2020},
publisher={Elsevier}
}
@article{chial2008mendelian,
title={Mendelian genetics: patterns of inheritance and single-gene disorders},
author={Chial, Heidi},
journal={Nature Education},
volume={1},
number={1},
pages={63},
year={2008}
}
@article{tian2019systematic,
title={Systematic functional interrogation of genes in GWAS loci identified ATF1 as a key driver in colorectal cancer modulated by a promoter-enhancer interaction},
author={Tian, Jianbo and Chang, Jiang and Gong, Jing and Lou, Jiao and Fu, Mingpeng and Li, Jiaoyuan and Ke, Juntao and Zhu, Ying and Gong, Yajie and Yang, Yang and others},
journal={The American Journal of Human Genetics},
volume={105},
number={1},
pages={29--47},
year={2019},
publisher={Elsevier}
}
@article{bojesen2013multiple,
title={Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer},
author={Bojesen, Stig E and Pooley, Karen A and Johnatty, Sharon E and Beesley, Jonathan and Michailidou, Kyriaki and Tyrer, Jonathan P and Edwards, Stacey L and Pickett, Hilda A and Shen, Howard C and Smart, Chanel E and others},
journal={Nature genetics},
volume={45},
number={4},
pages={371--384},
year={2013},
publisher={Nature Publishing Group US New York}
}
@article{michailidou2017association,
title={Association analysis identifies 65 new breast cancer risk loci},
author={Michailidou, Kyriaki and Lindstr{\"o}m, Sara and Dennis, Joe and Beesley, Jonathan and Hui, Shirley and Kar, Siddhartha and Lema{\c{c}}on, Audrey and Soucy, Penny and Glubb, Dylan and Rostamianfar, Asha and others},
journal={Nature},
volume={551},
number={7678},
pages={92--94},
year={2017},
publisher={Nature Publishing Group UK London}
}
% read
@article{pagni2022non,
title={Non-coding regulatory elements: Potential roles in disease and the case of epilepsy},
author={Pagni, Susanna and Mills, James D and Frankish, Adam and Mudge, Jonathan M and Sisodiya, Sanjay M},
journal={Neuropathology and Applied Neurobiology},
volume={48},
number={3},
pages={e12775},
year={2022},
publisher={Wiley Online Library}
}
@article{kapoor2014enhancer,
title={An enhancer polymorphism at the cardiomyocyte intercalated disc protein NOS1AP locus is a major regulator of the QT interval},
author={Kapoor, Ashish and Sekar, Rajesh B and Hansen, Nancy F and Fox-Talbot, Karen and Morley, Michael and Pihur, Vasyl and Chatterjee, Sumantra and Brandimarto, Jeffrey and Moravec, Christine S and Pulit, Sara L and others},
journal={The American Journal of Human Genetics},
volume={94},
number={6},
pages={854--869},
year={2014},
publisher={Elsevier}
}
@article{mcculloch1943logical,
title={A logical calculus of the ideas immanent in nervous activity},
author={McCulloch, Warren S and Pitts, Walter},
journal={The bulletin of mathematical biophysics},
volume={5},
pages={115--133},
year={1943},
publisher={Springer}
}
% read
@article{caudai2021ai,
title={AI applications in functional genomics},
author={Caudai, Claudia and Galizia, Antonella and Geraci, Filippo and Le Pera, Loredana and Morea, Veronica and Salerno, Emanuele and Via, Allegra and Colombo, Teresa},
journal={Computational and Structural Biotechnology Journal},
volume={19},
pages={5762--5790},
year={2021},
publisher={Elsevier}
}
% DeepSEA
@article{zhou2015predicting,
title={Predicting effects of noncoding variants with deep learning--based sequence model},
author={Zhou, Jian and Troyanskaya, Olga G},
journal={Nature methods},
volume={12},
number={10},
pages={931--934},
year={2015},
publisher={Nature Publishing Group US New York}
}
% Basset
@article{kelley2016basset,
title={Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks},
author={Kelley, David R and Snoek, Jasper and Rinn, John L},
journal={Genome research},
volume={26},
number={7},
pages={990--999},
year={2016},
publisher={Cold Spring Harbor Lab}
}
% DeepSATA
@article{ma2023deepsata,
title={DeepSATA: A Deep Learning-Based Sequence Analyzer Incorporating the Transcription Factor Binding Affinity to Dissect the Effects of Non-Coding Genetic Variants},
author={Ma, Wenlong and Fu, Yang and Bao, Yongzhou and Wang, Zhen and Lei, Bowen and Zheng, Weigang and Wang, Chao and Liu, Yuwen},
journal={International Journal of Molecular Sciences},
volume={24},
number={15},
pages={12023},
year={2023},
publisher={MDPI}
}
@article{watson1953molecular,
title={Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid},
author={Watson, James D and Crick, Francis HC},
journal={Nature},
volume={171},
number={4356},
pages={737--738},
year={1953},
publisher={Nature Publishing Group UK London}
}
@article{travers2015dna,
title={DNA structure and function},
author={Travers, Andrew and Muskhelishvili, Georgi},
journal={The FEBS journal},
volume={282},
number={12},
pages={2279--2295},
year={2015},
publisher={Wiley Online Library}
}
@article{crick1954complementary,
title={The complementary structure of deoxyribonucleic acid},
author={Crick, Francis Harry Compton and Watson, James Dewey},
journal={Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences},
volume={223},
number={1152},
pages={80--96},
year={1954},
publisher={The Royal Society London}
}
@book{clark2012molecular,
title={Molecular biology},
author={Clark, David P and Pazdernik, Nanette J},
year={2012},
publisher={Elsevier}
}
@article{donohue1960base,
title={Base pairing in DNA},
author={Donohue, Jerry and Trueblood, Kenneth N},
journal={Journal of Molecular Biology},
volume={2},
number={6},
pages={363--371},
year={1960},
publisher={Elsevier}
}
@article{fonseca2000hydrogen,
title={Hydrogen bonding in DNA base pairs: reconciliation of theory and experiment},
author={Fonseca Guerra, C{\'e}lia and Bickelhaupt, F Matthias and Snijders, Jaap G and Baerends, Evert Jan},
journal={Journal of the American Chemical Society},
volume={122},
number={17},
pages={4117--4128},
year={2000},
publisher={ACS Publications}
}
@article{li2021cell,
title={The cell as matter: Connecting molecular biology to cellular functions},
author={Li, Yiwei and Tang, Wenhui and Guo, Ming},
journal={Matter},
volume={4},
number={6},
pages={1863--1891},
year={2021},
publisher={Elsevier}
}
@article{ren2020identifying,
title={Identifying viruses from metagenomic data using deep learning},
author={Ren, Jie and Song, Kai and Deng, Chao and Ahlgren, Nathan A and Fuhrman, Jed A and Li, Yi and Xie, Xiaohui and Poplin, Ryan and Sun, Fengzhu},
journal={Quantitative Biology},
volume={8},
number={1},
pages={64--77},
year={2020},
publisher={Wiley Online Library}
}
@book{alberts2015essential,
title={Essential cell biology},
author={Alberts, Bruce and Bray, Dennis and Hopkin, Karen and Johnson, Alexander D and Lewis, Julian and Raff, Martin and Roberts, Keith and Walter, Peter},
year={2015},
publisher={Garland Science}
}
@article{Huseynova2020CELLOA,
title={CELL ORGANIZATION AND LIFE -BASES OF LIFE ON THE EARTH},
author={Nazaket Tagi kızı Huseynova and Rena Firudin kızı Mamedova},
journal={Biological journal},
year={2020},
url={https://api.semanticscholar.org/CorpusID:213655664}
}
@article{bell2002dna,
title={DNA replication in eukaryotic cells},
author={Bell, Stephen P and Dutta, Anindya},
journal={Annual review of biochemistry},
volume={71},
number={1},
pages={333--374},
year={2002},
publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}
}
@article{ernster1981mitochondria,
title={Mitochondria: a historical review.},
author={Ernster, Lars and Schatz, Gottfried},
journal={The Journal of cell biology},
volume={91},
number={3},
pages={227s--255s},
year={1981}
}
@article{chinnery2003mitochondria,
title={Mitochondria},
author={Chinnery, Patrick F and Schon, Eric A},
journal={Journal of Neurology, Neurosurgery \& Psychiatry},
volume={74},
number={9},
pages={1188--1199},
year={2003},
publisher={BMJ Publishing Group Ltd}
}
@article{mcbride2006mitochondria,
title={Mitochondria: more than just a powerhouse},
author={McBride, Heidi M and Neuspiel, Margaret and Wasiak, Sylwia},
journal={Current biology},
volume={16},
number={14},
pages={R551--R560},
year={2006},
publisher={Elsevier}
}
@book{pollard2022cell,
title={Cell Biology E-Book: Cell Biology E-Book},
author={Pollard, Thomas D and Earnshaw, William C and Lippincott-Schwartz, Jennifer and Johnson, Graham},
year={2022},
publisher={Elsevier Health Sciences}
}
@article{pederson1998plurifunctional,
title={The plurifunctional nucleolus},
author={Pederson, Thoru},
journal={Nucleic acids research},
volume={26},
number={17},
pages={3871--3876},
year={1998},
publisher={Oxford University Press}
}
@article{voeltz2002structural,
title={Structural organization of the endoplasmic reticulum},
author={Voeltz, Gia K and Rolls, Melissa M and Rapoport, Tom A},
journal={EMBO reports},
volume={3},
number={10},
pages={944--950},
year={2002},
publisher={John Wiley \& Sons, Ltd}
}
@article{dell2000lysosome,
title={Lysosome-related organelles},
author={Dell'Angelica, Esteban C and Mullins, Chris and Caplan, Steve and Bonifacino, Juan S},
journal={The FASEB Journal},
volume={14},
number={10},
pages={1265--1278},
year={2000},
publisher={Wiley Online Library}
}
@article{ballabio2016awesome,
title={The awesome lysosome},
author={Ballabio, Andrea},
journal={EMBO molecular medicine},
volume={8},
number={2},
pages={73--76},
year={2016}
}
@article{yang2021lysosome,
title={Lysosome biogenesis: Regulation and functions},
author={Yang, Chonglin and Wang, Xiaochen},
journal={The Journal of cell biology},
volume={220},
number={6},
year={2021},
publisher={The Rockefeller University Press}
}
@article{islinger2012peroxisome,
title={The peroxisome: an update on mysteries},
author={Islinger, Markus and Grille, Sandra and Fahimi, H Dariush and Schrader, Michael},
journal={Histochemistry and cell biology},
volume={137},
pages={547--574},
year={2012},
publisher={Springer}
}
@article{jansen2011nucleosome,
title={Nucleosome positioning in Saccharomyces cerevisiae},
author={Jansen, An and Verstrepen, Kevin J},
journal={Microbiology and molecular biology reviews},
volume={75},
number={2},
pages={301--320},
year={2011},
publisher={Am Soc Microbiol}
}
@book{zheng2010packaging,
title={The packaging of DNA in chromatin},
author={Zheng, Guohui},
year={2010},
publisher={Rutgers The State University of New Jersey, School of Graduate Studies}
}
@article{fortin2015trx,
title={TRX-LOGOS-a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence},
author={Fortin, Connor H and Schulze, Katharina V and Babbitt, Gregory A},
journal={Source code for biology and medicine},
volume={10},
pages={1--11},
year={2015},
publisher={Springer}
}
@article{stormo1998specificity,
title={Specificity, free energy and information content in protein--DNA interactions},
author={Stormo, Gary D and Fields, Dana S},
journal={Trends in biochemical sciences},
volume={23},
number={3},
pages={109--113},
year={1998},
publisher={Elsevier}
}
@article{mcintosh2012biophysics,
title={Biophysics of mitosis},
author={McIntosh, J Richard and Molodtsov, Maxim I and Ataullakhanov, Fazly I},
journal={Quarterly reviews of biophysics},
volume={45},
number={2},
pages={147--207},
year={2012},
publisher={Cambridge University Press}
}
@book{rippe2012genome,
title={Genome organization and function in the cell nucleus},
author={Rippe, Karsten},
year={2012},
publisher={John Wiley \& Sons}
}
@article{gerstein2007gene,
title={What is a gene, post-ENCODE? History and updated definition},
author={Gerstein, Mark B and Bruce, Can and Rozowsky, Joel S and Zheng, Deyou and Du, Jiang and Korbel, Jan O and Emanuelsson, Olof and Zhang, Zhengdong D and Weissman, Sherman and Snyder, Michael},
journal={Genome research},
volume={17},
number={6},
pages={669--681},
year={2007},
publisher={Cold Spring Harbor Lab}
}
@article{lee2000transcription,
title={Transcription of eukaryotic protein-coding genes},
author={Lee, Tong Ihn and Young, Richard A},
journal={Annual review of genetics},
volume={34},
number={1},
pages={77--137},
year={2000},
publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}
}
@book{white2009gene,
title={Gene transcription: mechanisms and control},
author={White, Robert J},
year={2009},
publisher={John Wiley \& Sons}
}
@article{cramer2019organization,
title={Organization and regulation of gene transcription},
author={Cramer, Patrick},
journal={Nature},
volume={573},
number={7772},
pages={45--54},
year={2019},
publisher={Nature Publishing Group UK London}
}
@incollection{alberts2002dna,
title={From DNA to RNA},
author={Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Raff, Martin and Roberts, Keith and Walter, Peter},
booktitle={Molecular Biology of the Cell. 4th edition},
year={2002},
publisher={Garland Science}
}
@article{hocine2010rna,
title={RNA processing and export},
author={Hocine, Sami and Singer, Robert H and Gr{\"u}nwald, David},
journal={Cold Spring Harbor perspectives in biology},
volume={2},
number={12},
pages={a000752},
year={2010},
publisher={Cold Spring Harbor Lab}
}
@article{philips2000rna,
title={RNA processing and human disease},
author={Philips, AV and Cooper*, TA},
journal={Cellular and Molecular Life Sciences CMLS},
volume={57},
pages={235--249},
year={2000},
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% read
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% read
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