Add JOSS submission materials (paper.md, paper.bib)

Author: ammawla

joss/paper.bib

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+@article{encode2012,
+  author  = {{The ENCODE Project Consortium}},
+  title   = {An integrated encyclopedia of {DNA} elements in the human genome},
+  journal = {Nature},
+  volume  = {489},
+  number  = {7414},
+  pages   = {57--74},
+  year    = {2012},
+  doi     = {10.1038/nature11247}
+}
+
+@article{encode2020,
+  author  = {Moore, Jill E. and Purcaro, Michael J. and Pratt, Henry E. and Epstein, Charles B. and Shoresh, Noam and Adrian, Jessika and Kawli, Trupti and Davis, Carrie A. and Dobin, Alexander and Kaul, Rajinder and Halow, Jessica and Van Nostrand, Eric L. and Freese, Peter and Gorkin, David U. and Shen, Yin and He, Yupeng and Mackiewicz, Mark and Pauli-Behn, Florencia and Williams, Brian A. and Mortazavi, Ali and Kishi, Yuri and Shlyueva, Daria and Stamatoyannopoulos, John A. and Weng, Zhiping and Snyder, Michael P. and {The ENCODE Project Consortium}},
+  title   = {Expanded encyclopaedias of {DNA} elements in the human and mouse genomes},
+  journal = {Nature},
+  volume  = {583},
+  number  = {7818},
+  pages   = {699--710},
+  year    = {2020},
+  doi     = {10.1038/s41586-020-2493-4}
+}
+
+@article{landt2012,
+  author  = {Landt, Stephen G. and Marinov, Georgi K. and Kundaje, Anshul and Kheradpour, Pouya and Pauli, Florencia and Batzoglou, Serafim and Bernstein, Bradley E. and Bickel, Peter and Brown, James B. and Cayting, Philip and Chen, Yiwen and DeSalvo, Gilberto and Epstein, Charles and Fisher-Aylor, Katherine I. and Euskirchen, Ghia and Gerstein, Mark and Gertz, Jason and Harber, Anthony J. and Kellis, Manolis and Kirilusha, Alina and Lam, Ho Yan and Li, Guoyan and Li, Qunhua and Liu, X. Shirley and Mortazavi, Ali and Negre, Nicolas and Park, Peter J. and Pepke, Shirley and Raha, Debasish and Snyder, Michael P. and Wold, Barbara J. and Birney, Ewan and {The ENCODE Project Consortium}},
+  title   = {ChIP-seq guidelines and practices of the {ENCODE} and mod{ENCODE} consortia},
+  journal = {Genome Research},
+  volume  = {22},
+  number  = {9},
+  pages   = {1813--1831},
+  year    = {2012},
+  doi     = {10.1101/gr.136184.111}
+}
+
+@article{buenrostro2013,
+  author  = {Buenrostro, Jason D. and Giresi, Paul G. and Zaba, Lisa C. and Chang, Howard Y. and Greenleaf, William J.},
+  title   = {Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, {DNA}-binding proteins and nucleosome position},
+  journal = {Nature Methods},
+  volume  = {10},
+  number  = {12},
+  pages   = {1213--1218},
+  year    = {2013},
+  doi     = {10.1038/nmeth.2688}
+}
+
+@article{conesa2016,
+  author  = {Conesa, Ana and Madrigal, Pedro and Tarazona, Sonia and Gomez-Cabrero, David and Cervera, Alejandra and McPherson, Andrew and Szcze\'{s}niak, Micha\l{} Wojciech and Gaffney, Daniel J. and Elo, Laura L. and Zhang, Xuegong and Mortazavi, Ali},
+  title   = {A survey of best practices for {RNA}-seq data analysis},
+  journal = {Genome Biology},
+  volume  = {17},
+  pages   = {13},
+  year    = {2016},
+  doi     = {10.1186/s13059-016-0881-8}
+}
+
+@misc{mcp2024,
+  author  = {{Anthropic}},
+  title   = {Model Context Protocol Specification},
+  year    = {2024},
+  url     = {https://modelcontextprotocol.io/specification},
+  note    = {Accessed: 2026-03-20}
+}
+
+@article{ucsc2023,
+  author  = {Nassar, Luis R. and Barber, Galt P. and Benet-Pag\`{e}s, Anna and Casper, Jonathan and Clawson, Hiram and Diekhans, Mark and Fischer, Clay and Gonzalez, Jairo Navarro and Hinrichs, Angie S. and Lee, Brian T. and Lee, Christopher M. and Muthuraman, Pranav and Nguy, Beagan and Pereira, Terrence and Nejad, Parisa and Perez, Gerardo and Raney, Brian J. and Schmelter, Daniel and Speir, Matthew L. and Wick, Brett D. and Zweig, Ann S. and Haussler, David and Kuhn, Robert M. and Haeussler, Maximilian and Kent, W. James},
+  title   = {The {UCSC} Genome Browser database: 2023 update},
+  journal = {Nucleic Acids Research},
+  volume  = {51},
+  number  = {D1},
+  pages   = {D1188--D1195},
+  year    = {2023},
+  doi     = {10.1093/nar/gkac1072}
+}
+
+@article{gtex2020,
+  author  = {{The GTEx Consortium}},
+  title   = {The {GTEx} Consortium atlas of genetic regulatory effects across human tissues},
+  journal = {Science},
+  volume  = {369},
+  number  = {6509},
+  pages   = {1318--1330},
+  year    = {2020},
+  doi     = {10.1126/science.aaz1776}
+}
+
+@article{geo2013,
+  author  = {Barrett, Tanya and Wilhite, Stephen E. and Ledoux, Pierre and Evangelista, Carlos and Kim, Irene F. and Tomashevsky, Maxim and Marshall, Kimberly A. and Phillippy, Katherine H. and Sherman, Patti M. and Holko, Michelle and Yefanov, Andrey and Lee, Hyeseung and Zhang, Naigong and Robertson, Cynthia L. and Serova, Nadezhda and Davis, Sean and Soboleva, Alexandra},
+  title   = {{NCBI} {GEO}: archive for functional genomics data sets---update},
+  journal = {Nucleic Acids Research},
+  volume  = {41},
+  number  = {D1},
+  pages   = {D991--D995},
+  year    = {2013},
+  doi     = {10.1093/nar/gks1193}
+}
+
+@article{clinvar2018,
+  author  = {Landrum, Melissa J. and Lee, Jennifer M. and Benson, Mark and Brown, Garth R. and Chao, Chen and Chitipiralla, Shanmuga and Gu, Baoshan and Hart, Jennifer and Hoffman, Douglas and Jang, Wonhee and Karapetyan, Karen and Katz, Kenneth and Liu, Chunlei and Maddipatla, Zenith and Malheiro, Adriana and McDaniel, Kurt and Ovetsky, Michael and Riley, George and Zhou, George and Holmes, J. Bradley and Kattman, Brandi L. and Maglott, Donna R.},
+  title   = {{ClinVar}: improving access to variant interpretations and supporting evidence},
+  journal = {Nucleic Acids Research},
+  volume  = {46},
+  number  = {D1},
+  pages   = {D1062--D1067},
+  year    = {2018},
+  doi     = {10.1093/nar/gkx1153}
+}
+
+@article{gwas2023,
+  author  = {Sollis, Elliot and Mosaku, Abayomi and Abid, Ala and Buniello, Annalisa and Cerezo, Maria and Gil, Laurent and Groza, Tudor and G\"{u}ne\c{s}, Osman and Hall, Peggy and Hayhurst, James and Ibrahim, Arwa and Ji, Yue and John, Sajo and Lewis, Elizabeth and MacArthur, Jacqueline A. L. and McMahon, Aoife and Osumi-Sutherland, David and Panoutsopoulou, Kalliope and Pendlington, Zo\"{e} and Ramachandran, Santhi and Stefancsik, Ray and Stewart, Jonathan and Whetzel, Patricia and Wilson, Robert and Hindorff, Lucia and Cunningham, Fiona and Lambert, Samuel A. and Inouye, Michael and Parkinson, Helen and Harris, Laura W.},
+  title   = {The {NHGRI-EBI} {GWAS} Catalog: knowledgebase and deposition resource},
+  journal = {Nucleic Acids Research},
+  volume  = {51},
+  number  = {D1},
+  pages   = {D977--D985},
+  year    = {2023},
+  doi     = {10.1093/nar/gkac1010}
+}
+
+@article{gnomad2020,
+  author  = {Karczewski, Konrad J. and Francioli, Laurent C. and Tiao, Grace and Cummings, Beryl B. and Alf\"{o}ldi, Jessica and Wang, Qingbo and Collins, Ryan L. and Laricchia, Kristen M. and Ganna, Andrea and Birnbaum, Daniel P. and Gauthier, Laura D. and Brand, Harrison and Solomonson, Matthew and Watts, Nicholas A. and Rhodes, Daniel and Singer-Berk, Moriel and England, Eleanor M. and Seaby, Eleanor G. and Kosmicki, Jack A. and Walters, Raymond K. and Tashman, Katherine and Farjoun, Yossi and Banks, Eric and Poterba, Timothy and Wang, Arcturus and Seed, Cotton and Whiffin, Nicola and Chong, Jessica X. and Samocha, Kaitlin E. and Pierce-Hoffman, Emma and Zappala, Zachary and O'Donnell-Luria, Anne H. and Minikel, Eric Vallabh and Weisburd, Ben and Lek, Monkol and Ware, James S. and Vittal, Christopher and Armean, Irina M. and Bergelson, Louis and Cibulskis, Kristian and Connolly, Kristen M. and Covarrubias, Miguel and Donnelly, Stacey and Ferriera, Steven and Gabriel, Stacey and Gentry, Jeff and Gupta, Namrata and Jeandet, Thibault and Kaplan, Diane and Llanwarne, Christopher and Munshi, Ruchi and Novod, Sam and Petrillo, Nikelle and Roazen, David and Ruano-Rubio, Valentin and Saltzman, Andrea and Schleicher, Molly and Soto, Jose and Tibbetts, Kathleen and Tolonen, Charlotte and Wade, Gordon and Talkowski, Michael E. and Neale, Benjamin M. and Daly, Mark J. and MacArthur, Daniel G.},
+  title   = {The mutational constraint spectrum quantified from variation in 141,456 humans},
+  journal = {Nature},
+  volume  = {581},
+  number  = {7809},
+  pages   = {434--443},
+  year    = {2020},
+  doi     = {10.1038/s41586-020-2308-7}
+}
+
+@article{jaspar2024,
+  author  = {Rauluseviciute, Ieva and Riudavets-Puig, Rafael and Blanc-Mathieu, Romain and Castro-Mondragon, Jaime A. and Ferenc, Katalin and Kumar, Vipin and Lemma, Roza Berhanu and Lucas, J\'{e}r\'{e}my and Ch\`{e}neby, Jeanne and Baranasic, Damir and Khan, Aziz and Fornes, Oriol and Gundersen, Sveinung and Johansen, Morten and Hovig, Eivind and Lenhard, Boris and Sandelin, Albin and Wasserman, Wyeth W. and Parcy, Fran\c{c}ois and Mathelier, Anthony},
+  title   = {{JASPAR} 2024: 20th anniversary of the open-access database of transcription factor binding profiles},
+  journal = {Nucleic Acids Research},
+  volume  = {52},
+  number  = {D1},
+  pages   = {D174--D182},
+  year    = {2024},
+  doi     = {10.1093/nar/gkad1059}
+}
+
+@article{ensembl2023,
+  author  = {Martin, Fergal J. and Amode, M. Ridwan and Aneja, Alisha and Austine-Orimoloye, Olanrewaju and Azov, Andrey G. and Barnes, If and Becker, Arne and Bennett, Ruth and Berry, Andrew and Bhai, Jyothish and Bhurji, Simarpreet Kaur and Bignell, Alexandra and Boddu, Sanjay and Branco Lins, Paulo R. and Brooks, Lucy and Ramaraju, Shashank Budhanuru and Charkhchi, Mehrnaz and Cockburn, Alexander and Da Rin Fiorretto, Luca and Davidson, Claire and Dodiya, Kamalkumar and Donaldson, Sarah and El Houdaigui, Bilal and El Naboulsi, Tamara and Fatima, Reham and Giron, Carlos Garcia and Genez, Thiago and Ghattaoraya, Gurpreet S. and Martinez, Jose Gonzalez and Guijarro-Clarke, Cristi and Gyber, Aysegul and Hardy, Matthew and Hollis, Zoe and Hourlier, Thibaut and Hunt, Toby and Kay, Mike and Kaykala, Vinay and Le, Tuan and Lemos, Diana and Marques-Coelho, Diego and Marug\'{a}n, Jos\'{e} Carlos and Merino, Gabriela Alejandra and Mirabueno, Louisse Paola and Mushtaq, Aleena and Hossain, Syed Nakib and Ogeh, Denye N. and Sakthivel, Manoj Pandian and Parker, Anne and Perry, Malcolm and Pili\v{z}ota, Ivana and Prosovetskaia, Irina and P\'{e}rez-Silva, Jos\'{e} G. and Salam, Ahamed Imran Abdul and Saraiva-Agostinho, Nuno and Schuilenburg, Helen and Sheppard, Dan and Sinha, Swati and Siber, Botond and Steed, Emily and Suerber, Ruth and Szpak, Michal and Tate, John G. and Thormann, Anja and Trevanion, Stephen J. and Walts, Blake and Wiber, Andrea and Winterbottom, Andrea and Cunningham, Fiona and Flicek, Paul},
+  title   = {Ensembl 2023},
+  journal = {Nucleic Acids Research},
+  volume  = {51},
+  number  = {D1},
+  pages   = {D933--D941},
+  year    = {2023},
+  doi     = {10.1093/nar/gkac958}
+}
+
+@article{cellxgene2025,
+  author  = {{CZI Single-Cell Biology Program} and Abdulla, Shibla and Aevermann, Brian and Assis, Pedro and Badajoz, Seve and Bell, Sidney M. and Bezzi, Emanuele and Cakir, Batuhan and Chaffer, Jim and Chambers, Signe and Cherry, J. Michael and Chi, Tiffany and Chien, Jennifer and Dorman, Leah and Garcia-Nieto, Pablo and Gloria, Nayib and Hastie, Mim and Hegeman, Daniel and Hilton, Jason and Huang, Timmy and Infeld, Amanda and Istrate, Ana-Maria and Jelic, Ivana and Katsuya, Kuni and Kim, Yang Joon and Liang, Karen and Lin, Mike and Lombardo, Maximilian and Marshall, Bailey and Martin, Bruce and McDade, Fran and Megill, Colin and Patel, Nikhil and Predeus, Alexander and Raymor, Brian and Robatmili, Behnam and Rogers, Dave and Rutherford, Erica and Sadgat, Dana and Shin, Andrew and Small, Corinn and Smith, Trent and Sridharan, Prathap and Tarashansky, Alexander and Tavares, Norbert and Thomas, Harley and Tolopko, Andrew and Urisko, Meghan and Yan, Joyce and Yeretssian, Garabet and Zamanian, Jennifer and Mani, Arathi and Cool, Jonah and Carr, Ambrose},
+  title   = {{CZ} {CELLxGENE} Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data},
+  journal = {Nucleic Acids Research},
+  volume  = {53},
+  number  = {D1},
+  pages   = {D886--D900},
+  year    = {2025},
+  doi     = {10.1093/nar/gkae1142}
+}
+
+@article{opentargets2023,
+  author  = {Ochoa, David and Hercules, Andrew and Carmona, Miguel and Suveges, Daniel and Baker, Jarrod and Malangone, Cinzia and Lopez, Irene and Miranda, Alfredo and Cruz-Castillo, Carlos and Fumis, Luca and Bernal-Llinares, Manuel and Tsukanov, Kirill and Cornu, Helena and Tsirigos, Konstantinos and Razuvayevskaya, Olesya and Buniello, Annalisa and Schwartzentruber, Jeremy and Karim, Mohd and Ariano, Bruno and Martinez Osorio, Ricardo Esteban and Ferrer, Javier and Ge, Xiangyu and Machlitt-Northen, Sandra and Gonzalez-Uriarte, Asier and Saha, Shyamasree and Tirunagari, Santosh and Mehta, Chintan and Rold\'{a}n-Romero, Juan Mar\'{i}a and Horswell, Stuart and Young, Sarah and Ghoussaini, Maya and Hulcoop, David G. and Dunham, Ian and McDonagh, Ellen M.},
+  title   = {The next-generation {Open Targets} Platform: reimagined, redesigned, rebuilt},
+  journal = {Nucleic Acids Research},
+  volume  = {51},
+  number  = {D1},
+  pages   = {D1353--D1359},
+  year    = {2023},
+  doi     = {10.1093/nar/gkac1046}
+}
+
+@article{lister2009,
+  author  = {Lister, Ryan and Pelizzola, Mattia and Dowen, Robert H. and Hawkins, R. David and Hon, Gary and Tonti-Filippini, Julian and Nery, Joseph R. and Lee, Leonard and Ye, Zhen and Ngo, Que-Minh and Edsall, Lee and Antosiewicz-Bourget, Jessica and Stewart, Ron and Ruotti, Victor and Millar, A. Harvey and Thomson, James A. and Ren, Bing and Ecker, Joseph R.},
+  title   = {Human {DNA} methylomes at base resolution show widespread epigenomic differences},
+  journal = {Nature},
+  volume  = {462},
+  number  = {7271},
+  pages   = {315--322},
+  year    = {2009},
+  doi     = {10.1038/nature08514}
+}
+
+@article{lieberman2009,
+  author  = {Lieberman-Aiden, Erez and van Berkum, Nynke L. and Williams, Louise and Imakaev, Maxim and Ragoczy, Tobias and Telling, Agnes and Amit, Ido and Lajoie, Bryan R. and Sabo, Peter J. and Dorschner, Michael O. and Sandstrom, Richard and Bernstein, Bradley and Bender, M. A. and Groudine, Mark and Gnirke, Andreas and Stamatoyannopoulos, John and Mirny, Leonid A. and Lander, Eric S. and Dekker, Job},
+  title   = {Comprehensive mapping of long-range interactions reveals folding principles of the human genome},
+  journal = {Science},
+  volume  = {326},
+  number  = {5950},
+  pages   = {289--293},
+  year    = {2009},
+  doi     = {10.1126/science.1181369}
+}
+
+@article{thurman2012,
+  author  = {Thurman, Robert E. and Rynes, Eric and Humbert, Richard and Vierstra, Jeff and Maurano, Matthew T. and Haugen, Eric and Sheffield, Nathan C. and Stergachis, Andrew B. and Wang, Hao and Vernot, Benjamin and Garg, Kavita and John, Sam and Sandstrom, Richard and Bates, Daniel and Boatman, Lisa and Canfield, Theresa K. and Diegel, Morgan and Dunn, Douglas and Ebersol, Abigail K. and Frum, Tristan and Giste, Erika and Johnson, Audra K. and Johnson, Ericka M. and Kutyavin, Tanya and Laber, Brenae and Lee, Kristen and Lotakis, Dimitra and Neph, Shane and Neri, Fidencio and Nguyen, Eric D. and Qu, Hongzhu and Reynolds, Alex P. and Roach, Vaughn and Safi, Alexias and Sanchez, Minerva E. and Sanyal, Amartya and Shafer, Anthony and Simon, Jeremy M. and Song, Lingyun and Vong, Shinny and Weaver, Molly and Yan, Yongqi and Zhang, Zhancheng and Lenhard, Boris and Tewari, Muneesh and Dorschner, Michael O. and Hansen, R. Scott and Navas, Patrick A. and Stamatoyannopoulos, George and Iyer, Vishwanath R. and Lieb, Jason D. and Sunyaev, Shamil R. and Akey, Joshua M. and Sabo, Peter J. and Kaul, Rajinder and Furey, Terrence S. and Dekker, Job and Crawford, Gregory E. and Stamatoyannopoulos, John A.},
+  title   = {The accessible chromatin landscape of the human genome},
+  journal = {Nature},
+  volume  = {489},
+  number  = {7414},
+  pages   = {75--82},
+  year    = {2012},
+  doi     = {10.1038/nature11232}
+}
+
+@article{skene2017,
+  author  = {Skene, Peter J. and Henikoff, Steven},
+  title   = {An efficient targeted nuclease strategy for high-resolution mapping of {DNA} binding sites},
+  journal = {eLife},
+  volume  = {6},
+  pages   = {e21856},
+  year    = {2017},
+  doi     = {10.7554/eLife.21856}
+}
+
+@article{mawla2019,
+  author  = {Mawla, Alex M. and van der Meulen, Talitha and Huising, Mark O.},
+  title   = {Navigating the Depths and Avoiding the Shallows of Pancreatic Islet Cell Transcriptomes},
+  journal = {Diabetes},
+  volume  = {68},
+  number  = {7},
+  pages   = {1380--1393},
+  year    = {2019},
+  doi     = {10.2337/dbi18-0019}
+}
+
+@article{stuart2019,
+  author  = {Stuart, Tim and Butler, Andrew and Hoffman, Paul and Hafemeister, Christoph and Papalexi, Efthymia and Mauck, William M. and Hao, Yuhan and Stoeckius, Marlon and Smibert, Peter and Satija, Rahul},
+  title   = {Comprehensive Integration of Single-Cell Data},
+  journal = {Cell},
+  volume  = {177},
+  number  = {7},
+  pages   = {1888--1902.e21},
+  year    = {2019},
+  doi     = {10.1016/j.cell.2019.05.031}
+}
+
+@article{tran2020,
+  author  = {Tran, Hoa Thi Nhu and Ang, Kok Siong and Chevrier, Marion and Zhang, Xiaomeng and Lee, Nicole Yee Shin and Goh, Michelle and Chen, Jinmiao},
+  title   = {A benchmark of batch-effect correction methods for single-cell {RNA} sequencing data},
+  journal = {Genome Biology},
+  volume  = {21},
+  number  = {1},
+  pages   = {12},
+  year    = {2020},
+  doi     = {10.1186/s13059-019-1850-9}
+}
+
+@article{luecken2019,
+  author  = {Luecken, Malte D. and Theis, Fabian J.},
+  title   = {Current best practices in single-cell {RNA}-seq analysis: a tutorial},
+  journal = {Molecular Systems Biology},
+  volume  = {15},
+  number  = {6},
+  pages   = {e8746},
+  year    = {2019},
+  doi     = {10.15252/msb.20188746}
+}
+
+@article{ewels2020,
+  author  = {Ewels, Philip A. and Peltzer, Alexander and Fillinger, Sven and Patel, Harshil and Alneberg, Johannes and Wilm, Andreas and Garcia, Maxime Ulysse and Di Tommaso, Paolo and Nahnsen, Sven},
+  title   = {The nf-core framework for community-curated bioinformatics pipelines},
+  journal = {Nature Biotechnology},
+  volume  = {38},
+  number  = {3},
+  pages   = {276--278},
+  year    = {2020},
+  doi     = {10.1038/s41587-020-0439-x}
+}
+
+@article{afgan2018,
+  author  = {Afgan, Enis and Baker, Dannon and Batut, B\'{e}r\'{e}nice and van den Beek, Marius and Bouvier, Dave and \v{C}ech, Martin and Chilton, John and Clements, Dave and Coraor, Nate and Gr\"{u}ning, Bj\"{o}rn A. and Guerler, Aysam and Hillman-Jackson, Jennifer and Hiltemann, Saskia and Jalili, Vahid and Rasche, Helena and Soranzo, Nicola and Goecks, Jeremy and Taylor, James and Nekrutenko, Anton and Blankenberg, Daniel},
+  title   = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses: 2018 update},
+  journal = {Nucleic Acids Research},
+  volume  = {46},
+  number  = {W1},
+  pages   = {W537--W544},
+  year    = {2018},
+  doi     = {10.1093/nar/gky379}
+}