add new references to the project

docs/source/references.bib

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+@article {Herken2023,
+	author = {Benjamin W. Herken and Garrett T. Wong and Thomas M. Norman and Luke A. Gilbert},
+	title = {Environmental challenge rewires functional connections among human genes},
+	elocation-id = {2023.08.09.552346},
+	year = {2023},
+	doi = {10.1101/2023.08.09.552346},
+	publisher = {Cold Spring Harbor Laboratory},
+	abstract = {A fundamental question in biology is how a limited number of genes combinatorially govern cellular responses to environmental changes. While the prevailing hypothesis is that relationships between genes, processes, and ontologies could be plastic to achieve this adaptability, quantitatively comparing human gene functional connections between specific environmental conditions at scale is very challenging. Therefore, it remains unclear whether and how human genetic interaction networks are rewired in response to changing environmental conditions. Here, we developed a framework for mapping context-specific genetic interactions, enabling us to measure the plasticity of human genetic architecture upon environmental challenge for \~{}250,000 interactions, using cell cycle interruption, genotoxic perturbation, and nutrient deprivation as archetypes. We discover large-scale rewiring of human gene relationships across conditions, highlighted by dramatic shifts in the functional connections of epigenetic regulators (TIP60), cell cycle regulators (PP2A), and glycolysis metabolism. Our study demonstrates that upon environmental perturbation, intra-complex genetic rewiring is rare while inter-complex rewiring is common, suggesting a modular and flexible evolutionary genetic strategy that allows a limited number of human genes to enable adaptation to a large number of environmental conditions.One Sentence Summary Five human genetic interaction maps reveal how the landscape of genes{\textquoteright} functional relationships is rewired as cells experience environmental stress to DNA integrity, cell cycle regulation, and metabolism.Competing Interest StatementL.A.G and T.M.N. have filed patents on CRISPR functional genomics. L.A.G consults for, has equity in and is a co-founder of Chroma Medicine.},
+	URL = {https://www.biorxiv.org/content/early/2023/08/09/2023.08.09.552346},
+	eprint = {https://www.biorxiv.org/content/early/2023/08/09/2023.08.09.552346.full.pdf},
+	journal = {bioRxiv}
+}
+
+@article{Hsiung2023,
+  title = {Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics},
+  url = {http://dx.doi.org/10.1101/2023.09.18.558350},
+  DOI = {10.1101/2023.09.18.558350},
+  publisher = {Cold Spring Harbor Laboratory},
+  author = {Hsiung,  CC and Wilson,  CM and Sambold,  NA and Dai,  R and Chen,  Q and Misiukiewicz,  S and Arab,  A and Teyssier,  N and O’Loughlin,  T and Cofsky,  JC and Shi,  J and Gilbert,  LA},
+  year = {2023},
+  month = sep 
+}
+
+@article{Han2020,
+  title = {CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities},
+  volume = {580},
+  ISSN = {1476-4687},
+  url = {http://dx.doi.org/10.1038/s41586-020-2099-x},
+  DOI = {10.1038/s41586-020-2099-x},
+  number = {7801},
+  journal = {Nature},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Han,  Kyuho and Pierce,  Sarah E. and Li,  Amy and Spees,  Kaitlyn and Anderson,  Gray R. and Seoane,  Jose A. and Lo,  Yuan-Hung and Dubreuil,  Michael and Olivas,  Micah and Kamber,  Roarke A. and Wainberg,  Michael and Kostyrko,  Kaja and Kelly,  Marcus R. and Yousefi,  Maryam and Simpkins,  Scott W. and Yao,  David and Lee,  Keonil and Kuo,  Calvin J. and Jackson,  Peter K. and Sweet-Cordero,  Alejandro and Kundaje,  Anshul and Gentles,  Andrew J. and Curtis,  Christina and Winslow,  Monte M. and Bassik,  Michael C.},
+  year = {2020},
+  month = mar,
+  pages = {136–141}
+}
+
+@article{Han2017,
+  title = {Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions},
+  volume = {35},
+  ISSN = {1546-1696},
+  url = {http://dx.doi.org/10.1038/nbt.3834},
+  DOI = {10.1038/nbt.3834},
+  number = {5},
+  journal = {Nature Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Han,  Kyuho and Jeng,  Edwin E and Hess,  Gaelen T and Morgens,  David W and Li,  Amy and Bassik,  Michael C},
+  year = {2017},
+  month = mar,
+  pages = {463–474}
+}
+
+@article{Tian2019,
+  title = {CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons},
+  volume = {104},
+  ISSN = {0896-6273},
+  url = {http://dx.doi.org/10.1016/j.neuron.2019.07.014},
+  DOI = {10.1016/j.neuron.2019.07.014},
+  number = {2},
+  journal = {Neuron},
+  publisher = {Elsevier BV},
+  author = {Tian,  Ruilin and Gachechiladze,  Mariam A. and Ludwig,  Connor H. and Laurie,  Matthew T. and Hong,  Jason Y. and Nathaniel,  Diane and Prabhu,  Anika V. and Fernandopulle,  Michael S. and Patel,  Rajan and Abshari,  Mehrnoosh and Ward,  Michael E. and Kampmann,  Martin},
+  year = {2019},
+  month = oct,
+  pages = {239--255.e12}
+}
+
+@article{Horlbeck2016,
+  title = {Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation},
+  volume = {5},
+  ISSN = {2050-084X},
+  url = {http://dx.doi.org/10.7554/eLife.19760},
+  DOI = {10.7554/elife.19760},
+  journal = {eLife},
+  publisher = {eLife Sciences Publications,  Ltd},
+  author = {Horlbeck,  Max A and Gilbert,  Luke A and Villalta,  Jacqueline E and Adamson,  Britt and Pak,  Ryan A and Chen,  Yuwen and Fields,  Alexander P and Park,  Chong Yon and Corn,  Jacob E and Kampmann,  Martin and Weissman,  Jonathan S},
+  year = {2016},
+  month = sep 
+}
+
+@article{Gilbert2014,
+  title = {Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation},
+  volume = {159},
+  ISSN = {0092-8674},
+  url = {http://dx.doi.org/10.1016/j.cell.2014.09.029},
+  DOI = {10.1016/j.cell.2014.09.029},
+  number = {3},
+  journal = {Cell},
+  publisher = {Elsevier BV},
+  author = {Gilbert,  Luke A. and Horlbeck,  Max A. and Adamson,  Britt and Villalta,  Jacqueline E. and Chen,  Yuwen and Whitehead,  Evan H. and Guimaraes,  Carla and Panning,  Barbara and Ploegh,  Hidde L. and Bassik,  Michael C. and Qi,  Lei S. and Kampmann,  Martin and Weissman,  Jonathan S.},
+  year = {2014},
+  month = oct,
+  pages = {647–661}
+}
+
+@article{Kampmann2014NatureProtocols,
+  title = {Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps},
+  volume = {9},
+  ISSN = {1750-2799},
+  url = {http://dx.doi.org/10.1038/nprot.2014.103},
+  DOI = {10.1038/nprot.2014.103},
+  number = {8},
+  journal = {Nature Protocols},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Kampmann,  Martin and Bassik,  Michael C and Weissman,  Jonathan S},
+  year = {2014},
+  month = jul,
+  pages = {1825–1847}
+}
+
+@article{Kampmann2013PNAS,
+  title = {Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells},
+  volume = {110},
+  ISSN = {1091-6490},
+  url = {http://dx.doi.org/10.1073/pnas.1307002110},
+  DOI = {10.1073/pnas.1307002110},
+  number = {25},
+  journal = {Proceedings of the National Academy of Sciences},
+  publisher = {Proceedings of the National Academy of Sciences},
+  author = {Kampmann,  Martin and Bassik,  Michael C. and Weissman,  Jonathan S.},
+  year = {2013},
+  month = jun 
+}
+
+@article{Bassik2013,
+  title = {A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility},
+  volume = {152},
+  ISSN = {0092-8674},
+  url = {http://dx.doi.org/10.1016/j.cell.2013.01.030},
+  DOI = {10.1016/j.cell.2013.01.030},
+  number = {4},
+  journal = {Cell},
+  publisher = {Elsevier BV},
+  author = {Bassik,  Michael C. and Kampmann,  Martin and Lebbink,  Robert Jan and Wang,  Shuyi and Hein,  Marco Y. and Poser,  Ina and Weibezahn,  Jimena and Horlbeck,  Max A. and Chen,  Siyuan and Mann,  Matthias and Hyman,  Anthony A. and LeProust,  Emily M. and McManus,  Michael T. and Weissman,  Jonathan S.},
+  year = {2013},
+  month = feb,
+  pages = {909–922}
+}