Software for Computing and Annotating Genomic Ranges

Citations

Cited by:

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4. Maritere Uriostegui-Arcos & Steven T. Mick & Zhuo Shi & Rufuto Rahman & Ana Fiszbein, 2023. "Splicing activates transcription from weak promoters upstream of alternative exons," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
5. Gaylor Boulay & Liliane C. Broye & Rui Dong & Sowmya Iyer & Rajendran Sanalkumar & Yu-Hang Xing & Rémi Buisson & Shruthi Rengarajan & Beverly Naigles & Benoît Duc & Angela Volorio & Mary E. Awad & Raf, 2024. "EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in desmoplastic small round cell tumors," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
6. Yue Yuan & Qiang Huo & Ziru Zhang & Qun Wang & Juanxia Wang & Shuaikang Chang & Peng Cai & Karen M. Song & David W. Galbraith & Weixiao Zhang & Long Huang & Rentao Song & Zeyang Ma, 2024. "Decoding the gene regulatory network of endosperm differentiation in maize," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
7. Teresa Maria Rosaria Noviello & Anna Maria Giacomo & Francesca Pia Caruso & Alessia Covre & Roberta Mortarini & Giovanni Scala & Maria Claudia Costa & Sandra Coral & Wolf H. Fridman & Catherine Sautès, 2023. "Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
8. Raúl F. Pérez & Patricia Tezanos & Alfonso Peñarroya & Alejandro González-Ramón & Rocío G. Urdinguio & Javier Gancedo-Verdejo & Juan Ramón Tejedor & Pablo Santamarina-Ojeda & Juan José Alba-Linares & , 2024. "A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
9. Seppe Goovaerts & Hanne Hoskens & Ryan J. Eller & Noah Herrick & Anthony M. Musolf & Cristina M. Justice & Meng Yuan & Sahin Naqvi & Myoung Keun Lee & Dirk Vandermeulen & Heather L. Szabo-Rogers & Pau, 2023. "Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
10. Natsuko Otaki & Yasutaka Motomura & Tommy Terooatea & S. Thomas Kelly & Miho Mochizuki & Natsuki Takeno & Shigeo Koyasu & Miu Tamamitsu & Fuminori Sugihara & Junichi Kikuta & Hideya Kitamura & Yoshiki, 2023. "Activation of ILC2s through constitutive IFNγ signaling reduction leads to spontaneous pulmonary fibrosis," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
11. M d Mesbah Uddin & Ngoc Quynh H. Nguyen & Bing Yu & Jennifer A. Brody & Akhil Pampana & Tetsushi Nakao & Myriam Fornage & Jan Bressler & Nona Sotoodehnia & Joshua S. Weinstock & Michael C. Honigberg &, 2022. "Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
12. Michael R. Kelly & Kamila Wisniewska & Matthew J. Regner & Michael W. Lewis & Andrea A. Perreault & Eric S. Davis & Douglas H. Phanstiel & Joel S. Parker & Hector L. Franco, 2022. "A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
13. Yanming Ren & Zongyao Huang & Lingling Zhou & Peng Xiao & Junwei Song & Ping He & Chuanxing Xie & Ran Zhou & Menghan Li & Xiangqun Dong & Qing Mao & Chao You & Jianguo Xu & Yanhui Liu & Zhigang Lan & , 2023. "Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
14. Alessandra Castiglioni & Yagai Yang & Katherine Williams & Alvin Gogineni & Ryan S. Lane & Amber W. Wang & Justin A. Shyer & Zhe Zhang & Stephanie Mittman & Alan Gutierrez & Jillian L. Astarita & Minh, 2023. "Combined PD-L1/TGFβ blockade allows expansion and differentiation of stem cell-like CD8 T cells in immune excluded tumors," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
15. Youtao Lu & Jaehee Lee & Jifen Li & Srinivasa Rao Allu & Jinhui Wang & HyunBum Kim & Kevin L. Bullaughey & Stephen A. Fisher & C. Erik Nordgren & Jean G. Rosario & Stewart A. Anderson & Alexandra V. U, 2023. "CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
16. Helen M. Gunter & Scott E. Youlten & Andre L. M. Reis & Tim McCubbin & Bindu Swapna Madala & Ted Wong & Igor Stevanovski & Arcadi Cipponi & Ira W. Deveson & Nadia S. Santini & Sarah Kummerfeld & Peter, 2024. "A universal molecular control for DNA, mRNA and protein expression," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
17. Lucia Coscujuela Tarrero & Valeria Famà & Giacomo D’Andrea & Simone Maestri & Anna Polo & Stefano Biffo & Mattia Furlan & Mattia Pelizzola, 2024. "Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
18. XinYue Wang & William J. Jowsey & Chen-Yi Cheung & Caitlan J. Smart & Hannah R. Klaus & Noon EJ Seeto & Natalie JE Waller & Michael T. Chrisp & Amanda L. Peterson & Boatema Ofori-Anyinam & Emily Stron, 2024. "Whole genome CRISPRi screening identifies druggable vulnerabilities in an isoniazid resistant strain of Mycobacterium tuberculosis," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
19. Jeroen Kneppers & Tesa M. Severson & Joseph C. Siefert & Pieter Schol & Stacey E. P. Joosten & Ivan Pak Lok Yu & Chia-Chi Flora Huang & Tunç Morova & Umut Berkay Altıntaş & Claudia Giambartolomei & Ji, 2022. "Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
20. Gerard Llimos & Vincent Gardeux & Ute Koch & Judith F. Kribelbauer & Antonina Hafner & Daniel Alpern & Joern Pezoldt & Maria Litovchenko & Julie Russeil & Riccardo Dainese & Riccardo Moia & Abdurraouf, 2022. "A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
21. Sebastian Carrasco Pro & Heather Hook & David Bray & Daniel Berenzy & Devlin Moyer & Meimei Yin & Adam Thomas Labadorf & Ryan Tewhey & Trevor Siggers & Juan Ignacio Fuxman Bass, 2023. "Widespread perturbation of ETS factor binding sites in cancer," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
22. Kathryn Weinand & Saori Sakaue & Aparna Nathan & Anna Helena Jonsson & Fan Zhang & Gerald F. M. Watts & Majd Al Suqri & Zhu Zhu & Deepak A. Rao & Jennifer H. Anolik & Michael B. Brenner & Laura T. Don, 2024. "The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis," Nature Communications, Nature, vol. 15(1), pages 1-25, December.
23. Marko Dunjić & Felix Jonas & Gilad Yaakov & Roye More & Yoav Mayshar & Yoach Rais & Ayelet-Hashahar Orenbuch & Saifeng Cheng & Naama Barkai & Yonatan Stelzer, 2023. "Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
24. Julian Cheron & Leonardo Beccari & Perrine Hagué & Romain Icick & Chloé Despontin & Teresa Carusone & Matthieu Defrance & Sagar Bhogaraju & Elena Martin-Garcia & Roberto Capellan & Rafael Maldonado & , 2023. "USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
25. Brian M. Schilder & Alan E. Murphy & Nathan G. Skene, 2024. "rworkflows: automating reproducible practices for the R community," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
26. Anna Podleśny-Drabiniok & Gloriia Novikova & Yiyuan Liu & Josefine Dunst & Rose Temizer & Chiara Giannarelli & Samuele Marro & Taras Kreslavsky & Edoardo Marcora & Alison Mary Goate, 2024. "BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer’s disease and other disorders of lipid-rich tissues," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
27. Lisa-Marie Appel & Vedran Franke & Melania Bruno & Irina Grishkovskaya & Aiste Kasiliauskaite & Tanja Kaufmann & Ursula E. Schoeberl & Martin G. Puchinger & Sebastian Kostrhon & Carmen Ebenwaldner & M, 2021. "PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC," Nature Communications, Nature, vol. 12(1), pages 1-24, December.
28. C. W. Ryan & S. L. Regan & E. F. Mills & B. T. McGrath & E. Gong & Y. T. Lai & J. B. Sheingold & K. Patel & T. Horowitz & A. Moccia & Y. C. Tsan & A. Srivastava & S. L. Bielas, 2024. "RING1 missense variants reveal sensitivity of DNA damage repair to H2A monoubiquitination dosage during neurogenesis," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
29. Yasha Butt & Ramin Sakhtemani & Rukshana Mohamad-Ramshan & Michael S. Lawrence & Ashok S. Bhagwat, 2024. "Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
30. Maja Olecka & Alena Bömmel & Lena Best & Madlen Haase & Silke Foerste & Konstantin Riege & Thomas Dost & Stefano Flor & Otto W. Witte & Sören Franzenburg & Marco Groth & Björn Eyss & Christoph Kaleta , 2024. "Nonlinear DNA methylation trajectories in aging male mice," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
31. Tina Pekec & Jarosław Lewandowski & Alicja A. Komur & Daria Sobańska & Yanwu Guo & Karolina Świtońska-Kurkowska & Jędrzej M. Małecki & Abhishek Anil Dubey & Wojciech Pokrzywa & Marcin Frankowski & Mac, 2022. "Ferritin-mediated iron detoxification promotes hypothermia survival in Caenorhabditis elegans and murine neurons," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
32. Cheng Zeng & Jiwei Chen & Emmalee W. Cooke & Arijita Subuddhi & Eliana T. Roodman & Fei Xavier Chen & Kaixiang Cao, 2023. "Demethylase-independent roles of LSD1 in regulating enhancers and cell fate transition," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
33. Konsta Karttunen & Divyesh Patel & Jihan Xia & Liangru Fei & Kimmo Palin & Lauri Aaltonen & Biswajyoti Sahu, 2023. "Transposable elements as tissue-specific enhancers in cancers of endodermal lineage," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
34. Heta Desai & Katrina H. Andrews & Kristina V. Bergersen & Samuel Ofori & Fengchao Yu & Flowreen Shikwana & Mark A. Arbing & Lisa M. Boatner & Miranda Villanueva & Nicholas Ung & Elaine F. Reed & Alexe, 2024. "Chemoproteogenomic stratification of the missense variant cysteinome," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
35. Samir Rachid Zaim & Mark-Phillip Pebworth & Imran McGrath & Lauren Okada & Morgan Weiss & Julian Reading & Julie L. Czartoski & Troy R. Torgerson & M. Juliana McElrath & Thomas F. Bumol & Peter J. Ske, 2024. "MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
36. Sujun Chen & Jessica Petricca & Wenbin Ye & Jiansheng Guan & Yong Zeng & Nicholas Cheng & Linsey Gong & Shu Yi Shen & Junjie T. Hua & Megan Crumbaker & Michael Fraser & Stanley Liu & Scott V. Bratman , 2022. "The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
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38. Bartosz Mucha & Shuo Qie & Sagar Bajpai & Vincenzo Tarallo & J. Nathaniel Diehl & Frank Tedeschi & Gao Zhou & Zhaofeng Gao & Samuel Flashner & Andres J. Klein-Szanto & Hanina Hibshoosh & Shimonosono M, 2022. "Tumor suppressor mediated ubiquitylation of hnRNPK is a barrier to oncogenic translation," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
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42. Robert Schöpflin & Uirá Souto Melo & Hossein Moeinzadeh & David Heller & Verena Laupert & Jakob Hertzberg & Manuel Holtgrewe & Nico Alavi & Marius-Konstantin Klever & Julius Jungnitsch & Emel Comak & , 2022. "Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
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75. Ihab Ansari & Llorenç Solé-Boldo & Meshi Ridnik & Julian Gutekunst & Oliver Gilliam & Maria Korshko & Timur Liwinski & Birgit Jickeli & Noa Weinberg-Corem & Michal Shoshkes-Carmel & Eli Pikarsky & Era, 2023. "TET2 and TET3 loss disrupts small intestine differentiation and homeostasis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
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