Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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Items 101–154 of 154

1. Genetic, epigenetic, and environmental factors controlling oxytocin receptor gene expression
   Danoff, Joshua S., Wroblewski, Kelly L., Graves, Andrew J., Quinn, Graham C., Perkeybile, Allison M., Kenkel, William M., Lillard, Travis S., Parikh, Hardik I., Golino, Hudson F., Gregory, Simon G. et al. · 2021 · Clinical Epigenetics
2. Outer Membrane Vesicle‐Based Nanohybrids Target Tumor‐Associated Macrophages to Enhance Trained Immunity‐Related Vaccine‐Generated Antitumor Activity
   Liang, Jie, Zhu, Fei, Cheng, Keman, Ma, Nana, Ma, Xiaotu, Feng, Qingqing, Xu, Chen, Gao, Xiaoyu, Wang, Xinwei, Shi, Jian et al. · 2023 · Advanced Materials
3. Activating ERBB2/HER2 mutations indicate susceptibility to pan-HER inhibitors in Lynch and Lynch-like colorectal cancer
   Kloth, Michael, Ruesseler, Vanessa, Engel, Christoph, Koenig, Katharina, Peifer, Martin, Mariotti, Erika, Kuenstlinger, Helen, Florin, Alexandra, Rommerscheidt-Fuss, Ursula, Koitzsch, Ulrike et al. · 2016 · Gut
4. The IL-4/STAT6/PPARγ signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages
   Daniel, Bence, Nagy, Gergely, Horvath, Attila, Czimmerer, Zsolt, Cuaranta-Monroy, Ixchelt, Poliska, Szilard, Hays, Tristan T, Sauer, Sascha, Francois-Deleuze, Jean, Nagy, Laszlo · 2018 · Nucleic Acids Research
5. RNA Sequencing and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-Tolerant Bacterium Deinococcus deserti
   de Groot, Arjan, Roche, David, Fernandez, Bernard, Ludanyi, Monika, Cruveiller, Stéphane, Pignol, David, Vallenet, David, Armengaud, Jean, Blanchard, Laurence · 2014 · Genome Biology and Evolution
6. Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate
   Silberberg, Shanni N., Taher, Leila, Lindtner, Susan, Sandberg, Magnus, Nord, Alex S., Vogt, Daniel, Mckinsey, Gabriel L., Hoch, Renee, Pattabiraman, Kartik, Zhang, Dongji et al. · 2016 · Neuron
7. Dedifferentiation and neuronal repression define familial Alzheimer’s disease
   Caldwell, Andrew B., Liu, Qing, Schroth, Gary P., Galasko, Douglas R., Yuan, Shauna H., Wagner, Steven L., Subramaniam, Shankar · 2020 · Science Advances
8. Droplet-based single-cell joint profiling of histone modifications and transcriptomes
   Xie, Yang, Zhu, Chenxu, Wang, Zhaoning, Tastemel, Melodi, Chang, Lei, Li, Yang Eric, Ren, Bing · 2023 · Nature Structural & Molecular Biology
9. Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs
   Cates, Kitra, McCoy, Matthew J., Kwon, Ji-Sun, Liu, Yangjian, Abernathy, Daniel G., Zhang, Bo, Liu, Shaopeng, Gontarz, Paul, Kim, Woo Kyung, Chen, Shawei et al. · 2021 · Cell Stem Cell
10. Proteasome subunit PSMC3 variants cause neurosensory syndrome combining deafness and cataract due to proteotoxic stress
    Kröll‐Hermi, Ariane, Ebstein, Frédéric, Stoetzel, Corinne, Geoffroy, Véronique, Schaefer, Elise, Scheidecker, Sophie, Bär, Séverine, Takamiya, Masanari, Kawakami, Koichi, Zieba, Barbara A et al. · 2020 · EMBO Molecular Medicine
11. Recapitulation of Endogenous 4R Tau Expression and Formation of Insoluble Tau in Directly Reprogrammed Human Neurons
    Capano, Lucia S., Sato, Chihiro, Ficulle, Elena, Yu, Anan, Horie, Kanta, Kwon, Ji-Sun, Burbach, Kyle F., Barthélemy, Nicolas R., Fox, Susan G., Karch, Celeste M. et al. · 2022 · Cell Stem Cell
12. Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4
    van den Bulk, Jitske, Verdegaal, Els M. E., Ruano, Dina, Ijsselsteijn, Marieke E., Visser, Marten, van der Breggen, Ruud, Duhen, Thomas, van der Ploeg, Manon, de Vries, Natasja L., Oosting, Jan et al. · 2019 · Genome Medicine
13. The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research
    Reynolds, Sheila M., Miller, Michael, Lee, Phyliss, Leinonen, Kalle, Paquette, Suzanne M., Rodebaugh, Zack, Hahn, Abigail, Gibbs, David L., Slagel, Joseph, Longabaugh, William J. et al. · 2017 · Cancer Research
14. Multi-omics analysis reveals contextual tumor suppressive and oncogenic gene modules within the acute hypoxic response
    Andrysik, Zdenek, Bender, Heather, Galbraith, Matthew D., Espinosa, Joaquin M. · 2021 · Nature Communications
15. Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway
    Di Fruscio, Giuseppina, Schulz, Angela, De Cegli, Rossella, Savarese, Marco, Mutarelli, Margherita, Parenti, Giancarlo, Banfi, Sandro, Braulke, Thomas, Nigro, Vincenzo, Ballabio, Andrea · 2015 · Autophagy
16. The Exosome Component Rrp6 Is Required for RNA Polymerase II Termination at Specific Targets of the Nrd1-Nab3 Pathway
    Fox, Melanie J., Gao, Hongyu, Smith-Kinnaman, Whitney R., Liu, Yunlong, Mosley, Amber L. · 2015 · PLOS Genetics
17. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads
    Nariai, Naoki, Kojima, Kaname, Mimori, Takahiro, Sato, Yukuto, Kawai, Yosuke, Yamaguchi-Kabata, Yumi, Nagasaki, Masao · 2014 · BMC Genomics
18. Allele-specific transcriptional regulation of IRF4 in melanocytes is mediated by chromatin looping of the intronic rs12203592 enhancer to the IRF4 promoter
    Visser, Mijke, Palstra, Robert-Jan, Kayser, Manfred · 2015 · Human Molecular Genetics
19. Vitamin B12 is a limiting factor for induced cellular plasticity and tissue repair
    Kovatcheva, Marta, Melendez, Elena, Chondronasiou, Dafni, Pietrocola, Federico, Bernad, Raquel, Caballe, Adrià, Junza, Alexandra, Capellades, Jordi, Holguín-Horcajo, Adrián, Prats, Neus et al. · 2023 · Nature Metabolism
20. Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice
    Wu, Yuechao, Ren, Qiurong, Zhong, Zhaohui, Liu, Guanqing, Han, Yangshuo, Bao, Yu, Liu, Li, Xiang, Shuyue, Liu, Shuo, Tang, Xu et al. · 2022 · Plant Biotechnology Journal
21. HNF4A and HNF1A exhibit tissue specific target gene regulation in pancreatic beta cells and hepatocytes
    Ng, Natasha Hui Jin, Ghosh, Soumita, Bok, Chek Mei, Ching, Carmen, Low, Blaise Su Jun, Chen, Juin Ting, Lim, Euodia, Miserendino, María Clara, Tan, Yaw Sing, Hoon, Shawn et al. · 2024 · Nature Communications
22. Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation
    MN, Weedon, L, Jackson, JW, Harrison, KS, Ruth, J, Tyrrell, AT, Hattersley, CF, Wright · 2021 · BMJ
23. Genome Comparisons of Candida glabrata Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations
    Carreté, Laia, Ksiezopolska, Ewa, Gómez-Molero, Emilia, Angoulvant, Adela, Bader, Oliver, Fairhead, Cécile, Gabaldón, Toni · 2019 · Frontiers in Microbiology
24. Antifungal Drug Concentration Impacts the Spectrum of Adaptive Mutations in <i>Candida albicans</i>
    Todd, Robert T, Soisangwan, Natthapon, Peters, Sam, Kemp, Bailey, Crooks, Taylor, Gerstein, Aleeza, Selmecki, Anna · 2023 · Molecular Biology and Evolution
25. Regulation of angiopoietin-like protein 4 production during and after exercise
    Norheim, Frode, Hjorth, Marit, Langleite, Torgrim M., Lee, Sindre, Holen, Torgeir, Bindesbøll, Christian, Stadheim, Hans K., Gulseth, Hanne L., Birkeland, Kåre I., Kielland, Anders et al. · 2014 · Physiological Reports
26. Structural Variation and Introgression from Wild Populations in East Asian Cattle Genomes Confer Adaptation to Local Environment
    Xia, Xiaoting, Zhang, Fengwei, Li, Shuang, Luo, Xiaoyu, Peng, Lixin, Dong, Zheng, Pausch, Hubert, Leonard, Alexander S., Crysnanto, Danang, Wang, Shikang et al. · 2023 · Genome biology
27. Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans
    Mozhui, Khyobeni, Pandey, Ashutosh K. · 2017 · Mechanisms of Ageing and Development
28. An Updated Collection of Sequence Barcoded Temperature-Sensitive Alleles of Yeast Essential Genes
    Kofoed, Megan, Milbury, Karissa L, Chiang, Jennifer H, Sinha, Sunita, Ben-Aroya, Shay, Giaever, Guri, Nislow, Corey, Hieter, Philip, Stirling, Peter C · 2015 · G3 Genes|Genomes|Genetics
29. Parasex Generates Phenotypic Diversity <i>de Novo</i> and Impacts Drug Resistance and Virulence in <i>Candida albicans</i>
    Hirakawa, Matthew P, Chyou, Darius E, Huang, Denis, Slan, Aaron R, Bennett, Richard J · 2017 · Genetics
30. Reduced representation bisulfite sequencing (RRBS)
    Nakabayashi, Kazuhiko, Yamamura, Michihiro, Haseagawa, Keita, Hata, Kenichiro · 2023 · Methods in Molecular Biology
31. An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease
    Mäkeläinen, Suvi, Gòdia, Marta, Hellsand, Minas, Viluma, Agnese, Hahn, Daniela, Makdoumi, Karim, Zeiss, Caroline J., Mellersh, Cathryn, Ricketts, Sally L., Narfström, Kristina et al. · 2019 · PLOS Genetics
32. Acquisition of cross-azole tolerance and aneuploidy in <i>Candida albicans</i> strains evolved to posaconazole
    Kukurudz, Rebekah J, Chapel, Madison, Wonitowy, Quinn, Adamu Bukari, Abdul-Rahman, Sidney, Brooke, Sierhuis, Riley, Gerstein, Aleeza C · 2022 · G3
33. A network of paralogous stress response transcription factors in the human pathogen Candida glabrata
    Merhej, Jawad, Thiebaut, Antonin, Blugeon, Corinne, Pouch, Juliette, Ali Chaouche, Mohammed El Amine, Camadro, Jean-Michel, Le Crom, Stéphane, Lelandais, Gaëlle, Devaux, Frédéric · 2016 · Frontiers in Microbiology
34. Response of high-risk MDS to azacitidine and lenalidomide is impacted by baseline and acquired mutations in a cluster of three inositide-specific genes
    Follo, Matilde Y., Pellagatti, Andrea, Armstrong, Richard N., Ratti, Stefano, Mongiorgi, Sara, De Fanti, Sara, Bochicchio, Maria Teresa, Russo, Domenico, Gobbi, Marco, Miglino, Maurizio et al. · 2019 · Leukemia
35. Hybrid genome assembly and annotation of Danionella translucida
    Kadobianskyi, Mykola, Schulze, Lisanne, Schuelke, Markus, Judkewitz, Benjamin · 2019 · Scientific Data
36. DeepTrio: Variant Calling in Families Using Deep Learning
    Brambrink, Lucas, Kolesnikov, Alexey, Goel, Sidharth, Nattestad, Maria, Yun, Taedong, Baid, Gunjan, Yang, Howard, McLean, Cory, Shafin, Kishwar, Chang, Pi-Chuan et al. · 2021
37. Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion
    Bergenholm, David, Liu, Guodong, Holland, Petter, Nielsen, Jens · 2018 · mSystems
38. The vast majority of somatic mutations in plants are layer-specific
    Goel, Manish, Campoy, José A., Krause, Kristin, Baus, Lisa C., Sahu, Anshupa, Sun, Hequan, Walkemeier, Birgit, Marek, Magdalena, Beaudry, Randy, Ruiz, David et al. · 2024 · Genome Biology
39. Nucleotide excision repair removes thymidine analog 5-ethynyl-2′-deoxyuridine from the mammalian genome
    Wang, Li, Cao, Xuemei, Yang, Yanyan, Kose, Cansu, Kawara, Hiroaki, Lindsey-Boltz, Laura A., Selby, Christopher P., Sancar, Aziz · 2022 · Proceedings of the National Academy of Sciences
40. HSATII RNA is induced via a noncanonical ATM-regulated DNA damage response pathway and promotes tumor cell proliferation and movement
    Nogalski, Maciej T., Shenk, Thomas · 2020 · Proceedings of the National Academy of Sciences
41. Assessing the analytical validity of SNP-chips for detecting very rare pathogenic variants: implications for direct-to-consumer genetic testing
    Weedon, Michael N, Jackson, Leigh, Harrison, James W, Ruth, Kate S, Tyrrell, Jessica, Hattersley, Andrew T, Wright, Caroline F · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
42. Histone chip-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity
    Cheung, Kathleen, Barter, Matthew J., Falk, Julia, Proctor, Carole J., Reynard, Louise N., Young, David A. · 2020 · The FASEB Journal
43. Epigenetic changes associated with early life experiences: saliva, a biospecimen for dna methylation signatures
    Bearer, Elaine L., Mulligan, Brianna S. · 2018 · Current Genomics
44. NeuN+ neuronal nuclei in non-human primate prefrontal cortex and subcortical white matter after clozapine exposure
    Halene, Tobias B., Kozlenkov, Alexey, Jiang, Yan, Mitchell, Amanda C., Javidfar, Behnam, Dincer, Aslihan, Park, Royce, Wiseman, Jennifer, Croxson, Paula L., Giannaris, Eustathia Lela et al. · 2016 · Schizophrenia Research
45. Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
    Viner, Coby, Ishak, Charles A., Johnson, James, Walker, Nicolas J., Shi, Hui, Sjöberg-Herrera, Marcela K., Shen, Shu Yi, Lardo, Santana M., Adams, David J., Ferguson-Smith, Anne C. et al. · 2016
46. Discovery of a Novel CIP2A Variant (NOCIVA) with Clinical Relevance in Predicting TKI Resistance in Myeloid Leukemias
    Mäkelä, Eleonora, Pavic, Karolina, Varila, Taru, Salmenniemi, Urpu, Löyttyniemi, Eliisa, Nagelli, Srikar G., Ammunét, Tea, Kähäri, Veli-Matti, Clark, Richard E., Elo, Laura L. et al. · 2021 · Clinical Cancer Research
47. Enrichment of colibactin-associated mutational signatures in unexplained colorectal polyposis patients
    Terlouw, Diantha, Boot, Arnoud, Ducarmon, Quinten R., Nooij, Sam, Suerink, Manon, van Leerdam, Monique E., van Egmond, Demi, Tops, Carli M., Zwittink, Romy D., Ruano, Dina et al. · 2024 · BMC Cancer
48. Evolutionary rescue of phosphomannomutase deficiency in yeast models of human disease
    Vignogna, Ryan C, Allocca, Mariateresa, Monticelli, Maria, Norris, Joy W, Steet, Richard, Perlstein, Ethan O, Andreotti, Giuseppina, Lang, Gregory I · 2022 · eLife
49. Analysis and comparison of the STR genotypes called with HipSTR, STRait Razor and toaSTR by using next generation sequencing data in a Brazilian population sample
    Valle-Silva, Guilherme, Frontanilla, Tamara Soledad, Ayala, Jesús, Donadi, Eduardo Antonio, Simões, Aguinaldo Luiz, Castelli, Erick C., Mendes-Junior, Celso Teixeira · 2022 · Forensic Science International Genetics
50. Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle
    Xia, Xiaoting, Wang, Fuwen, Luo, Xiaoyu, Li, Shuang, Lyu, Yang, Zheng, Yining, Ma, Zhijie, Qu, Kaixing, Song, Rende, Liu, Jianyong et al. · 2025 · Advanced Science
51. Genome Engineering by RNA-Guided Transposition for <i>Anabaena</i> sp. PCC 7120
    Arévalo, Sergio, Pérez Rico, Daniel, Abarca, Dolores, Dijkhuizen, Laura W., Sarasa-Buisan, Cristina, Lindblad, Peter, Flores, Enrique, Nierzwicki-Bauer, Sandra, Schluepmann, Henriette · 2024 · ACS Synthetic Biology
52. The <i>Saccharomyces cerevisiae</i> Cdk8 Mediator Represses <i>AQY1</i> Transcription by Inhibiting Set1p-Dependent Histone Methylation
    Law, Michael J, Finger, Michael A · 2017 · G3 Genes|Genomes|Genetics
53. A structural variant at <i>ASIP</i> associated with the darkness of hair coat is found in multiple zebu cattle populations
    Trigo, Beatriz Batista, Alves, Natália Fonseca, Milanesi, Marco, Garcia, José Fernando, Terefe, Endashaw, Hanotte, Olivier, Tijjani, Abdulfatai, Utsunomiya, Yuri Tani · 2023 · Animal Genetics
54. Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
    Husser, Mathieu C, Pham, Nhat P, Law, Chris, Araujo, Flavia RB, Martin, Vincent JJ, Piekny, Alisa · 2024 · eLife