Fast gapped-read alignment with Bowtie 2

Cited by (908)

Items 601–700 of 908

1. Acinetobacter baumannii Response to Host-Mediated Zinc Limitation Requires the Transcriptional Regulator Zur
   Mortensen, Brittany L., Rathi, Subodh, Chazin, Walter J., Skaar, Eric P. · 2014 · Journal of Bacteriology
2. Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome
   Rubino, Francesco, Carberry, Ciara, Waters, Sinéad M, Kenny, David, McCabe, Matthew S, Creevey, Christopher J · 2017 · The ISME Journal
3. Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome
   Martinez-Ara, Miguel, Comoglio, Federico, van Arensbergen, Joris, van Steensel, Bas · 2022 · Molecular Cell
4. IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation
   Park, Sun-Mi, Cho, Hyunwoo, Thornton, Angela M., Barlowe, Trevor S., Chou, Timothy, Chhangawala, Sagar, Fairchild, Lauren, Taggart, James, Chow, Arthur, Schurer, Alexandria et al. · 2019 · Cell Stem Cell
5. Associations of the intestinal microbiome with the complement system in neovascular age-related macular degeneration
   Zysset-Burri, Denise C., Keller, Irene, Berger, Lieselotte E., Largiadèr, Carlo R., Wittwer, Matthias, Wolf, Sebastian, Zinkernagel, Martin S. · 2020 · npj Genomic Medicine
6. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition
   Deliu, Elena, Arecco, Niccolò, Morandell, Jasmin, Dotter, Christoph P., Contreras, Ximena, Girardot, Charles, Käsper, Eva-Lotta, Kozlova, Alena, Kishi, Kasumi, Chiaradia, Ilaria et al. · 2018 · Nature Neuroscience
7. RNA‐seq Data: Challenges in and Recommendations for Experimental Design and Analysis
   Williams, Alexander G., Thomas, Sean, Wyman, Stacia K., Holloway, Alisha K. · 2014 · Current Protocols in Human Genetics
8. Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load
   Pärnänen, Katariina MM, Hultman, Jenni, Markkanen, Melina, Satokari, Reetta, Rautava, Samuli, Lamendella, Regina, Wright, Justin, McLimans, Christopher J, Kelleher, Shannon L, Virta, Marko P · 2022 · The American Journal of Clinical Nutrition
9. <i>ABCA7</i> frameshift deletion associated with Alzheimer disease in African Americans
   Cukier, Holly N., Kunkle, Brian W., Vardarajan, Badri N., Rolati, Sophie, Hamilton-Nelson, Kara L., Kohli, Martin A., Whitehead, Patrice L., Dombroski, Beth A., Van Booven, Derek, Lang, Rosalyn et al. · 2016 · Neurology Genetics
10. Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
    Vockley, Christopher M., Guo, Cong, Majoros, William H., Nodzenski, Michael, Scholtens, Denise M., Hayes, M. Geoffrey, Lowe, William L., Reddy, Timothy E. · 2015 · Genome Research
11. Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage
    Kim, Mirang, Park, Young-Kyu, Kang, Tae-Wook, Lee, Sang-Hun, Rhee, Yong-Hee, Park, Jong-Lyul, Kim, Hee-Jin, Lee, Daeyoup, Lee, Doheon, Kim, Seon-Young et al. · 2014 · Human Molecular Genetics
12. Transcriptional activation of Jun and Fos members of the AP‐1 complex is a conserved signature of immune aging that contributes to inflammaging
    Karakaslar, Emin Onur, Katiyar, Neerja, Hasham, Muneer, Youn, Ahrim, Sharma, Siddhartha, Chung, Cheng‐han, Marches, Radu, Korstanje, Ron, Banchereau, Jacques, Ucar, Duygu · 2023 · Aging Cell
13. Inverse data-driven modeling and multiomics analysis reveals Phgdh as a metabolic checkpoint of macrophage polarization and proliferation
    Wilson, Jayne Louise, Nägele, Thomas, Linke, Monika, Demel, Florian, Fritsch, Stephanie D., Mayr, Hannah Katharina, Cai, Zhengnan, Katholnig, Karl, Sun, Xiaoliang, Fragner, Lena et al. · 2020 · Cell Reports
14. The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output
    Bulut-Karslioglu, Aydan, Macrae, Trisha A., Oses-Prieto, Juan A., Covarrubias, Sergio, Percharde, Michelle, Ku, Gregory, Diaz, Aaron, McManus, Michael T., Burlingame, Alma L., Ramalho-Santos, Miguel · 2018 · Cell Stem Cell
15. Epitope spreading toward wild-type melanocyte-lineage antigens rescues suboptimal immune checkpoint blockade responses
    Lo, Jennifer A., Kawakubo, Masayoshi, Juneja, Vikram R., Su, Mack Y., Erlich, Tal H., LaFleur, Martin W., Kemeny, Lajos V., Rashid, Mamunur, Malehmir, Mohsen, Rabi, S. Alireza et al. · 2021 · Science Translational Medicine
16. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility
    Meijer, Mandy, Agirre, Eneritz, Kabbe, Mukund, van Tuijn, Cassandra A., Heskol, Abeer, Zheng, Chao, Mendanha Falcão, Ana, Bartosovic, Marek, Kirby, Leslie, Calini, Daniela et al. · 2022 · Neuron
17. Hierarchical and stage-specific regulation of murine cardiomyocyte maturation by serum response factor
    Guo, Yuxuan, Jardin, Blake D., Zhou, Pingzhu, Sethi, Isha, Akerberg, Brynn N., Toepfer, Christopher N, Ai, Yulan, Li, Yifei, Ma, Qing, Guatimosim, Silvia et al. · 2018 · Nature Communications
18. Interaction between STAT3 and GLI1/tGLI1 oncogenic transcription factors promotes the aggressiveness of triple-negative breast cancers and HER2-enriched breast cancer
    Sirkisoon, Sherona R., Carpenter, Richard L., Rimkus, Tadas, Anderson, Ashley, Harrison, Alexandria, Lange, Allison M., Jin, Guangxu, Watabe, Kounosuke, Lo, Hui-Wen · 2018 · Oncogene
19. Genetic and Genomic Architecture of the Evolution of Resistance to Antifungal Drug Combinations
    Hill, Jessica A., Ammar, Ron, Torti, Dax, Nislow, Corey, Cowen, Leah E. · 2013 · PLoS Genetics
20. E2f8 mediates tumor suppression in postnatal liver development
    Kent, Lindsey N., Rakijas, Jessica B., Pandit, Shusil K., Westendorp, Bart, Chen, Hui-Zi, Huntington, Justin T., Tang, Xing, Bae, Sooin, Srivastava, Arunima, Senapati, Shantibhusan et al. · 2016 · Journal of Clinical Investigation
21. Disruption of <i>SUV39H1</i> -Mediated H3K9 Methylation Sustains CAR T-cell Function
    Jain, Nayan, Zhao, Zeguo, Koche, Richard P., Antelope, Chenling, Gozlan, Yosi, Montalbano, Antonino, Brocks, David, Lopez, Michael, Dobrin, Anton, Shi, Yuzhe et al. · 2024 · Cancer Discovery
22. Iron in micronutrient Powder promotes an Unfavorable gut microbiota in Kenyan infants
    Tang, Minghua, Frank, Daniel, Hendricks, Audrey, Ir, Diana, Esamai, Fabian, Liechty, Edward, Hambidge, K., Krebs, Nancy · 2017 · Nutrients
23. Association of a common genetic variant with Parkinson’s disease is mediated by microglia
    Langston, Rebekah G., Beilina, Alexandra, Reed, Xylena, Kaganovich, Alice, Singleton, Andrew B., Blauwendraat, Cornelis, Gibbs, J. Raphael, Cookson, Mark R. · 2022 · Science Translational Medicine
24. Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci
    Liu, Boxiang, Pjanic, Milos, Wang, Ting, Nguyen, Trieu, Gloudemans, Michael, Rao, Abhiram, Castano, Victor G., Nurnberg, Sylvia, Rader, Daniel J., Elwyn, Susannah et al. · 2018 · The American Journal of Human Genetics
25. Exceptional Evolutionary Divergence of Human Muscle and Brain Metabolomes Parallels Human Cognitive and Physical Uniqueness
    Bozek, Katarzyna, Wei, Yuning, Yan, Zheng, Liu, Xiling, Xiong, Jieyi, Sugimoto, Masahiro, Tomita, Masaru, Pääbo, Svante, Pieszek, Raik, Sherwood, Chet C. et al. · 2014 · PLoS Biology
26. Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq
    Deatherage, Daniel E., Traverse, Charles C., Wolf, Lindsey N., Barrick, Jeffrey E. · 2015 · Frontiers in Genetics
27. Histone H3K4me1 and H3K27ac play roles in nucleosome eviction and eRNA transcription, respectively, at enhancers
    Kang, Yujin, Kim, Yea Woon, Kang, Jin, Kim, AeRi · 2021 · The FASEB Journal
28. Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans
    Muñoz, José F., Delorey, Toni, Ford, Christopher B., Li, Bi Yu, Thompson, Dawn A., Rao, Reeta P., Cuomo, Christina A. · 2019 · Nature Communications
29. AtrR Is an Essential Determinant of Azole Resistance in Aspergillus fumigatus
    Paul, Sanjoy, Stamnes, Mark, Thomas, Grace Heredge, Liu, Hong, Hagiwara, Daisuke, Gomi, Katsuya, Filler, Scott G., Moye-Rowley, W. Scott · 2019 · mBio
30. Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans
    Kaasinen, Eevi, Kuismin, Outi, Rajamäki, Kristiina, Ristolainen, Heikki, Aavikko, Mervi, Kondelin, Johanna, Saarinen, Silva, Berta, Davide G., Katainen, Riku, Hirvonen, Elina A. M. et al. · 2019 · Nature Communications
31. Diagnosis of traumatic brain injury using miRNA signatures in nanomagnetically isolated brain-derived extracellular vesicles
    Ko, J., Hemphill, M., Yang, Z., Sewell, E., Na, Y. J., Sandsmark, D. K., Haber, M., Fisher, S. A., Torre, E. A., Svane, K. C. et al. · 2018 · Lab on a Chip
32. Exercise-induced microbiota metabolite enhances CD8 T cell antitumor immunity promoting immunotherapy efficacy
    Phelps, Catherine M., Willis, Nathaniel B., Duan, Tingting, Lee, Amanda H., Zhang, Yue, Rodriguez J, Daphne M., Pandey, Surya P., Laughlin, Colin R., Rosen, Aaron B.I., McPherson, Alex C. et al. · 2025 · Cell
33. Alleviation of reactive oxygen species enhances PUFA accumulation in Schizochytrium sp. through regulating genes involved in lipid metabolism
    Zhang, Sai, He, Yaodong, Sen, Biswarup, Chen, Xiaohong, Xie, Yunxuan, Keasling, Jay D., Wang, Guangyi · 2018 · Metabolic Engineering Communications
34. Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq
    Bottini, Silvia, Hamouda-Tekaya, Nedra, Mategot, Raphael, Zaragosi, Laure-Emmanuelle, Audebert, Stephane, Pisano, Sabrina, Grandjean, Valerie, Mauduit, Claire, Benahmed, Mohamed, Barbry, Pascal et al. · 2017 · Nature Communications
35. Postnatal colonization with human "infant-type" Bifidobacterium species alters behavior of adult gnotobiotic mice
    Luk, Berkley, Veeraragavan, Surabi, Engevik, Melinda, Balderas, Miriam, Major, Angela, Runge, Jessica, Luna, Ruth Ann, Versalovic, James · 2018 · PLOS ONE
36. Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain
    Zhang, Yanxiao, Amaral, Maria Luisa, Zhu, Chenxu, Grieco, Steven Francis, Hou, Xiaomeng, Lin, Lin, Buchanan, Justin, Tong, Liqi, Preissl, Sebastian, Xu, Xiangmin et al. · 2022 · Cell Research
37. Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere
    Zadjelovic, Vinko, Wright, Robyn J., Borsetto, Chiara, Quartey, Jeannelle, Cairns, Tyler N., Langille, Morgan G. I., Wellington, Elizabeth M. H., Christie-Oleza, Joseph A. · 2023 · Microbiome
38. Analysis of antifungal resistance genes in Candida albicans and Candida glabrata using next generation sequencing
    Spettel, Kathrin, Barousch, Wolfgang, Makristathis, Athanasios, Zeller, Iris, Nehr, Marion, Selitsch, Brigitte, Lackner, Michaela, Rath, Peter-Michael, Steinmann, Joerg, Willinger, Birgit · 2019 · PLoS ONE
39. Pathogenic Potential of Hic1-Expressing Cardiac Stromal Progenitors
    Soliman, Hesham, Paylor, Ben, Scott, R. Wilder, Lemos, Dario R., Chang, ChihKai, Arostegui, Martin, Low, Marcela, Lee, Christina, Fiore, Daniela, Braghetta, Paola et al. · 2020 · Cell Stem Cell
40. Haplotype-aware pantranscriptome analyses using spliced pangenome graphs
    Sibbesen, Jonas A., Eizenga, Jordan M., Novak, Adam M., Sirén, Jouni, Chang, Xian, Garrison, Erik, Paten, Benedict · 2023 · Nature Methods
41. A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice
    Abdel-Haq, Reem, Schlachetzki, Johannes CM, Boktor, Joseph C, Cantu-Jungles, Thaisa M, Thron, Taren, Zhang, Mengying, Bostick, John W, Khazaei, Tahmineh, Chilakala, Sujatha, Morais, Livia H et al. · 2022 · eLife
42. Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae
    Djukovic, Ana, Garzón, María José, Canlet, Cécile, Cabral, Vitor, Lalaoui, Rym, García-Garcerá, Marc, Rechenberger, Julia, Tremblay-Franco, Marie, Peñaranda, Iván, Puchades-Carrasco, Leonor et al. · 2022 · Nature Communications
43. Mechanism of Virus Attenuation by Codon Pair Deoptimization
    Groenke, Nicole, Trimpert, Jakob, Merz, Sophie, Conradie, Andelé M., Wyler, Emanuel, Zhang, Hongwei, Hazapis, Orsalia-Georgia, Rausch, Sebastian, Landthaler, Markus, Osterrieder, Nikolaus et al. · 2020 · Cell Reports
44. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation
    Bravo González-Blas, Carmen, Matetovici, Irina, Hillen, Hanne, Taskiran, Ibrahim Ihsan, Vandepoel, Roel, Christiaens, Valerie, Sansores-García, Leticia, Verboven, Elisabeth, Hulselmans, Gert, Poovathingal, Suresh et al. · 2024 · Nature Cell Biology
45. Bacterially produced metabolites protect C. elegans neurons from degeneration
    Urrutia, Arles, García-Angulo, Víctor A., Fuentes, Andrés, Caneo, Mauricio, Legüe, Marcela, Urquiza, Sebastián, Delgado, Scarlett E., Ugalde, Juan, Burdisso, Paula, Calixto, Andrea · 2020 · PLOS Biology
46. Genome-Wide Signatures of Adaptation to Extreme Environments in Red Algae
    Cho, Chung Hyun, Park, Seung In, Huang, Tzu-Yen, Lee, Yongsung, Ciniglia, Claudia, Yadavalli, Hari Chandana, Yang, Seong Wook, Bhattacharya, Debashish, Yoon, Hwan Su · 2023 · Nature Communications
47. Multi-metal restriction by calprotectin impacts de novo flavin biosynthesis in Acinetobacter baumannii
    Wang, Jiefei, Lonergan, Zachery R., Gonzalez-Gutierrez, Giovanni, Nairn, Brittany L., Maxwell, Christina N., Zhang, Yixiang, Andreini, Claudia, Karty, Jonathan A., Chazin, Walter J., Trinidad, Jonathan C. et al. · 2019 · Cell chemical biology
48. Generation of human adult hepatocyte organoids with metabolic functions
    Igarashi, Ryo, Oda, Mayumi, Okada, Ryo, Yano, Tomoki, Takahashi, Sirirat, Pastuhov, Strahil, Matano, Mami, Masuda, Norio, Togasaki, Kazuhiro, Ohta, Yuki et al. · 2025 · Nature
49. Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance
    Calabrese, Francesco Maria, Ameur, Hana, Nikoloudaki, Olga, Celano, Giuseppe, Vacca, Mirco, Junior, Wilson JFLemos, Manzari, Caterina, Vertè, Fabienne, Di Cagno, Raffaella, Pesole, Graziano et al. · 2022 · Microbiome
50. The Evf2 ultraconserved enhancer lncRNA functionally and spatially organizes megabase distant genes in the developing forebrain
    Cajigas, Ivelisse, Chakraborty, Abhijit, Swyter, Kelsey R., Luo, Hao, Bastidas, Monique, Nigro, Maximilliano, Morris, Elizabeth R., Chen, Sean, VanGompel, Michael J.W., Leib, David et al. · 2018 · Molecular Cell
51. Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression
    Blankvoort, Stefan, Witter, Menno P., Noonan, James, Cotney, Justin, Kentros, Cliff · 2018 · Current Biology
52. Activation of endogenous retroviruses during brain development causes an inflammatory response
    Jönsson, Marie E, Garza, Raquel, Sharma, Yogita, Petri, Rebecca, Södersten, Erik, Johansson, Jenny G, Johansson, Pia A, Atacho, Diahann AM, Pircs, Karolina, Madsen, Sofia et al. · 2021 · The EMBO Journal
53. Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency
    Mor, Nofar, Rais, Yoach, Sheban, Daoud, Peles, Shani, Aguilera-Castrejon, Alejandro, Zviran, Asaf, Elinger, Dalia, Viukov, Sergey, Geula, Shay, Krupalnik, Vladislav et al. · 2018 · Cell Stem Cell
54. Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration
    Chen, Tianyi, Oh, Sehhoon, Gregory, Simon, Shen, Xiling, Diehl, Anna Mae · 2020 · JCI Insight
55. Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis
    Shcherbina, Anna, Larouche, Jacqueline, Fraczek, Paula, Yang, Benjamin A., Brown, Lemuel A., Markworth, James F., Chung, Carolina H., Khaliq, Mehwish, de Silva, Kanishka, Choi, Jeongmoon J. et al. · 2020 · Cell Reports
56. Computational design of epitope-specific functional antibodies
    Nimrod, Guy, Fischman, Sharon, Austin, Mark, Herman, Asael, Keyes, Feenagh, Leiderman, Olga, Hargreaves, David, Strajbl, Marek, Breed, Jason, Klompus, Shelley et al. · 2018 · Cell Reports
57. Comparison of whole genome amplification techniques for human single cell exome sequencing
    Borgström, Erik, Paterlini, Marta, Mold, Jeff E., Frisen, Jonas, Lundeberg, Joakim · 2017 · PLOS ONE
58. Enhancer and transcription factor dynamics during myeloid differentiation reveal an early differentiation block in Cebpa null progenitors
    Pundhir, Sachin, Bratt Lauridsen, Felicia Kathrine, Schuster, Mikkel Bruhn, Jakobsen, Janus Schou, Ge, Ying, Schoof, Erwin Marten, Rapin, Nicolas, Waage, Johannes, Hasemann, Marie Sigurd, Porse, Bo Torben · 2018 · Cell Reports
59. An evolutionary trade-off between host immunity and metabolism drives fatty liver in male mice
    Nikkanen, Joni, Leong, Yew Ann, Krause, William C., Dermadi, Denis, Maschek, J. Alan, Van Ry, Tyler, Cox, James E., Weiss, Ethan J., Gokcumen, Omer, Chawla, Ajay et al. · 2022 · Science
60. TGFβ-induced fibroblast activation requires persistent and targeted HDAC-mediated gene repression
    Jones, Dakota L., Haak, Andrew J., Caporarello, Nunzia, Choi, Kyoung M., Ye, Zhenqing, Yan, Huihuang, Varelas, Xaralabos, Ordog, Tamas, Ligresti, Giovanni, Tschumperlin, Daniel J. · 2019 · Journal of Cell Science
61. Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
    Luo, Chongyuan, Lee, Qian Yi, Wapinski, Orly, Castanon, Rosa, Nery, Joseph R, Mall, Moritz, Kareta, Michael S, Cullen, Sean M, Goodell, Margaret A, Chang, Howard Y et al. · 2019 · eLife
62. Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence
    Olan, Ioana, Parry, Aled J., Schoenfelder, Stefan, Narita, Masako, Ito, Yoko, Chan, Adelyne S. L., Slater, Guy St.C., Bihary, Dóra, Bando, Masashige, Shirahige, Katsuhiko et al. · 2020 · Nature Communications
63. Transcription elongation rate affects nascent histone pre-mRNA folding and 3′ end processing
    Saldi, Tassa, Fong, Nova, Bentley, David L. · 2018 · Genes &amp; Development
64. Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation
    Fitz, Johanna, Neumann, Tobias, Pavri, Rushad · 2018 · The EMBO Journal
65. Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice
    Kundu, Payel, Torres, Eileen Ruth S., Stagaman, Keaton, Kasschau, Kristin, Okhovat, Mariam, Holden, Sarah, Ward, Samantha, Nevonen, Kimberly A., Davis, Brett A., Saito, Takashi et al. · 2021 · Scientific Reports
66. Next-generation data filtering in the genomics era
    Hemstrom, William, Grummer, Jared A., Luikart, Gordon, Christie, Mark R. · 2024 · Nature Reviews Genetics
67. Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
    Pękowska, Aleksandra, Klaus, Bernd, Xiang, Wanqing, Severino, Jacqueline, Daigle, Nathalie, Klein, Felix A., Oleś, Małgorzata, Casellas, Rafael, Ellenberg, Jan, Steinmetz, Lars M. et al. · 2018 · Cell Systems
68. Sex Differences in the Effects of Prenatal Bisphenol A Exposure on Genes Associated with Autism Spectrum Disorder in the Hippocampus
    Thongkorn, Surangrat, Kanlayaprasit, Songphon, Jindatip, Depicha, Tencomnao, Tewin, Hu, Valerie W., Sarachana, Tewarit · 2019 · Scientific Reports
69. The cis-regulatory effects of modern human-specific variants
    Weiss, Carly V, Harshman, Lana, Inoue, Fumitaka, Fraser, Hunter B, Petrov, Dmitri A, Ahituv, Nadav, Gokhman, David · 2021 · eLife
70. Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization.
    Peddu, Vikas, Shean, Ryan C, Xie, Hong, Shrestha, Lasata, Perchetti, Garrett A, Minot, Samuel S, Roychoudhury, Pavitra, Huang, Meei-Li, Nalla, Arun, Reddy, Shriya B et al. · 2020 · Clinical Chemistry
71. Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs
    Janssens, Derek H., Wu, Steven J., Sarthy, Jay F., Meers, Michael P., Myers, Carrie H., Olson, James M., Ahmad, Kami, Henikoff, Steven · 2018 · Epigenetics &amp; Chromatin
72. Cabazitaxel versus abiraterone or enzalutamide in poor prognosis metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase II trial
    Annala, M., Fu, S., Bacon, J.V.W., Sipola, J., Iqbal, N., Ferrario, C., Ong, M., Wadhwa, D., Hotte, S.J., Lo, G. et al. · 2021 · Annals of Oncology
73. Histone chaperone HIRA deposits histone H3.3 onto foreign viral DNA and contributes to anti-viral intrinsic immunity
    Rai, Taranjit Singh, Glass, Mandy, Cole, John J., Rather, Mohammad I., Marsden, Morgan, Neilson, Matthew, Brock, Claire, Humphreys, Ian R., Everett, Roger D., Adams, Peter D. · 2017 · Nucleic Acids Research
74. Deletion of aryl hydrocarbon receptor AHR in mice leads to subretinal accumulation of microglia and RPE atrophy.
    Kim, Soo-Young, Yang, Hyun-Jin, Chang, Yi-Sheng, Kim, Jung-Woong, Brooks, Matthew, Chew, Emily Y., Wong, Wai T., Fariss, Robert N., Rachel, Rivka A., Cogliati, Tiziana et al. · 2014 · Investigative Opthalmology &amp; Visual Science
75. Broad antifungal resistance mediated by RNAi-dependent epimutation in the basal human fungal pathogen Mucor circinelloides
    Chang, Zanetta, Billmyre, R. Blake, Lee, Soo Chan, Heitman, Joseph · 2019 · PLOS Genetics
76. Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females
    Huang, Yu-Feng, Chen, Yen-Ju, Fan, Tan-Chi, Chang, Nai-Chuan, Chen, Yi-Jie, Midha, Mohit K., Chen, Tzu-Han, Yang, Hsiao-Hsiang, Wang, Yu-Tai, Yu, Alice L. et al. · 2018 · BMC Medical Genomics
77. New genomic data and analyses challenge the traditional vision of animal epithelium evolution
    Belahbib, Hassiba, Renard, Emmanuelle, Santini, Sébastien, Jourda, Cyril, Claverie, Jean-Michel, Borchiellini, Carole, Le Bivic, André · 2018 · BMC Genomics
78. A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome
    Zhang, Dengwei, Zhang, Jian, Kalimuthu, Shanthini, Liu, Jing, Song, Zhi-Man, He, Bei-bei, Cai, Peiyan, Zhong, Zheng, Feng, Chenchen, Neelakantan, Prasanna et al. · 2023 · Microbiome
79. Actin is an evolutionarily-conserved damage-associated molecular pattern that signals tissue injury in Drosophila melanogaster
    Srinivasan, Naren, Gordon, Oliver, Ahrens, Susan, Franz, Anna, Deddouche, Safia, Chakravarty, Probir, Phillips, David, Yunus, Ali A, Rosen, Michael K, Valente, Rita S et al. · 2016 · eLife
80. Intersecting transcription networks constrain gene regulatory evolution
    Sorrells, Trevor R., Booth, Lauren N., Tuch, Brian B., Johnson, Alexander D. · 2015 · Nature
81. Iron Regulation in Clostridioides difficile
    Berges, Mareike, Michel, Annika-Marisa, Lassek, Christian, Nuss, Aaron M., Beckstette, Michael, Dersch, Petra, Riedel, Katharina, Sievers, Susanne, Becher, Dörte, Otto, Andreas et al. · 2018 · Frontiers in Microbiology
82. Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in <i>Drosophila melanogaster</i>
    Liu, Xiaochuan, Freitas, Jaime, Zheng, Dinghai, Oliveira, Marta S., Hoque, Mainul, Martins, Torcato, Henriques, Telmo, Tian, Bin, Moreira, Alexandra · 2017 · RNA
83. The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease
    Bendl, Jaroslav, Hauberg, Mads E., Girdhar, Kiran, Im, Eunju, Vicari, James M., Rahman, Samir, Fernando, Michael B., Townsley, Kayla G., Dong, Pengfei, Misir, Ruth et al. · 2022 · Nature Neuroscience
84. DOT1L modulates the senescence-associated secretory phenotype through epigenetic regulation of IL1A
    Leon, Kelly E., Buj, Raquel, Lesko, Elizabeth, Dahl, Erika S., Chen, Chi-Wei, Tangudu, Naveen Kumar, Imamura-Kawasawa, Yuka, Kossenkov, Andrew V., Hobbs, Ryan P., Aird, Katherine M. · 2021 · Journal of Cell Biology
85. HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy
    Jiang, Qinqin, Braun, David A., Clauser, Karl R., Ramesh, Vijyendra, Shirole, Nitin H., Duke-Cohan, Joseph E., Nabilsi, Nancy, Kramer, Nicholas J., Forman, Cleo, Lippincott, Isabelle E. et al. · 2025 · Cell
86. 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
87. Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers
    Byrd, Allyson L., Liu, Menghan, Fujimura, Kei E., Lyalina, Svetlana, Nagarkar, Deepti R., Charbit, Bruno, Bergstedt, Jacob, Patin, Etienne, Harrison, Oliver J., Quintana-Murci, Lluís et al. · 2021 · Journal of Experimental Medicine
88. Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge)
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89. A Functional riboSNitch in the 3′ Untranslated Region of<i>FKBP5</i>Alters MicroRNA-320a Binding Efficiency and Mediates Vulnerability to Chronic Post-Traumatic Pain
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