Fast gapped-read alignment with Bowtie 2

Cited by (909)

Items 201–300 of 909

1. Synaptic dysregulation in a human iPS cell model of mental disorders
   Wen, Zhexing, Nguyen, Ha Nam, Guo, Ziyuan, Lalli, Matthew A., Wang, Xinyuan, Su, Yijing, Kim, Nam-Shik, Yoon, Ki-Jun, Shin, Jaehoon, Zhang, Ce et al. · 2014 · Nature
2. Widespread and Functional RNA Circularization in Localized Prostate Cancer
   Chen, Sujun, Huang, Vincent, Xu, Xin, Livingstone, Julie, Soares, Fraser, Jeon, Jouhyun, Zeng, Yong, Hua, Junjie Tony, Petricca, Jessica, Guo, Haiyang et al. · 2019 · Cell
3. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
   Jacobs, Frank M. J., Greenberg, David, Nguyen, Ngan, Haeussler, Maximilian, Ewing, Adam D., Katzman, Sol, Paten, Benedict, Salama, Sofie R., Haussler, David · 2014 · Nature
4. m6A facilitates hippocampus-dependent learning and memory through YTHDF1
   Shi, Hailing, Zhang, Xuliang, Weng, Yi-Lan, Lu, Zongyang, Liu, Yajing, Lu, Zhike, Li, Jianan, Hao, Piliang, Zhang, Yu, Zhang, Feng et al. · 2018 · Nature
5. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
   Olm, Matthew R., Crits-Christoph, Alexander, Bouma-Gregson, Keith, Firek, Brian A., Morowitz, Michael J., Banfield, Jillian F. · 2021 · Nature Biotechnology
6. Proteogenomic Characterization of Endometrial Carcinoma
   Dou, Yongchao, Kawaler, Emily A., Cui Zhou, Daniel, Gritsenko, Marina A., Huang, Chen, Blumenberg, Lili, Karpova, Alla, Petyuk, Vladislav A., Savage, Sara R., Satpathy, Shankha et al. · 2020 · Cell
7. Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
   Castelle, Cindy J., Wrighton, Kelly C., Thomas, Brian C., Hug, Laura A., Brown, Christopher T., Wilkins, Michael J., Frischkorn, Kyle R., Tringe, Susannah G., Singh, Andrea, Markillie, Lye Meng et al. · 2015 · Current Biology
8. <i>SMN2</i> splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy
   Naryshkin, Nikolai A., Weetall, Marla, Dakka, Amal, Narasimhan, Jana, Zhao, Xin, Feng, Zhihua, Ling, Karen K. Y., Karp, Gary M., Qi, Hongyan, Woll, Matthew G. et al. · 2014 · Science
9. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions
   Narunsky-Haziza, Lian, Sepich-Poore, Gregory D., Livyatan, Ilana, Asraf, Omer, Martino, Cameron, Nejman, Deborah, Gavert, Nancy, Stajich, Jason E., Amit, Guy, González, Antonio et al. · 2022 · Cell
10. The outer mucus layer hosts a distinct intestinal microbial niche
    Li, Hai, Limenitakis, Julien P., Fuhrer, Tobias, Geuking, Markus B., Lawson, Melissa A., Wyss, Madeleine, Brugiroux, Sandrine, Keller, Irene, Macpherson, Jamie A., Rupp, Sandra et al. · 2015 · Nature Communications
11. Gut vascular barrier impairment leads to intestinal bacteria dissemination and colorectal cancer metastasis to liver
    Bertocchi, Alice, Carloni, Sara, Ravenda, Paola Simona, Bertalot, Giovanni, Spadoni, Ilaria, Lo Cascio, Antonino, Gandini, Sara, Lizier, Michela, Braga, Daniele, Asnicar, Francesco et al. · 2021 · Cancer Cell
12. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations
    Tett, Adrian, Huang, Kun D., Asnicar, Francesco, Fehlner-Peach, Hannah, Pasolli, Edoardo, Karcher, Nicolai, Armanini, Federica, Manghi, Paolo, Bonham, Kevin, Zolfo, Moreno et al. · 2019 · Cell Host &amp; Microbe
13. Metabolic modeling of single Th17 cells reveals regulators of autoimmunity
    Wagner, Allon, Wang, Chao, Fessler, Johannes, DeTomaso, David, Avila-Pacheco, Julian, Kaminski, James, Zaghouani, Sarah, Christian, Elena, Thakore, Pratiksha, Schellhaass, Brandon et al. · 2021 · Cell
14. Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
    Whalen, Sean, Truty, Rebecca M, Pollard, Katherine S · 2016 · Nature Genetics
15. The structural basis for cohesin–CTCF-anchored loops
    Li, Yan, Haarhuis, Judith H. I., Sedeño Cacciatore, Ángela, Oldenkamp, Roel, van Ruiten, Marjon S., Willems, Laureen, Teunissen, Hans, Muir, Kyle W., de Wit, Elzo, Rowland, Benjamin D. et al. · 2020 · Nature
16. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
    Nédélec, Yohann, Sanz, Joaquín, Baharian, Golshid, Szpiech, Zachary A., Pacis, Alain, Dumaine, Anne, Grenier, Jean-Christophe, Freiman, Andrew, Sams, Aaron J., Hebert, Steven et al. · 2016 · Cell
17. Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth
    Zhu, Jiajun, Sammons, Morgan A., Donahue, Greg, Dou, Zhixun, Vedadi, Masoud, Getlik, Matthäus, Barsyte-Lovejoy, Dalia, Al-awar, Rima, Katona, Bryson W., Shilatifard, Ali et al. · 2015 · Nature
18. Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity
    Paul, Anirban, Crow, Megan, Raudales, Ricardo, He, Miao, Gillis, Jesse, Huang, Z. Josh · 2017 · Cell
19. Profiling the human intestinal environment under physiological conditions
    Shalon, Dari, Culver, Rebecca Neal, Grembi, Jessica A., Folz, Jacob, Treit, Peter V., Shi, Handuo, Rosenberger, Florian A., Dethlefsen, Les, Meng, Xiandong, Yaffe, Eitan et al. · 2023 · Nature
20. Mapping the genomic landscape of CRISPR-Cas9 cleavage
    Cameron, Peter, Fuller, Chris K, Donohoue, Paul D, Jones, Brittnee N, Thompson, Matthew S, Carter, Matthew M, Gradia, Scott, Vidal, Bastien, Garner, Elizabeth, Slorach, Euan M et al. · 2017 · Nature Methods
21. CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome
    Klann, Tyler S, Black, Joshua B, Chellappan, Malathi, Safi, Alexias, Song, Lingyun, Hilton, Isaac B, Crawford, Gregory E, Reddy, Timothy E, Gersbach, Charles A · 2017 · Nature Biotechnology
22. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance
    Cirelli, Kimberly M., Carnathan, Diane G., Nogal, Bartek, Martin, Jacob T., Rodriguez, Oscar L., Upadhyay, Amit A., Enemuo, Chiamaka A., Gebru, Etse H., Choe, Yury, Viviano, Federico et al. · 2019 · Cell
23. The person-to-person transmission landscape of the gut and oral microbiomes
    Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D., Manara, Serena et al. · 2023 · Nature
24. Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma
    Hashizume, Rintaro, Andor, Noemi, Ihara, Yuichiro, Lerner, Robin, Gan, Haiyun, Chen, Xiaoyue, Fang, Dong, Huang, Xi, Tom, Maxwell W, Ngo, Vy et al. · 2014 · Nature Medicine
25. Evaluating the Information Content of Shallow Shotgun Metagenomics
    Hillmann, Benjamin, Al-Ghalith, Gabriel A., Shields-Cutler, Robin R., Zhu, Qiyun, Gohl, Daryl M., Beckman, Kenneth B., Knight, Rob, Knights, Dan · 2018 · mSystems
26. Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1
    McCulloch, John A., Davar, Diwakar, Rodrigues, Richard R., Badger, Jonathan H., Fang, Jennifer R., Cole, Alicia M., Balaji, Ascharya K., Vetizou, Marie, Prescott, Stephanie M., Fernandes, Miriam R. et al. · 2022 · Nature Medicine
27. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma
    Lee, Karla A., Thomas, Andrew Maltez, Bolte, Laura A., Björk, Johannes R., de Ruijter, Laura Kist, Armanini, Federica, Asnicar, Francesco, Blanco-Miguez, Aitor, Board, Ruth, Calbet-Llopart, Neus et al. · 2022 · Nature Medicine
28. Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract
    Kommineni, Sushma, Bretl, Daniel J., Lam, Vy, Chakraborty, Rajrupa, Hayward, Michael, Simpson, Pippa, Cao, Yumei, Bousounis, Pavlos, Kristich, Christopher J., Salzman, Nita H. · 2015 · Nature
29. Premature Termination of Reprogramming In Vivo Leads to Cancer Development through Altered Epigenetic Regulation
    Ohnishi, Kotaro, Semi, Katsunori, Yamamoto, Takuya, Shimizu, Masahito, Tanaka, Akito, Mitsunaga, Kanae, Okita, Keisuke, Osafune, Kenji, Arioka, Yuko, Maeda, Toshiyuki et al. · 2014 · Cell
30. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
    Nayfach, Stephen, Rodriguez-Mueller, Beltran, Garud, Nandita, Pollard, Katherine S. · 2016 · Genome Research
31. Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species
    Muñoz, José F., Gade, Lalitha, Chow, Nancy A., Loparev, Vladimir N., Juieng, Phalasy, Berkow, Elizabeth L., Farrer, Rhys A., Litvintseva, Anastasia P., Cuomo, Christina A. · 2018 · Nature Communications
32. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
    Naccache, Samia N., Federman, Scot, Veeraraghavan, Narayanan, Zaharia, Matei, Lee, Deanna, Samayoa, Erik, Bouquet, Jerome, Greninger, Alexander L., Luk, Ka-Cheung, Enge, Barryett et al. · 2014 · Genome Research
33. Dynamic profiling of the protein life cycle in response to pathogens
    Jovanovic, Marko, Rooney, Michael S., Mertins, Philipp, Przybylski, Dariusz, Chevrier, Nicolas, Satija, Rahul, Rodriguez, Edwin H., Fields, Alexander P., Schwartz, Schraga, Raychowdhury, Raktima et al. · 2015 · Science
34. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
    Achim, Kaia, Pettit, Jean-Baptiste, Saraiva, Luis R, Gavriouchkina, Daria, Larsson, Tomas, Arendt, Detlev, Marioni, John C · 2015 · Nature Biotechnology
35. Transcription Elongation Can Affect Genome 3D Structure
    Heinz, Sven, Texari, Lorane, Hayes, Michael G.B., Urbanowski, Matthew, Chang, Max W., Givarkes, Ninvita, Rialdi, Alexander, White, Kris M., Albrecht, Randy A., Pache, Lars et al. · 2018 · Cell
36. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq
    Wienert, Beeke, Wyman, Stacia K., Richardson, Christopher D., Yeh, Charles D., Akcakaya, Pinar, Porritt, Michelle J., Morlock, Michaela, Vu, Jonathan T., Kazane, Katelynn R., Watry, Hannah L. et al. · 2019 · Science
37. Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis
    Seidman, Jason S., Troutman, Ty D., Sakai, Mashito, Gola, Anita, Spann, Nathanael J., Bennett, Hunter, Bruni, Cassi M., Ouyang, Zhengyu, Li, Rick Z., Sun, Xiaoli et al. · 2020 · Immunity
38. Combinatorial labeling of single cells for gene expression cytometry
    Fan, H. Christina, Fu, Glenn K., Fodor, Stephen P. A. · 2015 · Science
39. Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life
    Yassour, Moran, Jason, Eeva, Hogstrom, Larson J., Arthur, Timothy D., Tripathi, Surya, Siljander, Heli, Selvenius, Jenni, Oikarinen, Sami, Hyöty, Heikki, Virtanen, Suvi M. et al. · 2018 · Cell Host &amp; Microbe
40. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche
    Zepeda-Rivera, Martha, Minot, Samuel S., Bouzek, Heather, Wu, Hanrui, Blanco-Míguez, Aitor, Manghi, Paolo, Jones, Dakota S., LaCourse, Kaitlyn D., Wu, Ying, McMahon, Elsa F. et al. · 2024 · Nature
41. Human cardiac organoids for the modelling of myocardial infarction and drug cardiotoxicity
    Richards, Dylan J., Li, Yang, Kerr, Charles M., Yao, Jenny, Beeson, Gyda C., Coyle, Robert C., Chen, Xun, Jia, Jia, Damon, Brooke, Wilson, Robert et al. · 2020 · Nature Biomedical Engineering
42. Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling
    Asnicar, Francesco, Manara, Serena, Zolfo, Moreno, Truong, Duy Tin, Scholz, Matthias, Armanini, Federica, Ferretti, Pamela, Gorfer, Valentina, Pedrotti, Anna, Tett, Adrian et al. · 2017 · mSystems
43. Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders
    Johmura, Yoshikazu, Yamanaka, Takehiro, Omori, Satotaka, Wang, Teh-Wei, Sugiura, Yuki, Matsumoto, Masaki, Suzuki, Narumi, Kumamoto, Soichiro, Yamaguchi, Kiyoshi, Hatakeyama, Seira et al. · 2021 · Science
44. Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate
    Chakraborty, Abhishek A., Laukka, Tuomas, Myllykoski, Matti, Ringel, Alison E., Booker, Matthew A., Tolstorukov, Michael Y., Meng, Yuzhong Jeff, Meier, Samuel R., Jennings, Rebecca B., Creech, Amanda L. et al. · 2019 · Science
45. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
    Tubio, Jose M. C., Li, Yilong, Ju, Young Seok, Martincorena, Inigo, Cooke, Susanna L., Tojo, Marta, Gundem, Gunes, Pipinikas, Christodoulos P., Zamora, Jorge, Raine, Keiran et al. · 2014 · Science
46. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
    Schep, Alicia N., Buenrostro, Jason D., Denny, Sarah K., Schwartz, Katja, Sherlock, Gavin, Greenleaf, William J. · 2015 · Genome Research
47. Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity
    Sakai, Mashito, Troutman, Ty D., Seidman, Jason S., Ouyang, Zhengyu, Spann, Nathanael J., Abe, Yohei, Ego, Kaori M., Bruni, Cassi M., Deng, Zihou, Schlachetzki, Johannes C.M. et al. · 2019 · Immunity
48. The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity
    Simsek, Deniz, Tiu, Gerald C., Flynn, Ryan A., Byeon, Gun W., Leppek, Kathrin, Xu, Adele F., Chang, Howard Y., Barna, Maria · 2017 · Cell
49. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
    Chen, Lei, Qiu, Qiang, Jiang, Yu, Wang, Kun, Lin, Zeshan, Li, Zhipeng, Bibi, Faysal, Yang, Yongzhi, Wang, Jinhuan, Nie, Wenhui et al. · 2019 · Science
50. Adaptive Evolution within Gut Microbiomes of Healthy People
    Zhao, Shijie, Lieberman, Tami D., Poyet, Mathilde, Kauffman, Kathryn M., Gibbons, Sean M., Groussin, Mathieu, Xavier, Ramnik J., Alm, Eric J. · 2019 · Cell Host &amp; Microbe
51. SMN2 splice modulators enhance U1–pre-mRNA association and rescue SMA mice
    Palacino, James, Swalley, Susanne E, Song, Cheng, Cheung, Atwood K, Shu, Lei, Zhang, Xiaolu, Van Hoosear, Mailin, Shin, Youngah, Chin, Donovan N, Keller, Caroline Gubser et al. · 2015 · Nature Chemical Biology
52. Accurate and complete genomes from metagenomes
    Chen, Lin-Xing, Anantharaman, Karthik, Shaiber, Alon, Eren, A. Murat, Banfield, Jillian F. · 2020 · Genome Research
53. Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration
    Moiseeva, Victoria, Cisneros, Andrés, Sica, Valentina, Deryagin, Oleg, Lai, Yiwei, Jung, Sascha, Andrés, Eva, An, Juan, Segalés, Jessica, Ortet, Laura et al. · 2023 · Nature
54. Gut microbiome function predicts response to anti-integrin biologic therapy in Inflammatory Bowel diseases
    Ananthakrishnan, Ashwin N., Luo, Chengwei, Yajnik, Vijay, Khalili, Hamed, Garber, John J., Stevens, Betsy W., Cleland, Thomas, Xavier, Ramnik J. · 2017 · Cell Host &amp; Microbe
55. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases
    Altae-Tran, Han, Kannan, Soumya, Demircioglu, F. Esra, Oshiro, Rachel, Nety, Suchita P., McKay, Luke J., Dlakić, Mensur, Inskeep, William P., Makarova, Kira S., Macrae, Rhiannon K. et al. · 2021 · Science
56. The cis-regulatory dynamics of embryonic development at single-cell resolution
    Cusanovich, Darren A., Reddington, James P., Garfield, David A., Daza, Riza M., Aghamirzaie, Delasa, Marco-Ferreres, Raquel, Pliner, Hannah A., Christiansen, Lena, Qiu, Xiaojie, Steemers, Frank J. et al. · 2018 · Nature
57. Structure and function of the healthy pre-adolescent pediatric gut microbiome
    Hollister, Emily B., Riehle, Kevin, Luna, Ruth Ann, Weidler, Erica M., Rubio-Gonzales, Michelle, Mistretta, Toni-Ann, Raza, Sabeen, Doddapaneni, Harsha V., Metcalf, Ginger A., Muzny, Donna M. et al. · 2015 · Microbiome
58. Ancient DNA analysis
    Orlando, Ludovic, Allaby, Robin, Skoglund, Pontus, Der Sarkissian, Clio, Stockhammer, Philipp W., Ávila-Arcos, María C., Fu, Qiaomei, Krause, Johannes, Willerslev, Eske, Stone, Anne C. et al. · 2021 · Nature Reviews Methods Primers
59. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults
    Langelier, Charles, Kalantar, Katrina L., Moazed, Farzad, Wilson, Michael R., Crawford, Emily D., Deiss, Thomas, Belzer, Annika, Bolourchi, Samaneh, Caldera, Saharai, Fung, Monica et al. · 2018 · Proceedings of the National Academy of Sciences
60. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements
    Hoyt, Savannah J., Storer, Jessica M., Hartley, Gabrielle A., Grady, Patrick G. S., Gershman, Ariel, de Lima, Leonardo G., Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias et al. · 2022 · Science
61. Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare
    Chng, Kern Rei, Tay, Angeline Su Ling, Li, Chenhao, Ng, Amanda Hui Qi, Wang, Jingjing, Suri, Bani Kaur, Matta, Sri Anusha, McGovern, Naomi, Janela, Baptiste, Wong, Xuan Fei Colin C. et al. · 2016 · Nature Microbiology
62. Alzheimer’s disease microbiome is associated with dysregulation of the anti-inflammatory p-glycoprotein pathway
    Haran, John P., Bhattarai, Shakti K., Foley, Sage E., Dutta, Protiva, Ward, Doyle V., Bucci, Vanni, McCormick, Beth A. · 2019 · mBio
63. Genome graphs and the evolution of genome inference
    Paten, Benedict, Novak, Adam M., Eizenga, Jordan M., Garrison, Erik · 2017 · Genome Research
64. Necroptosis microenvironment directs lineage commitment in liver cancer
    Seehawer, Marco, Heinzmann, Florian, D’Artista, Luana, Harbig, Jule, Roux, Pierre-François, Hoenicke, Lisa, Dang, Hien, Klotz, Sabrina, Robinson, Lucas, Doré, Grégory et al. · 2018 · Nature
65. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
    Sirén, Jouni, Monlong, Jean, Chang, Xian, Novak, Adam M., Eizenga, Jordan M., Markello, Charles, Sibbesen, Jonas A., Hickey, Glenn, Chang, Pi-Chuan, Carroll, Andrew et al. · 2021 · Science
66. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia
    Giustacchini, Alice, Thongjuea, Supat, Barkas, Nikolaos, Woll, Petter S, Povinelli, Benjamin J, Booth, Christopher A G, Sopp, Paul, Norfo, Ruggiero, Rodriguez-Meira, Alba, Ashley, Neil et al. · 2017 · Nature Medicine
67. Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation
    Dorighi, Kristel M., Swigut, Tomek, Henriques, Telmo, Bhanu, Natarajan V., Scruggs, Benjamin S., Nady, Nataliya, Still, Christopher D., Garcia, Benjamin A., Adelman, Karen, Wysocka, Joanna · 2017 · Molecular Cell
68. Genomic epidemiology reveals multiple introductions of Zika virus into the United States
    Grubaugh, Nathan D., Ladner, Jason T., Kraemer, Moritz U. G., Dudas, Gytis, Tan, Amanda L., Gangavarapu, Karthik, Wiley, Michael R., White, Stephen, Thézé, Julien, Magnani, Diogo M. et al. · 2017 · Nature
69. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
    Leppek, Kathrin, Byeon, Gun Woo, Kladwang, Wipapat, Wayment-Steele, Hannah K., Kerr, Craig H., Xu, Adele F., Kim, Do Soon, Topkar, Ved V., Choe, Christian, Rothschild, Daphna et al. · 2022 · Nature Communications
70. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
    Leppek, Kathrin, Byeon, Gun Woo, Kladwang, Wipapat, Wayment-Steele, Hannah K., Kerr, Craig H., Xu, Adele F., Kim, Do Soon, Topkar, Ved V., Choe, Christian, Rothschild, Daphna et al. · 2021
71. Different Neuronal Activity Patterns Induce Different Gene Expression Programs
    Tyssowski, Kelsey M., DeStefino, Nicholas R., Cho, Jin-Hyung, Dunn, Carissa J., Poston, Robert G., Carty, Crista E., Jones, Richard D., Chang, Sarah M., Romeo, Palmyra, Wurzelmann, Mary K. et al. · 2018 · Neuron
72. Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks
    Michelini, Flavia, Pitchiaya, Sethuramasundaram, Vitelli, Valerio, Sharma, Sheetal, Gioia, Ubaldo, Pessina, Fabio, Cabrini, Matteo, Wang, Yejun, Capozzo, Ilaria, Iannelli, Fabio et al. · 2017 · Nature Cell Biology
73. Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer
    Arthur, Janelle C., Gharaibeh, Raad Z., Mühlbauer, Marcus, Perez-Chanona, Ernesto, Uronis, Joshua M., McCafferty, Jonathan, Fodor, Anthony A., Jobin, Christian · 2014 · Nature Communications
74. LTR-Retrotransposon Control by tRNA-Derived Small RNAs
    Schorn, Andrea J., Gutbrod, Michael J., LeBlanc, Chantal, Martienssen, Rob · 2017 · Cell
75. T cell-mediated regulation of the microbiota protects against obesity
    Petersen, Charisse, Bell, Rickesha, Klag, Kendra A., Lee, Soh-Hyun, Soto, Raymond, Ghazaryan, Arevik, Buhrke, Kaitlin, Ekiz, H. Atakan, Ost, Kyla S., Boudina, Sihem et al. · 2019 · Science
76. Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells
    Bulut-Karslioglu, Aydan, De La Rosa-Velázquez, Inti A., Ramirez, Fidel, Barenboim, Maxim, Onishi-Seebacher, Megumi, Arand, Julia, Galán, Carmen, Winter, Georg E., Engist, Bettina, Gerle, Borbala et al. · 2014 · Molecular Cell
77. The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk
    Wang, Dong D., Nguyen, Long H., Li, Yanping, Yan, Yan, Ma, Wenjie, Rinott, Ehud, Ivey, Kerry L., Shai, Iris, Willett, Walter C., Hu, Frank B. et al. · 2021 · Nature Medicine
78. C2H2 zinc finger proteins greatly expand the human regulatory lexicon
    Najafabadi, Hamed S, Mnaimneh, Sanie, Schmitges, Frank W, Garton, Michael, Lam, Kathy N, Yang, Ally, Albu, Mihai, Weirauch, Matthew T, Radovani, Ernest, Kim, Philip M et al. · 2015 · Nature Biotechnology
79. Developmental barcoding of whole mouse via homing CRISPR
    Kalhor, Reza, Kalhor, Kian, Mejia, Leo, Leeper, Kathleen, Graveline, Amanda, Mali, Prashant, Church, George M. · 2018 · Science
80. Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity
    Mills, Robert H., Dulai, Parambir S., Vázquez-Baeza, Yoshiki, Sauceda, Consuelo, Daniel, Noëmie, Gerner, Romana R., Batachari, Lakshmi E., Malfavon, Mario, Zhu, Qiyun, Weldon, Kelly et al. · 2022 · Nature Microbiology
81. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
    Zhu, Chenxu, Yu, Miao, Huang, Hui, Juric, Ivan, Abnousi, Armen, Hu, Rong, Lucero, Jacinta, Behrens, M. Margarita, Hu, Ming, Ren, Bing · 2019 · Nature Structural &amp; Molecular Biology
82. Metatranscriptomics of the Human Oral Microbiome during Health and Disease
    Jorth, Peter, Turner, Keith H., Gumus, Pinar, Nizam, Nejat, Buduneli, Nurcan, Whiteley, Marvin · 2014 · mBio
83. DNA methylation changes in plasticity genes accompany the formation and maintenance of memory
    Halder, Rashi, Hennion, Magali, Vidal, Ramon O, Shomroni, Orr, Rahman, Raza-Ur, Rajput, Ashish, Centeno, Tonatiuh Pena, van Bebber, Frauke, Capece, Vincenzo, Vizcaino, Julio C Garcia et al. · 2016 · Nature Neuroscience
84. An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease
    Nativio, Raffaella, Lan, Yemin, Donahue, Greg, Sidoli, Simone, Berson, Amit, Srinivasan, Ananth R., Shcherbakova, Oksana, Amlie-Wolf, Alexandre, Nie, Ji, Cui, Xiaolong et al. · 2020 · Nature Genetics
85. The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic
    Kadosh, Eliran, Snir-Alkalay, Irit, Venkatachalam, Avanthika, May, Shahaf, Lasry, Audrey, Elyada, Ela, Zinger, Adar, Shaham, Maya, Vaalani, Gitit, Mernberger, Marco et al. · 2020 · Nature
86. Extremely High Mutation Rate of HIV-1 In Vivo
    Cuevas, José M., Geller, Ron, Garijo, Raquel, López-Aldeguer, José, Sanjuán, Rafael · 2015 · PLOS Biology
87. Rational discovery of molecular glue degraders via scalable chemical profiling
    Mayor-Ruiz, Cristina, Bauer, Sophie, Brand, Matthias, Kozicka, Zuzanna, Siklos, Marton, Imrichova, Hana, Kaltheuner, Ines H., Hahn, Elisa, Seiler, Kristina, Koren, Anna et al. · 2020 · Nature Chemical Biology
88. Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases
    Ianiro, Gianluca, Punčochář, Michal, Karcher, Nicolai, Porcari, Serena, Armanini, Federica, Asnicar, Francesco, Beghini, Francesco, Blanco-Míguez, Aitor, Cumbo, Fabio, Manghi, Paolo et al. · 2022 · Nature Medicine
89. Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies
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