Fast gapped-read alignment with Bowtie 2

Cited by (908)

Items 401–500 of 908

1. Metagenomic Identification of Microbial Signatures Predicting Pancreatic Cancer From a Multinational Study
   Nagata, Naoyoshi, Nishijima, Suguru, Kojima, Yasushi, Hisada, Yuya, Imbe, Koh, Miyoshi-Akiyama, Tohru, Suda, Wataru, Kimura, Moto, Aoki, Ryo, Sekine, Katsunori et al. · 2022 · Gastroenterology
2. A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
   O'Geen, Henriette, Henry, Isabelle M., Bhakta, Mital S., Meckler, Joshua F., Segal, David J. · 2015 · Nucleic Acids Research
3. Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy
   Lee, Jaecheol, Termglinchan, Vittavat, Diecke, Sebastian, Itzhaki, Ilanit, Lam, Chi Keung, Garg, Priyanka, Lau, Edward, Greenhaw, Matthew, Seeger, Timon, Wu, Haodi et al. · 2019 · Nature
4. Neuronal enhancers are hotspots for DNA single-strand break repair
   Wu, Wei, Kargbo-Hill, Sarah E., Nathan, William J., Paiano, Jacob, Callen, Elsa, Wang, Dongpeng, Shinoda, Kenta, van Wietmarschen, Niek, Colón-Mercado, Jennifer M., Zong, Dali et al. · 2021 · Nature
5. Altered microbiome composition in individuals with fibromyalgia
   Minerbi, Amir, Gonzalez, Emmanuel, Brereton, Nicholas J.B., Anjarkouchian, Abraham, Dewar, Ken, Fitzcharles, Mary-Ann, Chevalier, Stéphanie, Shir, Yoram · 2019 · Pain
6. DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in <i>Arabidopsis</i>
   Yelina, Nataliya E., Lambing, Christophe, Hardcastle, Thomas J., Zhao, Xiaohui, Santos, Bruno, Henderson, Ian R. · 2015 · Genes &amp; Development
7. Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome
   Brooks, Brandon, Olm, Matthew R., Firek, Brian A., Baker, Robyn, Thomas, Brian C., Morowitz, Michael J., Banfield, Jillian F. · 2017 · Nature Communications
8. Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells
   Johnson, John L., Georgakilas, Georgios, Petrovic, Jelena, Kurachi, Makoto, Cai, Stanley, Harly, Christelle, Pear, Warren S., Bhandoola, Avinash, Wherry, E. John, Vahedi, Golnaz · 2018 · Immunity
9. Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption
   Romano, Kymberleigh A., Martinez-del Campo, Ana, Kasahara, Kazuyuki, Chittim, Carina L., Vivas, Eugenio I., Amador-Noguez, Daniel, Balskus, Emily P., Rey, Federico E. · 2017 · Cell Host &amp; Microbe
10. Identification and Quantification of Proteoforms by Mass Spectrometry
    Schaffer, Leah V., Millikin, Robert J., Miller, Rachel M., Anderson, Lissa C., Fellers, Ryan T., Ge, Ying, Kelleher, Neil L., LeDuc, Richard D., Liu, Xiaowen, Payne, Samuel H. et al. · 2019 · PROTEOMICS
11. Trained Immunity-Promoting Nanobiologic Therapy Suppresses Tumor Growth and Potentiates Checkpoint Inhibition
    Priem, Bram, van Leent, Mandy M.T., Teunissen, Abraham J.P., Sofias, Alexandros Marios, Mourits, Vera P., Willemsen, Lisa, Klein, Emma D., Oosterwijk, Roderick S., Meerwaldt, Anu E., Munitz, Jazz et al. · 2020 · Cell
12. Oncogenic KRAS-Driven Metabolic Reprogramming in Pancreatic Cancer Cells Utilizes Cytokines from the Tumor Microenvironment
    Dey, Prasenjit, Li, Jun, Zhang, Jianhua, Chaurasiya, Surendra, Strom, Anders, Wang, Huamin, Liao, Wen-Ting, Cavallaro, Frederick, Denz, Parker, Bernard, Vincent et al. · 2020 · Cancer Discovery
13. Microbiome-derived ethanol in nonalcoholic fatty liver disease
    Meijnikman, Abraham S., Davids, Mark, Herrema, Hilde, Aydin, Omrum, Tremaroli, Valentina, Rios-Morales, Melany, Levels, Han, Bruin, Sjoerd, de Brauw, Maurits, Verheij, Joanne et al. · 2022 · Nature Medicine
14. Hic1 Defines Quiescent Mesenchymal Progenitor Subpopulations with Distinct Functions and Fates in Skeletal Muscle Regeneration
    Scott, R. Wilder, Arostegui, Martin, Schweitzer, Ronen, Rossi, Fabio M.V., Underhill, T. Michael · 2019 · Cell Stem Cell
15. A Thermostable Cas9 with Increased Lifetime in Human Plasma
    Harrington, Lucas B., Paez-Espino, David, Staahl, Brett T., Chen, Janice S., Ma, Enbo, Kyrpides, Nikos C., Doudna, Jennifer A. · 2017 · Nature Communications
16. Neurogenesis and prolongevity signaling in young germ-free mice transplanted with the gut microbiota of old mice
    Kundu, Parag, Lee, Hae Ung, Garcia-Perez, Isabel, Tay, Emmy Xue Yun, Kim, Hyejin, Faylon, Llanto Elma, Martin, Katherine A., Purbojati, Rikky, Drautz-Moses, Daniela I., Ghosh, Sujoy et al. · 2019 · Science Translational Medicine
17. CoBATCH for High-Throughput Single-Cell Epigenomic Profiling
    Wang, Qianhao, Xiong, Haiqing, Ai, Shanshan, Yu, Xianhong, Liu, Yaxi, Zhang, Jiejie, He, Aibin · 2019 · Molecular Cell
18. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function
    Link, Verena M., Duttke, Sascha H., Chun, Hyun B., Holtman, Inge R., Westin, Emma, Hoeksema, Marten A., Abe, Yohei, Skola, Dylan, Romanoski, Casey E., Tao, Jenhan et al. · 2018 · Cell
19. Super-enhancers include classical enhancers and facilitators to fully activate gene expression
    Blayney, Joseph W., Francis, Helena, Rampasekova, Alexandra, Camellato, Brendan, Mitchell, Leslie, Stolper, Rosa, Cornell, Lucy, Babbs, Christian, Boeke, Jef D., Higgs, Douglas R. et al. · 2023 · Cell
20. Interferon-γ Represses M2 Gene Expression in Human Macrophages by Disassembling Enhancers Bound by the Transcription Factor MAF
    Kang, Kyuho, Park, Sung Ho, Chen, Janice, Qiao, Yu, Giannopoulou, Eugenia, Berg, Karen, Hanidu, Adedayo, Li, Jun, Nabozny, Gerald, Kang, Keunsoo et al. · 2017 · Immunity
21. Subtype-specific 3D genome alteration in acute myeloid leukaemia
    Xu, Jie, Song, Fan, Lyu, Huijue, Kobayashi, Mikoto, Zhang, Baozhen, Zhao, Ziyu, Hou, Ye, Wang, Xiaotao, Luan, Yu, Jia, Bei et al. · 2022 · Nature
22. Interrogation of human hematopoiesis at single-cell and single-variant resolution
    Ulirsch, Jacob C., Lareau, Caleb A., Bao, Erik L., Ludwig, Leif S., Guo, Michael H., Benner, Christian, Satpathy, Ansuman T., Kartha, Vinay K., Salem, Rany M., Hirschhorn, Joel N. et al. · 2019 · Nature Genetics
23. Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel
    Dey, Neelendu, Wagner, Vitas E., Blanton, Laura V., Cheng, Jiye, Fontana, Luigi, Haque, Rashidul, Ahmed, Tahmeed, Gordon, Jeffrey I. · 2015 · Cell
24. Pathway analysis of systemic transcriptome responses to injected polystyrene particles in zebrafish larvae
    Veneman, Wouter J., Spaink, Herman P., Brun, Nadja R., Bosker, Thijs, Vijver, Martina G. · 2017 · Aquatic Toxicology
25. Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in genomic DNA
    Gombolay, Alli L, Vannberg, Fredrik O, Storici, Francesca · 2019 · Nucleic Acids Research
26. Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome
    Taylor, Bryn C., Lejzerowicz, Franck, Poirel, Marion, Shaffer, Justin P., Jiang, Lingjing, Aksenov, Alexander, Litwin, Nicole, Humphrey, Gregory, Martino, Cameron, Miller-Montgomery, Sandrine et al. · 2020 · mSystems
27. APOE4 impairs the microglial response in Alzheimer’s disease by inducing TGFβ-mediated checkpoints
    Yin, Zhuoran, Rosenzweig, Neta, Kleemann, Kilian L., Zhang, Xiaoming, Brandão, Wesley, Margeta, Milica A., Schroeder, Caitlin, Sivanathan, Kisha N., Silveira, Sebastian, Gauthier, Christian et al. · 2023 · Nature Immunology
28. Large-scale comparative metagenomics of <i>Blastocystis</i>, a common member of the human gut microbiome
    Beghini, Francesco, Pasolli, Edoardo, Truong, Tin Duy, Putignani, Lorenza, Cacciò, Simone M, Segata, Nicola · 2017 · The ISME Journal
29. Fate-Mapping of GM-CSF Expression Identifies a Discrete Subset of Inflammation-Driving T Helper Cells Regulated by Cytokines IL-23 and IL-1β
    Komuczki, Juliana, Tuzlak, Selma, Friebel, Ekaterina, Hartwig, Tom, Spath, Sabine, Rosenstiel, Philip, Waisman, Ari, Opitz, Lennart, Oukka, Mohammed, Schreiner, Bettina et al. · 2019 · Immunity
30. The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation
    Wang, Dapeng, Diao, Huitian, Getzler, Adam J., Rogal, Walter, Frederick, Megan A., Milner, Justin, Yu, Bingfei, Crotty, Shane, Goldrath, Ananda W., Pipkin, Matthew E. · 2018 · Immunity
31. Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation
    Rubio, Claudia A, Weisburd, Benjamin, Holderfield, Matthew, Arias, Carolina, Fang, Eric, DeRisi, Joseph L, Fanidi, Abdallah · 2014 · Genome Biology
32. Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells
    Hu, Gangqing, Cui, Kairong, Fang, Difeng, Hirose, Satoshi, Wang, Xun, Wangsa, Darawalee, Jin, Wenfei, Ried, Thomas, Liu, Pentao, Zhu, Jinfang et al. · 2018 · Immunity
33. Integrated genomic, epidemiologic investigation of Candida auris skin colonization in a skilled nursing facility
    Proctor, Diana M., Dangana, Thelma, Sexton, D. Joseph, Fukuda, Christine, Yelin, Rachel D., Stanley, Mary, Bell, Pamela B., Baskaran, Sangeetha, Deming, Clay, Chen, Qiong et al. · 2021 · Nature Medicine
34. Targeted gene addition in human CD34+ hematopoietic cells for correction of X-linked chronic granulomatous disease
    De Ravin, Suk See, Reik, Andreas, Liu, Pei-Qi, Li, Linhong, Wu, Xiaolin, Su, Ling, Raley, Castle, Theobald, Narda, Choi, Uimook, Song, Alexander H et al. · 2016 · Nature Biotechnology
35. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate.
    De Filippis, Francesca, Genovese, Alessandro, Ferranti, Pasquale, Gilbert, Jack A., Ercolini, Danilo · 2016 · Scientific Reports
36. Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex
    Mich, John K., Graybuck, Lucas T., Hess, Erik E., Mahoney, Joseph T., Kojima, Yoshiko, Ding, Yi, Somasundaram, Saroja, Miller, Jeremy A., Kalmbach, Brian E., Radaelli, Cristina et al. · 2021 · Cell Reports
37. Spatially resolved epigenomic profiling of single cells in complex tissues
    Lu, Tian, Ang, Cheen Euong, Zhuang, Xiaowei · 2022 · Cell
38. Multiparameter functional diversity of human C2H2 zinc finger proteins
    Schmitges, Frank W., Radovani, Ernest, Najafabadi, Hamed S., Barazandeh, Marjan, Campitelli, Laura F., Yin, Yimeng, Jolma, Arttu, Zhong, Guoqing, Guo, Hongbo, Kanagalingam, Tharsan et al. · 2016 · Genome Research
39. Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia
    Bryois, Julien, Garrett, Melanie E., Song, Lingyun, Safi, Alexias, Giusti-Rodriguez, Paola, Johnson, Graham D., Shieh, Annie W., Buil, Alfonso, Fullard, John F., Roussos, Panos et al. · 2018 · Nature Communications
40. Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis
    Avagyan, S., Henninger, J. E., Mannherz, W. P., Mistry, M., Yoon, J., Yang, S., Weber, M. C., Moore, J. L., Zon, L. I. · 2021 · Science
41. Novel Fecal Biomarkers That Precede Clinical Diagnosis of Ulcerative Colitis
    Galipeau, Heather J., Caminero, Alberto, Turpin, Williams, Bermudez-Brito, Miriam, Santiago, Alba, Libertucci, Josie, Constante, Marco, Raygoza Garay, Juan Antonio, Rueda, Gaston, Armstrong, Sarah et al. · 2021 · Gastroenterology
42. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer
    Risom, Tyler, Langer, Ellen M., Chapman, Margaret P., Rantala, Juha, Fields, Andrew J., Boniface, Christopher, Alvarez, Mariano J., Kendsersky, Nicholas D., Pelz, Carl R., Johnson-Camacho, Katherine et al. · 2018 · Nature Communications
43. Loss of SATB1 Induces p21-Dependent Cellular Senescence in Post-mitotic Dopaminergic Neurons
    Riessland, Markus, Kolisnyk, Benjamin, Kim, Tae Wan, Cheng, Jia, Ni, Jason, Pearson, Jordan A., Park, Emily J., Dam, Kevin, Acehan, Devrim, Ramos-Espiritu, Lavoisier S. et al. · 2019 · Cell Stem Cell
44. Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells
    Rhodes, James D.P., Feldmann, Angelika, Hernández-Rodríguez, Benjamín, Díaz, Noelia, Brown, Jill M., Fursova, Nadezda A., Blackledge, Neil P., Prathapan, Praveen, Dobrinic, Paula, Huseyin, Miles K. et al. · 2020 · Cell Reports
45. Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells
    Bodogai, Monica, O’Connell, Jennifer, Kim, Ki, Kim, Yoo, Moritoh, Kanako, Chen, Chen, Gusev, Fedor, Vaughan, Kelli, Shulzhenko, Natalia, Mattison, Julie A. et al. · 2018 · Science Translational Medicine
46. Population-level Metagenomics Uncovers Distinct Effects of Multiple Medications on the Human Gut Microbiome
    Nagata, Naoyoshi, Nishijima, Suguru, Miyoshi-Akiyama, Tohru, Kojima, Yasushi, Kimura, Moto, Aoki, Ryo, Ohsugi, Mitsuru, Ueki, Kohjiro, Miki, Kuniko, Iwata, Eri et al. · 2022 · Gastroenterology
47. The BET Family of Proteins Targets Moloney Murine Leukemia Virus Integration near Transcription Start Sites
    De Rijck, Jan, de Kogel, Christine, Demeulemeester, Jonas, Vets, Sofie, El Ashkar, Sara, Malani, Nirav, Bushman, Frederic D., Landuyt, Bart, Husson, Steven J., Busschots, Katrien et al. · 2013 · Cell Reports
48. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration
    Wang, Jie, Zibetti, Cristina, Shang, Peng, Sripathi, Srinivasa R., Zhang, Pingwu, Cano, Marisol, Hoang, Thanh, Xia, Shuli, Ji, Hongkai, Merbs, Shannath L. et al. · 2018 · Nature Communications
49. Characterization of Distinct Subpopulations of Hepatic Macrophages in HFD/Obese Mice
    Morinaga, Hidetaka, Mayoral, Rafael, Heinrichsdorff, Jan, Osborn, Olivia, Franck, Niclas, Hah, Nasun, Walenta, Evelyn, Bandyopadhyay, Gautam, Pessentheiner, Ariane R., Chi, Tyler J. et al. · 2015 · Diabetes
50. A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq
    Li, Bin, Qing, Tao, Zhu, Jinhang, Wen, Zhuo, Yu, Ying, Fukumura, Ryutaro, Zheng, Yuanting, Gondo, Yoichi, Shi, Leming · 2017 · Scientific Reports
51. Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells
    Delacher, Michael, Simon, Malte, Sanderink, Lieke, Hotz-Wagenblatt, Agnes, Wuttke, Marina, Schambeck, Kathrin, Schmidleithner, Lisa, Bittner, Sebastian, Pant, Asmita, Ritter, Uwe et al. · 2021 · Immunity
52. HRas Signal Transduction Promotes Hepatitis C Virus Cell Entry by Triggering Assembly of the Host Tetraspanin Receptor Complex
    Zona, Laetitia, Lupberger, Joachim, Sidahmed-Adrar, Nazha, Thumann, Christine, Harris, Helen J., Barnes, Amy, Florentin, Jonathan, Tawar, Rajiv G., Xiao, Fei, Turek, Marine et al. · 2013 · Cell Host &amp; Microbe
53. Host genetic regulation of human gut microbial structural variation
    Zhernakova, Daria V., Wang, Daoming, Liu, Lei, Andreu-Sánchez, Sergio, Zhang, Yue, Ruiz-Moreno, Angel J., Peng, Haoran, Plomp, Niels, Del Castillo-Izquierdo, Ángela, Gacesa, Ranko et al. · 2024 · Nature
54. Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition
    Mamantopoulos, Michail, Ronchi, Francesca, Van Hauwermeiren, Filip, Vieira-Silva, Sara, Yilmaz, Bahtiyar, Martens, Liesbet, Saeys, Yvan, Drexler, Stefan K., Yazdi, Amir S., Raes, Jeroen et al. · 2017 · Immunity
55. Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification
    Ku, Wai Lim, Nakamura, Kosuke, Gao, Weiwu, Cui, Kairong, Hu, Gangqing, Tang, Qingsong, Ni, Bing, Zhao, Keji · 2019 · Nature Methods
56. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome
    Vockley, Christopher M., D’Ippolito, Anthony M., McDowell, Ian C., Majoros, William H., Safi, Alexias, Song, Lingyun, Crawford, Gregory E., Reddy, Timothy E. · 2016 · Cell
57. Probiotics for gastrointestinal symptoms and quality of life in autism: a placebo-controlled pilot trial
    Arnold, L. Eugene, Luna, Ruth Ann, Williams, Kent, Chan, James, Parker, Robert A., Wu, Qinglong, Hollway, Jill A., Jeffs, Adelina, Lu, Frances, Coury, Daniel L. et al. · 2019 · Journal of Child and Adolescent Psychopharmacology
58. FOXA2 drives lineage plasticity and KIT pathway activation in neuroendocrine prostate cancer
    Han, Ming, Li, Fei, Zhang, Yehan, Dai, Pengfei, He, Juan, Li, Yunguang, Zhu, Yiqin, Zheng, Junke, Huang, Hai, Bai, Fan et al. · 2022 · Cancer Cell
59. Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak
    Ottesen, Andrea, Ramachandran, Padmini, Reed, Elizabeth, White, James R., Hasan, Nur, Subramanian, Poorani, Ryan, Gina, Jarvis, Karen, Grim, Christopher, Daquiqan, Ninalynn et al. · 2016 · BMC Microbiology
60. A selective HDAC8 inhibitor potentiates antitumor immunity and efficacy of immune checkpoint blockade in hepatocellular carcinoma
    Yang, Weiqin, Feng, Yu, Zhou, Jingying, Cheung, Otto Ka-Wing, Cao, Jianquan, Wang, Jing, Tang, Wenshu, Tu, Yalin, Xu, Liangliang, Wu, Feng et al. · 2021 · Science Translational Medicine
61. High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids
    Oliver, Andrew, Chase, Alexander B., Weihe, Claudia, Orchanian, Stephanie B., Riedel, Stefan F., Hendrickson, Clark L., Lay, Mi, Sewall, Julia Massimelli, Martiny, Jennifer B. H., Whiteson, Katrine · 2021 · mSystems
62. A comparative atlas of single-cell chromatin accessibility in the human brain
    Li, Yang Eric, Preissl, Sebastian, Miller, Michael, Johnson, Nicholas D., Wang, Zihan, Jiao, Henry, Zhu, Chenxu, Wang, Zhaoning, Xie, Yang, Poirion, Olivier et al. · 2023 · Science
63. Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment
    Terrisse, Safae, Derosa, Lisa, Iebba, Valerio, Ghiringhelli, François, Vaz-Luis, Ines, Kroemer, Guido, Fidelle, Marine, Christodoulidis, Stergios, Segata, Nicola, Thomas, Andrew Maltez et al. · 2021 · Cell Death &amp; Differentiation
64. Expression profiling of budding cells in colorectal cancer reveals an EMT-like phenotype and molecular subtype switching
    De Smedt, Linde, Palmans, Sofie, Andel, Daan, Govaere, Olivier, Boeckx, Bram, Smeets, Dominiek, Galle, Eva, Wouters, Jasper, Barras, David, Suffiotti, Madeleine et al. · 2017 · British Journal of Cancer
65. Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility
    Lio, Chan-Wang, Zhang, Jiayuan, González-Avalos, Edahí, Hogan, Patrick G, Chang, Xing, Rao, Anjana · 2016 · eLife
66. Altered neuronal migratory trajectories in human cerebral organoids derived from individuals with neuronal heterotopia
    Klaus, Johannes, Kanton, Sabina, Kyrousi, Christina, Ayo-Martin, Ane Cristina, Di Giaimo, Rossella, Riesenberg, Stephan, O’Neill, Adam C., Camp, J. Gray, Tocco, Chiara, Santel, Malgorzata et al. · 2019 · Nature Medicine
67. Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition
    Hogg, Simon J., Motorna, Olga, Cluse, Leonie A., Johanson, Timothy M., Coughlan, Hannah D., Raviram, Ramya, Myers, Robert M., Costacurta, Matteo, Todorovski, Izabela, Pijpers, Lizzy et al. · 2021 · Molecular Cell
68. Systematic Analysis of Gut Microbiome Reveals the Role of Bacterial Folate and Homocysteine Metabolism in Parkinson’s Disease
    Rosario, Dorines, Bidkhori, Gholamreza, Lee, Sunjae, Bedarf, Janis, Hildebrand, Falk, Le Chatelier, Emmanuelle, Uhlen, Mathias, Ehrlich, Stanislav Dusko, Proctor, Gordon, Wüllner, Ullrich et al. · 2021 · Cell Reports
69. Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
    Karcher, Nicolai, Nigro, Eleonora, Punčochář, Michal, Blanco-Míguez, Aitor, Ciciani, Matteo, Manghi, Paolo, Zolfo, Moreno, Cumbo, Fabio, Manara, Serena, Golzato, Davide et al. · 2021 · Genome Biology
70. Tau exacerbates excitotoxic brain damage in an animal model of stroke
    Bi, Mian, Gladbach, Amadeus, van Eersel, Janet, Ittner, Arne, Przybyla, Magdalena, van Hummel, Annika, Chua, Sook Wern, van der Hoven, Julia, Lee, Wei S., Müller, Julius et al. · 2017 · Nature Communications
71. The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection
    Sultana, Tania, van Essen, Dominic, Siol, Oliver, Bailly-Bechet, Marc, Philippe, Claude, Zine El Aabidine, Amal, Pioger, Léo, Nigumann, Pilvi, Saccani, Simona, Andrau, Jean-Christophe et al. · 2019 · Molecular Cell
72. Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans
    Gibbons, John G., Branco, Alan T., Yu, Shoukai, Lemos, Bernardo · 2014 · Nature Communications
73. Targeted degradation of the enhancer lysine acetyltransferases CBP and p300
    Vannam, Raghu, Sayilgan, Jan, Ojeda, Samuel, Karakyriakou, Barbara, Hu, Eileen, Kreuzer, Johannes, Morris, Robert, Herrera Lopez, Xcanda Ixchel, Rai, Sumit, Haas, Wilhelm et al. · 2021 · Cell Chemical Biology
74. Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic islands
    Maguire, Finlay, Jia, Baofeng, Gray, Kristen L., Lau, Wing Yin Venus, Beiko, Robert G., Brinkman, Fiona S. L. · 2020 · Microbial Genomics
75. Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability
    Rizzardi, Lindsay F., Hickey, Peter F., Rodriguez DiBlasi, Varenka, Tryggvadóttir, Rakel, Callahan, Colin M., Idrizi, Adrian, Hansen, Kasper D., Feinberg, Andrew P. · 2019 · Nature Neuroscience
76. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
    Steenwyk, Jacob L., Opulente, Dana A., Kominek, Jacek, Shen, Xing-Xing, Zhou, Xiaofan, Labella, Abigail L., Bradley, Noah P., Eichman, Brandt F., Čadež, Neža, Libkind, Diego et al. · 2019 · PLoS Biology
77. Inflammation-driven senescence-associated secretory phenotype in cancer-associated fibroblasts enhances peritoneal dissemination
    Yasuda, Tadahito, Koiwa, Mayu, Yonemura, Atsuko, Miyake, Keisuke, Kariya, Ryusho, Kubota, Sho, Yokomizo-Nakano, Takako, Yasuda-Yoshihara, Noriko, Uchihara, Tomoyuki, Itoyama, Rumi et al. · 2021 · Cell Reports
78. SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
    Krueger, Felix, Andrews, Simon R. · 2016 · F1000Research
79. CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions
    Gasperini, Molly, Findlay, Gregory M., McKenna, Aaron, Milbank, Jennifer H., Lee, Choli, Zhang, Melissa D., Cusanovich, Darren A., Shendure, Jay · 2017 · The American Journal of Human Genetics
80. Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus
    Fernandez-Albert, Jordi, Lipinski, Michal, Lopez-Cascales, María T., Rowley, M. Jordan, Martin-Gonzalez, Ana M., del Blanco, Beatriz, Corces, Victor G., Barco, Angel · 2019 · Nature Neuroscience
81. Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms
    Rusu, Victor, Hoch, Eitan, Mercader, Josep M., Tenen, Danielle E., Gymrek, Melissa, Hartigan, Christina R., DeRan, Michael, von Grotthuss, Marcin, Fontanillas, Pierre, Spooner, Alexandra et al. · 2017 · Cell
82. Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen
    Marcellin, Esteban, Behrendorff, James B., Nagaraju, Shilpa, DeTissera, Sashini, Segovia, Simon, Palfreyman, Robin W., Daniell, James, Licona-Cassani, Cuauhtemoc, Quek, Lake-ee, Speight, Robert et al. · 2016 · Green Chemistry
83. 5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes
    Mellén, Marian, Ayata, Pinar, Heintz, Nathaniel · 2017 · Proceedings of the National Academy of Sciences
84. Evidence Suggesting Absence of Mitochondrial DNA Methylation
    Mechta, Mie, Ingerslev, Lars R., Fabre, Odile, Picard, Martin, Barrès, Romain · 2017 · Frontiers in Genetics
85. CowPI: a rumen microbiome focussed version of the PICRUSt functional inference software
    Wilkinson, Toby J., Huws, Sharon A., Edwards, Joan E., Kingston-Smith, Alison H., Siu-Ting, Karen, Hughes, Martin, Rubino, Francesco, Friedersdorff, Maximillian, Creevey, Christopher J. · 2018 · Frontiers in Microbiology
86. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble
    Marco, Asaf, Meharena, Hiruy S., Dileep, Vishnu, Raju, Ravikiran M., Davila-Velderrain, Jose, Zhang, Amy Letao, Adaikkan, Chinnakkaruppan, Young, Jennie Z., Gao, Fan, Kellis, Manolis et al. · 2020 · Nature Neuroscience
87. Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract
    Burnham, Philip, Dadhania, Darshana, Heyang, Michael, Chen, Fanny, Westblade, Lars F., Suthanthiran, Manikkam, Lee, John Richard, De Vlaminck, Iwijn · 2018 · Nature Communications
88. HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains
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