featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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1. IL-1-driven stromal–neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies
   Matthias Friedrich, Mathilde Pohin, Matthew A Jackson, Ilya Korsunsky, Samuel J. Bullers, Kévin Rue-Albrecht, Zoe Christoforidou, Dharshan Sathananthan, Tom R Thomas, Rahul Prashanth Ravindran et al. · 2021 · Nature Medicine
2. Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities
   Abrar Choudhury, Stephen T. Magill, Charlotte D. Eaton, Briana C. Prager, William Chen, Martha A. Cady, Kyounghee Seo, Calixto‐Hope G. Lucas, Tim Casey-Clyde, Harish N. Vasudevan et al. · 2022 · Nature Genetics
3. Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
   Rodriguez-Meira, Alba, Buck, Gemma, Clark, Sally-Ann, Povinelli, Benjamin J., Alcolea, Veronica, Louka, Eleni, McGowan, Simon, Hamblin, Angela, Sousos, Nikolaos, Barkas, Nikolaos et al. · 2019 · Molecular Cell
4. A non-canonical tricarboxylic acid cycle underlies cellular identity
   Arnold, Paige K., Jackson, Benjamin T., Paras, Katrina I., Brunner, Julia S., Hart, Madeleine L., Newsom, Oliver J., Alibeckoff, Sydney P., Endress, Jennifer, Drill, Esther, Sullivan, Lucas B. et al. · 2022 · Nature
5. Sterol regulatory element binding protein 1 couples mechanical cues and lipid metabolism
   Rebecca Bertolio, Francesco Napoletano, Miguel Mano, Sebastian Maurer‐Stroh, Marco Fantuz, Alessandro Zannini, Silvio Bicciato, Giovanni Sorrentino, Giannino Del Sal · 2019 · Nature Communications
6. m6A RNA methylation regulates the fate of endogenous retroviruses
   Tomasz Chełmicki, Emeline Roger, Aurélie Teissandier, Mathilde Dura, Lorraine Bonneville, Sofia Rucli, François Dossin, Camille Fouassier, Sonia Lameiras, Déborah Bourc’his · 2021 · Nature
7. Mitochondrial RNA modifications shape metabolic plasticity in metastasis
   Sylvain Delaunay, Gloria Pascual, Bohai Feng, Kevin Klann, Mikaela Behm, Agnes Hotz‐Wagenblatt, Karsten Richter, Karim Zaoui, Esther Herpel, Christian Münch et al. · 2022 · Nature
8. Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency
   Mehdipour, Parinaz, Marhon, Sajid A., Ettayebi, Ilias, Chakravarthy, Ankur, Hosseini, Amir, Wang, Yadong, de Castro, Fabíola Attié, Loo Yau, Helen, Ishak, Charles, Abelson, Sagi et al. · 2020 · Nature
9. Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution
   Daniel Dar, Nina Dar, Long Cai, Dianne K. Newman · 2021 · Science
10. Single-cell RNA sequencing reveals evolution of immune landscape during glioblastoma progression
    Alan T. Yeo, Shruti Rawal, Bethany Delcuze, Anthos Christofides, Agata M. P. Atayde, Laura Strauss, Leonora Balaj, Vaughn A. Rogers, Erik J. Uhlmann, Hemant Varma et al. · 2022 · Nature Immunology
11. Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes
    Robertson, Catherine C., Inshaw, Jamie R. J., Onengut-Gumuscu, Suna, Chen, Wei-Min, Santa Cruz, David Flores, Yang, Hanzhi, Cutler, Antony J., Crouch, Daniel J. M., Farber, Emily, Bridges, S. Louis et al. · 2021 · Nature Genetics
12. Advanced Applications of RNA Sequencing and Challenges
    Yixing Han, Shouguo Gao, Kathrin Muegge, Wei Zhang, Bing Zhou · 2015 · Bioinformatics and Biology Insights
13. High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation
    Song Li, Masashi Yamada, Xinwei Han, Uwe Ohler, Philip N. Benfey · 2016 · Developmental Cell
14. Tumor-derived exosomes modulate PD-L1 expression in monocytes
    Franziska Haderk, Ralph Schulz, Murat Iskar, Laura Llaó Cid, Thomas Stefan Worst, Karolin V. Willmund, Angela Schulz, Uwe H. Warnken, Jana Seiler, Axel Benner et al. · 2017 · Science Immunology
15. Two subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans
    Galletti, Giovanni, De Simone, Gabriele, Mazza, Emilia M. C., Puccio, Simone, Mezzanotte, Claudia, Bi, Timothy M., Davydov, Alexey N., Metsger, Maria, Scamardella, Eloise, Alvisi, Giorgia et al. · 2020 · Nature Immunology
16. Polyamine metabolism is a central determinant of helper T cell lineage fidelity
    Daniel J. Puleston, Francesc Baixauli, David E. Sanin, Joy Edwards-Hicks, Matteo Villa, Agnieszka Martyna Kabat, Marcin M. Kamiński, Michal Stanckzak, Hauke J. Weiss, Katarzyna M. Grzes et al. · 2021 · Cell
17. Replicative senescence dictates the emergence of disease-associated microglia and contributes to Aβ pathology
    Hu, Yanling, Fryatt, Gemma L., Ghorbani, Mohammadmersad, Obst, Juliane, Menassa, David A., Martin-Estebane, Maria, Muntslag, Tim A.O., Olmos-Alonso, Adrian, Guerrero-Carrasco, Monica, Thomas, Daniel et al. · 2021 · Cell Reports
18. Time of exercise specifies the impact on muscle metabolic pathways and systemic energy homeostasis
    Sato, Shogo, Basse, Astrid Linde, Schönke, Milena, Chen, Siwei, Samad, Muntaha, Altıntaş, Ali, Laker, Rhianna C., Dalbram, Emilie, Barrès, Romain, Baldi, Pierre et al. · 2019 · Cell Metabolism
19. MicroRNA and mRNA cargo of extracellular vesicles from porcine adipose tissue-derived mesenchymal stem cells
    Alfonso Eirin, Scott M. Riester, Xiang yang Zhu, Hui Ru Tang, Jared M. Evans, Daniel R. O’Brien, André J. van Wijnen, Lilach O. Lerman · 2014 · Gene
20. Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma
    Selina Jansky, Ashwini Kumar Sharma, Verena Körber, Andrés Quintero, Umut H. Toprak, Elisa M. Wecht, Moritz Gartlgruber, Alessandro Greco, Elad Chomsky, Thomas G. P. Grünewald et al. · 2021 · Nature Genetics
21. Reversible reprogramming of cardiomyocytes to a fetal state drives heart regeneration in mice
    Chen, Yanpu, Lüttmann, Felipe F., Schoger, Eric, Schöler, Hans R., Zelarayán, Laura C., Kim, Kee-Pyo, Haigh, Jody J., Kim, Johnny, Braun, Thomas · 2021 · Science
22. Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex
    Christine Grossen, Frédéric Guillaume, Lukas F. Keller, Daniel Croll · 2020 · Nature Communications
23. α-Ketoglutarate links p53 to cell fate during tumour suppression
    Morris, John P., Yashinskie, Jossie J., Koche, Richard, Chandwani, Rohit, Tian, Sha, Chen, Chi-Chao, Baslan, Timour, Marinkovic, Zoran S., Sánchez-Rivera, Francisco J., Leach, Steven D. et al. · 2019 · Nature
24. Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes
    Xue, Ruidong, Chen, Lu, Zhang, Chong, Fujita, Masashi, Li, Ruoyan, Yan, Shu-Mei, Ong, Choon Kiat, Liao, Xiwen, Gao, Qiang, Sasagawa, Shota et al. · 2019 · Cancer Cell
25. M3Drop: dropout-based feature selection for scRNASeq
    Tallulah S. Andrews, Martin Hemberg · 2018 · Bioinformatics
26. The Implication of Early Chromatin Changes in X Chromosome Inactivation
    Jan Jakub Żylicz, Aurélie Bousard, Kristina Žumer, François Dossin, Eusra Mohammad, Simão Teixeira da Rocha, Björn Schwalb, Laurène Syx, Florent Dingli, Damarys Loew et al. · 2018 · Cell
27. Integrative analyses of metabolome and genome‐wide transcriptome reveal the regulatory network governing flavor formation in kiwifruit ( Actinidia chinensis )
    Ruochen Wang, Peng Shu, Chi Zhang, Junlin Zhang, Ya Chen, Yaoxin Zhang, Kui Du, Yue Xie, Mingzhang Li, Tao Ma et al. · 2021 · New Phytologist
28. FTO mediates LINE1 m 6 A demethylation and chromatin regulation in mESCs and mouse development
    Jiangbo Wei, Xianbin Yu, Lei Yang, Xuelian Liu, Boyang Gao, Boxian Huang, Xiaoyang Dou, Jun Liu, Zhongyu Zou, Xiaolong Cui et al. · 2022 · Science
29. Deep learning-based prediction of the T cell receptor–antigen binding specificity
    Lu, Tianshi, Zhang, Ze, Zhu, James, Wang, Yunguan, Jiang, Peixin, Xiao, Xue, Bernatchez, Chantale, Heymach, John V., Gibbons, Don L., Wang, Jun et al. · 2021 · Nature Machine Intelligence
30. Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration
    Shih-Lei Lai, Rubén Marín‐Juez, Pedro Luís Moura, Carsten Tobias Kuenne, Jason Kuan Han Lai, Ayele Taddese Tsedeke, Stefan Günther, Mario Looso, Didier Y. R. Stainier · 2017 · eLife
31. Stalled developmental programs at the root of pediatric brain tumors
    Selin Jessa, Alexis Blanchet-Cohen, Brian Krug, Maria Claudia Vladoiu, Marie Coutelier, Damien Faury, Brice Poreau, Nicolas De Jay, Steven Hébert, Jean Monlong et al. · 2019 · Nature Genetics
32. Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease
    Feargal J. Ryan, Anna M. Ahern, Rachel S. Fitzgerald, Emilio José Laserna Mendieta, E. M. Power, Adam G. Clooney, KEITH O'DONOGHUE, Paul J. McMurdie, Shoko Iwai, Alexander Crits‐Christoph et al. · 2020 · Nature Communications
33. Androgen signaling negatively controls group 2 innate lymphoid cells
    Sophie Laffont, Eve Blanquart, Magali Savignac, Claire Cénac, Gilles LAVERNY, Daniel METZGER, Jean‐Philippe Girard, Gabrielle Therese Belz, Lucette Pelletier, Cyril Seillet et al. · 2017 · The Journal of Experimental Medicine
34. Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential
    Wampach, Linda, Heintz-Buschart, Anna, Fritz, Joëlle V., Ramiro-Garcia, Javier, Habier, Janine, Herold, Malte, Narayanasamy, Shaman, Kaysen, Anne, Hogan, Angela H., Bindl, Lutz et al. · 2018 · Nature Communications
35. Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes
    Brian David Lehmann, Antonio Colaprico, Tiago C. Silva, Jianjiao Chen, Hanbing An, Yuguang J. Ban, Hanchen Huang, Lily Hui-Ching Wang, Jamaal L. James, Justin Micah Balko et al. · 2021 · Nature Communications
36. Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states
    Ma, Peijun, Amemiya, Haley M., He, Lorrie L., Gandhi, Shivam J., Nicol, Robert, Bhattacharyya, Roby P., Smillie, Christopher S., Hung, Deborah T. · 2023 · Cell
37. Novel Alzheimer risk genes determine the microglia response to amyloid-β but not to TAU pathology
    Sierksma, Annerieke, Lu, Ashley, Mancuso, Renzo, Fattorelli, Nicola, Thrupp, Nicola, Salta, Evgenia, Zoco, Jesus, Blum, David, Buée, Luc, De Strooper, Bart et al. · 2020 · EMBO Molecular Medicine
38. NODULE INCEPTION Recruits the Lateral Root Developmental Program for Symbiotic Nodule Organogenesis in Medicago truncatula
    Katharina Schiessl, Jodi L. Stewart Lilley, Tak H. Lee, Ioannis Tamvakis, Wouter Kohlen, Paul C. E. Bailey, Aaron Thomas, Jakub Lupták, Ramakrishnan Karunakaran, Matthew D. Carpenter et al. · 2019 · Current Biology
39. Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development
    Marques, Sueli, van Bruggen, David, Vanichkina, Darya Pavlovna, Floriddia, Elisa Mariagrazia, Munguba, Hermany, Väremo, Leif, Giacomello, Stefania, Falcão, Ana Mendanha, Meijer, Mandy, Björklund, Åsa Kristina et al. · 2018 · Developmental Cell
40. Thymic tuft cells promote an IL-4-enriched medulla and shape thymocyte development
    Miller, Corey N., Proekt, Irina, von Moltke, Jakob, Wells, Kristen L., Rajpurkar, Aparna R., Wang, Haiguang, Rattay, Kristin, Khan, Imran S., Metzger, Todd C., Pollack, Joshua L. et al. · 2018 · Nature
41. An atlas of β-glucuronidases in the human intestinal microbiome
    Pollet, Rebecca M., D'Agostino, Emma H., Walton, William G., Xu, Yongmei, Little, Michael S., Biernat, Kristen A., Pellock, Samuel J., Patterson, Loraine M., Creekmore, Benjamin C., Isenberg, Hanna N. et al. · 2017 · Structure
42. Thermophilic archaea activate butane via alkyl-coenzyme M formation
    Rafael Laso-Pérez, Gunter Wegener, Katrin Knittel, Friedrich Widdel, Katie J. Harding, Viola Krukenberg, Dimitri V. Meier, Michael Richter, Halina E. Tegetmeyer, Dietmar Riedel et al. · 2016 · Nature
43. F. nucleatum targets lncRNA ENO1-IT1 to promote glycolysis and oncogenesis in colorectal cancer
    Jie Hong, Fangfang Guo, Shiyuan Lu, Chaoqin Shen, Dan Ma, Xinyu Zhang, Yile Xie, Tingting Yan, TaChung Yu, Tiantian Sun et al. · 2020 · Gut
44. A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event
    Zheng Fan, Yuan Tao, Piao Liu, Lu-Yu Wang, Jian-Feng Jin, Feng Zhang, Zhi‐Sheng Zhang · 2021 · GigaScience
45. SARS-CoV-2 receptor and entry genes are expressed by sustentacular cells in the human olfactory neuroepithelium
    Fodoulian, Leon, Tuberosa, Joel, Rossier, Daniel, Boillat, Madlaina, Kan, Chenda, Pauli, Véronique, Egervari, Kristof, Lobrinus, Johannes A., Landis, Basile N., Carleton, Alan et al. · 2020
46. Commensal-driven immune zonation of the liver promotes host defence
    Anita Gola, Michael G. Dorrington, Emily E. Speranza, Claudia Sala, Rochelle M. Shih, Andrea J. Radtke, Harikesh S. Wong, António P. Baptista, Jonathan Matthew Hernandez, Gastone Castellani et al. · 2020 · Nature
47. PD-1-cis IL-2R agonism yields better effectors from stem-like CD8+ T cells
    Laura Codarri Deak, Valeria Nicolini, Masao Hashimoto, Maria Karagianni, Petra Catalina Schwalie, Laura Lauener, Eleni Maria Varypataki, Marine Richard, Esther Bommer, Johannes Sam et al. · 2022 · Nature
48. Transposable elements are the primary source of novelty in primate gene regulation
    Marco Trizzino, YoSon Park, Márcia Holsbach Beltrame, Katherine A Aracena, Katelyn M. Mika, Minal Çalışkan, George H. Perry, Vincent J. Lynch, Christopher D. Brown · 2017 · Genome Research
49. LAG-3 Inhibitory Receptor Expression Identifies Immunosuppressive Natural Regulatory Plasma Cells
    Andreia C. Lino, Van Duc Dang, Vicky Lampropoulou, Anna Welle, Jara J. Joedicke, Jelka Pohar, Quentin Simon, Jessie Thalmensi, Aurélia Baures, Vinciane Flühler et al. · 2018 · Immunity
50. Generation and persistence of human tissue-resident memory T cells in lung transplantation
    Mark E. Snyder, Michael O. Finlayson, Thomas J. Connors, Pranay Dogra, Takashi Senda, Erin C. Bush, Dustin J. Carpenter, Charles C. Marboe, Luke J. Benvenuto, Lori Shah et al. · 2019 · Science Immunology
51. SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples
    Ze Zhang, Danni Luo, Xue Yun Zhong, Jin Huk Choi, Yuanqing Ma, Stacy Wang, Elena Mahrt, Wei Guo, Eric W. Stawiski, Zora D. Modrusan et al. · 2019 · Genes
52. Rare driver mutations in head and neck squamous cell carcinomas converge on NOTCH signaling
    Sampath K. Loganathan, Krista Schleicher, Ahmad Malik, Rene Quevedo, Ellen R. Langille, Katie Teng, Robin Hyunseo Oh, Bhavisha Rathod, Ricky Tsai, Payman Samavarchi‐Tehrani et al. · 2020 · Science
53. Long-term perturbation of the peripheral immune system months after SARS-CoV-2 infection
    Feargal J. Ryan, Christopher M. Hope, Makutiro Ghislain Masavuli, Miriam Anne Lynn, Zelalem Addis Mekonnen, Arthur Eng Lip Yeow, Pablo García-Valtanen, Zahraa Al-Delfi, Jason Gummow, Catherine Craun Ferguson et al. · 2022 · BMC Medicine
54. Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer
    Parolia, Abhijit, Cieslik, Marcin, Chu, Shih-Chun, Xiao, Lanbo, Ouchi, Takahiro, Zhang, Yuping, Wang, Xiaoju, Vats, Pankaj, Cao, Xuhong, Pitchiaya, Sethuramasundaram et al. · 2019 · Nature
55. Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs
    Tetsutaro Hayashi, Haruka Ozaki, Yohei Sasagawa, Mana Umeda, Hiroki Danno, Itoshi Nikaido · 2018 · Nature Communications
56. Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma
    Jasper Wouters, Zeynep Kalender Atak, Liesbeth Minnoye, Katina I. Spanier, Maxime De Waegeneer, Carmen Bravo González‐Blas, David Mauduit, Kristofer Davie, Gert J. Hulselmans, Ahmad Najem et al. · 2020 · Nature Cell Biology
57. The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants
    Anders B. Dohlman, Diana Arguijo Mendoza, Shengli Ding, Michael C. Gao, Holly Kloos Dressman, Iliyan Dimitrov Iliev, Steven M. Lipkin, Xiling Shen · 2021 · Cell Host & Microbe
58. Reconstruction of the human blood–brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes
    Blanchard, Joel W., Bula, Michael, Davila-Velderrain, Jose, Akay, Leyla Anne, Zhu, Lena, Frank, Alexander, Victor, Matheus B., Bonner, Julia Maeve, Mathys, Hansruedi, Lin, Yuan-Ta et al. · 2020 · Nature Medicine
59. Monosomes actively translate synaptic mRNAs in neuronal processes
    Anne Biever, Caspar Glock, Georgi Tushev, Elena Ciirdaeva, Tamas Dalmay, Julian D. Langer, Erin Margaret Schuman · 2020 · Science
60. Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis
    Florian J. Weisel, Steven J. Mullett, Rebecca A. Elsner, Ashley V. Menk, Nikita H Trivedi, Wei Luo, Daniel J. Wikenheiser, William F. Hawse, Maria D. Chikina, Shuchi Smita et al. · 2020 · Nature Immunology
61. The stepwise assembly of the neonatal virome is modulated by breastfeeding
    Guanxiang Liang, Chunyu Zhao, Huanjia Zhang, Lisa M. Mattei, Scott A. Sherrill-Mix, Kyle L. Bittinger, Lyanna R. Kessler, Gary D. Wu, Robert N. Baldassano, Patricia A. DeRusso et al. · 2020 · Nature
62. Pathogen-Induced TLR4-TRIF Innate Immune Signaling in Hematopoietic Stem Cells Promotes Proliferation but Reduces Competitive Fitness
    Hitoshi Takizawa, Kristin Fritsch, Larisa V. Kovtonyuk, Yasuyuki Saito, Chakradhar Yakkala, Kurt Jacobs, Akshay Kumar Ahuja, Massimo Lopes, Annika Hausmann, Wolf‐Dietrich Hardt et al. · 2017 · Cell stem cell
63. A compendium of genetic regulatory effects across pig tissues
    Jinyan Teng, Yahui Gao, Hongwei Holly Yin, Zhonghao Bai, Shuli Liu, Haonan Zeng, Lijing Bai, Zexi Cai, Bingru Zhao, Xiujin Li et al. · 2024 · Nature Genetics
64. Prolonged sleep deprivation induces a cytokine-storm-like syndrome in mammals
    Di Sang, Keteng Lin, Yini Yang, Guangdi Ran, Bohan Li, Chen Chen, Qi Li, Yan Ma, Lihui Lu, Xi‐Yang Cui et al. · 2023 · Cell
65. Selection of GalNAc-conjugated siRNAs with limited off-target-driven rat hepatotoxicity
    Janas, Maja M., Schlegel, Mark K., Harbison, Carole E., Yilmaz, Vedat O., Jiang, Yongfeng, Parmar, Rubina, Zlatev, Ivan, Castoreno, Adam, Xu, Huilei, Shulga-Morskaya, Svetlana et al. · 2018 · Nature Communications
66. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
    Ling Xu, Zhaobin Dong, Dawn M. Chiniquy, Grady Pierroz, Siwen Deng, Cheng Da Gao, Spencer Diamond, Tuesday Simmons, Heidi M.‐L. Wipf, Daniel F. Caddell et al. · 2021 · Nature Communications
67. Human Pluripotent Stem Cell-Derived Organoids as Models of Liver Disease
    Ramli, Muhammad Nadzim Bin, Lim, Yee Siang, Koe, Chwee Tat, Demircioglu, Deniz, Tng, Weiquan, Gonzales, Kevin Andrew Uy, Tan, Cheng Peow, Szczerbinska, Iwona, Liang, Hongqing, Soe, Einsi Lynn et al. · 2020 · Gastroenterology
68. Single-Cell Multiomics Sequencing Reveals Prevalent Genomic Alterations in Tumor Stromal Cells of Human Colorectal Cancer
    Yuan Zhou, Shuhui Bian, Xin Zhou, Yueli Cui, Wendong Wang, Lu Wen, Limei Guo, Wei Fu, Fuchou Tang · 2020 · Cancer Cell
69. The neurotranscriptome of the Aedes aegypti mosquito
    Benjamin John Matthews, Carolyn S. McBride, Matthew DeGennaro, Orion Despo, Leslie B. Vosshall · 2016 · BMC Genomics
70. Heat stress directly impairs gut integrity and recruits distinct immune cell populations into the bovine intestine
    Franziska Koch, Ulrike Thom, Elke Albrecht, Rosemarie Weikard, Wietje Nolte, Björn Kuhla, Christa Kuehn · 2019 · Proceedings of the National Academy of Sciences
71. Microglia and macrophages promote corralling, wound compaction and recovery after spinal cord injury via Plexin-B2
    Zhou, Xiang, Wahane, Shalaka, Friedl, Marie-Sophie, Kluge, Michael, Friedel, Caroline C., Avrampou, Kleopatra, Zachariou, Venetia, Guo, Lei, Zhang, Bin, He, Xijing et al. · 2020 · Nature Neuroscience
72. Neutrophil extracellular traps formed during chemotherapy confer treatment resistance via TGF-β activation
    Alexandra Mousset, Enora Lecorgne, Isabelle Bourget, Pascal Lopez, Kitti Jenovai, Julien Cherfils‐Vicini, Chloé Dominici, Géraldine Rios, Cédric Girard-Riboulleau, Bodu Liu et al. · 2023 · Cancer Cell
73. Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines
    Cano-Gamez, Kiki, Soskic, Blagoje, Roumeliotis, Theodoros I., So, Ernest, Smyth, Deborah J., Baldrighi, Marta, Willé, David, Nakic, Nikolina, Esparza-Gordillo, Jorge, Larminie, Christopher G. C. et al. · 2020 · Nature Communications
74. Myocardial infarction accelerates breast cancer via innate immune reprogramming
    Graeme J. Koelwyn, Alexandra A. C. Newman, Milessa Silva Afonso, Coen V Solingen, Emma M. Corr, Emily J. Brown, Kathleen B. Albers, Naoko Yamaguchi, Deven Narke, Martin Schlegel et al. · 2020 · Nature Medicine
75. Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer
    Jae-Won Cho, Min Hee Hong, Sang‐Jun Ha, Young‐Joon Kim, Byoung Chul Cho, Insuk Lee, Hye Ryun Kim · 2020 · Experimental & Molecular Medicine
76. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses
    Xu, Heping, Ding, Jiarui, Porter, Caroline B.M., Wallrapp, Antonia, Tabaka, Marcin, Ma, Sai, Fu, Shujie, Guo, Xuanxuan, Riesenfeld, Samantha J., Su, Chienwen et al. · 2019 · Immunity
77. Novel antigen-presenting cell imparts Treg-dependent tolerance to gut microbiota
    Akagbosu, Blossom, Tayyebi, Zakieh, Shibu, Gayathri, Paucar Iza, Yoselin A., Deep, Deeksha, Parisotto, Yollanda Franco, Fisher, Logan, Pasolli, H. Amalia, Thevin, Valentin, Elmentaite, Rasa et al. · 2022 · Nature
78. Hacking macrophage-associated immunosuppression for regulating glioblastoma angiogenesis
    Xin Cui, Renee‐Tyler T. Morales, Weiyi Qian, Haoyu Wang, Jean‐Pierre Gagner, Igor Dolgalev, Dimitris G. Placantonakis, David Zagzag, Luisa Cimmino, Matija Snuderl et al. · 2018 · Biomaterials
79. A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes
    Charlotte Soneson, Yao Yao, Anna Bratus-Neuenschwander, Andrea Patrignani, Mark D. Robinson, Shobbir Hussain · 2019 · Nature Communications
80. Identification of a choroid plexus vascular barrier closing during intestinal inflammation
    Sara Carloni, Alice Bertocchi, Sara Mancinelli, Martina Bellini, Marco Erreni, Antonella Borreca, Daniele Braga, Silvia Giugliano, Alessandro Mauro Mozzarelli, Daria Manganaro et al. · 2021 · Science
81. KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements
    Zhang, Shang-Min, Cai, Wesley L., Liu, Xiaoni, Thakral, Durga, Luo, Jiesi, Chan, Lok Hei, McGeary, Meaghan K., Song, Eric, Blenman, Kim R. M., Micevic, Goran et al. · 2021 · Nature
82. pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
    Fédérico Marini, Harald Binder · 2019 · BMC Bioinformatics
83. Personalized neoantigen pulsed dendritic cell vaccine for advanced lung cancer
    Zhenyu Ding, Qing Li, Rui Zhang, Li Xie, Yang Shu, Song Gao, Peipei Wang, Xiaoqing Su, Yun Qin, Yuelan Wang et al. · 2021 · Signal Transduction and Targeted Therapy
84. Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
    Avi Srivastava, Laraib Iqbal Malik, Tom S. Smith, Ian M. Sudbery, Rob Patro · 2019 · Genome biology
85. Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21
    Dae-Seok Kim, Cristel V. Camacho, Anusha Nagari, Venkat S. Malladi, Sridevi Challa, W. Lee Kraus · 2019 · Molecular Cell
86. Inhibition of fatty acid oxidation enables heart regeneration in adult mice
    Xiang Li, Fan Wu, Stefan Günther, Mario Looso, Carsten Tobias Kuenne, Ting Zhang, Marion Wiesnet, Stephan Klatt, Sven Zukunft, Ingrid Fleming et al. · 2023 · Nature
87. Inflammatory macrophage dependence on NAD+ salvage is a consequence of reactive oxygen species–mediated DNA damage
    Cameron, Alanna M., Castoldi, Angela, Sanin, David E., Flachsmann, Lea J., Field, Cameron S., Puleston, Daniel. J., Kyle, Ryan L., Patterson, Annette E., Hässler, Fabian, Buescher, Joerg M. et al. · 2019 · Nature Immunology
88. Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes
    Irene Miguel-Escalada, Sílvia Bonàs‐Guarch, Inês Cebola, Joan Ponsa-Cobas, Julen Mendieta-Esteban, Goutham Atla, Biola M. Javierre, Delphine Rolando, Irene Farabella, Claire C. Morgan et al. · 2019 · Nature Genetics
89. recount3: summaries and queries for large-scale RNA-seq expression and splicing
    Christopher Wilks, Shijie Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie L. Imada, David Zhang, Lance Joseph, Jeffrey T. Leek et al. · 2021 · Genome biology
90. An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence
    Eugen Dhimolea, Ricardo De Matos Simoes, Dhvanir N. Kansara, Aziz M. Al’Khafaji, Juliette Bouyssou, Xiang Weng, Shruti Sharma, Joseline Raja, Pallavi Awate, Ryosuke Shirasaki et al. · 2021 · Cancer Cell
91. Activating a collaborative innate-adaptive immune response to control metastasis
    Lijuan Sun, Tim Kees, Ana Santos Almeida, Bodu Liu, Xue‐Yan He, David Chee‐Eng Ng, Xiao Han, David L. Spector, Iain A. McNeish, Phyllis A. Gimotty et al. · 2021 · Cancer Cell
92. Germline Chd8 haploinsufficiency alters brain development in mouse
    Gompers, Andrea L, Su-Feher, Linda, Ellegood, Jacob, Copping, Nycole A, Riyadh, M Asrafuzzaman, Stradleigh, Tyler W, Pride, Michael C, Schaffler, Melanie D, Wade, A Ayanna, Catta-Preta, Rinaldo et al. · 2017 · Nature Neuroscience
93. The macrophage IRF8/IRF1 regulome is required for protection against infections and is associated with chronic inflammation
    David Langlais, Luis Bruno Barreiro, Philippe Gros · 2016 · The Journal of Experimental Medicine
94. Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere
    Yan Yan, Eiko E. Kuramae, Mattias de Hollander, Peter G. L. Klinkhamer, Johannes A. van Veen · 2016 · The ISME Journal
95. Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity
    Ivan Carcamo‐Orive, Gabriel E. Hoffman, Paige Cundiff, Noam D. Beckmann, Sunita L. D’Souza, Joshua W. Knowles, Achchhe Patel, Caroline Hendry, Dimitri Papatsenko, Fahim Abbasi et al. · 2016 · Cell stem cell
96. The impact of amplification on differential expression analyses by RNA-seq
    Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann · 2016 · Scientific Reports
97. Initiation of a conserved trophectoderm program in human, cow and mouse embryos
    Claudia Gerri, Afshan McCarthy, Gregorio Alanis‐Lobato, Andrej Demtschenko, Alexandre Bruneau, Sophie Loubersac, Norah M. E. Fogarty, Daniel Hampshire, Kay T. Elder, Phil Snell et al. · 2020 · Nature
98. H3.3K27M Cooperates with Trp53 Loss and PDGFRA Gain in Mouse Embryonic Neural Progenitor Cells to Induce Invasive High-Grade Gliomas
    Pathania, Manav, De Jay, Nicolas, Maestro, Nicola, Harutyunyan, Ashot S., Nitarska, Justyna, Pahlavan, Pirasteh, Henderson, Stephen, Mikael, Leonie G., Richard-Londt, Angela, Zhang, Ying et al. · 2017 · Cancer Cell
99. Evaluation of variability in human kidney organoids
    Belinda Phipson, Pei Xuan Er, Alexander N. Combes, Thomas A. Forbes, Sara E. Howden, Luke Zappia, Hsan-Jan Yen, Kynan T. Lawlor, Lorna J. Hale, Jane Q. J. Sun et al. · 2018 · Nature Methods
100. MYB orchestrates T cell exhaustion and response to checkpoint inhibition
     Carlson Tsui, Lorenz Kretschmer, Svenja Rapelius, Sarah S. Gabriel, David Chisanga, Konrad Knöpper, Daniel T. Utzschneider, Simone Nüssing, Yang Liao, Teisha Mason et al. · 2022 · Nature