Salmon provides fast and bias-aware quantification of transcript expression

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Items 101–141 of 141

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3. A clinically applicable gene-expression classifier reveals intrinsic and extrinsic contributions to consensus molecular subtypes in primary and metastatic colon cancer
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   The Dominantly Inherited Alzheimer Network (DIAN), Li, Zeran, Del-Aguila, Jorge L., Dube, Umber, Budde, John, Martinez, Rita, Black, Kathleen, Xiao, Qingli, Cairns, Nigel J., Dougherty, Joseph D. et al. · 2018 · Genome Medicine
5. Aberrant RNA methylation triggers recruitment of an alkylation repair complex
   Tsao, Ning, Brickner, Joshua R., Rodell, Rebecca, Ganguly, Adit, Wood, Matthew, Oyeniran, Clement, Ahmad, Tanveer, Sun, Hua, Bacolla, Albino, Zhang, Lisheng et al. · 2021 · Molecular Cell
6. New insights into diosgenin biosynthesis pathway and its regulation in <scp> <i>Trigonella foenum‐graecum</i> </scp> L.
   Mohammadi, Mohammad, Mashayekh, Tooba, Rashidi‐Monfared, Sajad, Ebrahimi, Amin, Abedini, Davar · 2020 · Phytochemical Analysis
7. Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses
   Sardar, Puspendu, Beresford-Jones, Benjamin S., Xia, Wangmingyu, Shabana, Omar, Suyama, Satoshi, Ramos, Ruben J. F., Soderholm, Amelia T., Tourlomousis, Panagiotis, Kuo, Paula, Evans, Alexander C. et al. · 2025 · Nature Microbiology
8. Androgen signaling uses a writer and a reader of ADP-ribosylation to regulate protein complex assembly
   Yang, Chun-Song, Jividen, Kasey, Kamata, Teddy, Dworak, Natalia, Oostdyk, Luke, Remlein, Bartlomiej, Pourfarjam, Yasin, Kim, In-Kwon, Du, Kang-Ping, Abbas, Tarek et al. · 2021 · Nature Communications
9. Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis
   Tian, Ruilin, Abarientos, Anthony, Hong, Jason, Hashemi, Sayed Hadi, Yan, Rui, Dräger, Nina, Leng, Kun, Nalls, Mike A., Singleton, Andrew B., Xu, Ke et al. · 2020
10. Transcriptome dynamics over a lunar month in a broadcast spawning acroporid coral
    Oldach, Matthew J., Workentine, Matthew, Matz, Mikhail V., Fan, Tung‐Yung, Vize, Peter D. · 2017 · Molecular Ecology
11. Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissue
    Holzscheck, Nicholas, Söhle, Jörn, Kristof, Boris, Grönniger, Elke, Gallinat, Stefan, Wenck, Horst, Winnefeld, Marc, Falckenhayn, Cassandra, Kaderali, Lars · 2020 · Aging
12. Highly accurate isoform identification for the human transcriptome
    Sommer, Markus J., Cha, Sooyoung, Varabyou, Ales, Rincon, Natalia, Park, Sukhwan, Minkin, Ilia, Pertea, Mihaela, Steinegger, Martin, Salzberg, Steven L. · 2022
13. Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton
    Alexander, Harriet, Hu, Sarah K., Krinos, Arianna I., Pachiadaki, Maria, Tully, Benjamin J., Neely, Christopher J., Reiter, Taylor · 2021
14. Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency
    Jakab, Moritz, Lee, Ki Hong, Uvarovskii, Alexey, Ovchinnikova, Svetlana, Kulkarni, Shubhada R., Jakab, Sevinç, Rostalski, Till, Spegg, Carleen, Anders, Simon, Augustin, Hellmut G. · 2024 · Nature Cancer
15. CRISPRi-based screen of autism spectrum disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning
    Teter, Olivia M., McQuade, Amanda, Hagan, Venus, Liang, Weiwei, Dräger, Nina M., Sattler, Sydney M., Holmes, Brandon B., Castillo, Vincent Cele, Papakis, Vasileios, Leng, Kun et al. · 2025 · Molecular Psychiatry
16. Nuclear actin structure regulates chromatin accessibility
    Sen, Buer, Xie, Zhihui, Thomas, Michelle D., Pattenden, Samantha G., Howard, Sean, McGrath, Cody, Styner, Maya, Uzer, Gunes, Furey, Terrence S., Rubin, Janet · 2024 · Nature Communications
17. X chromosome dosage and the genetic impact across human tissues
    Viuff, Mette, Skakkebæk, Anne, Johannsen, Emma B., Chang, Simon, Pedersen, Steen Bønlykke, Lauritsen, Katrine Meyer, Pedersen, Mette Glavind Bülow, Trolle, Christian, Just, Jesper, Gravholt, Claus H. · 2023 · Genome Medicine
18. Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity
    Katsuda, Takeshi, Sussman, Jonathan H., Ito, Kenji, Katznelson, Andrew, Yuan, Salina, Takenaka, Naomi, Li, Jinyang, Merrell, Allyson J., Cure, Hector, Li, Qinglan et al. · 2024 · Nature Communications
19. Single-cell transcriptomic analysis of retinal immune regulation and blood-retinal barrier function during experimental autoimmune uveitis
    Quinn, Joel, Salman, Ahmed, Paluch, Christopher, Jackson-Wood, Matthew, McClements, Michelle E., Luo, Jian, Davis, Simon J., Cornall, Richard J., MacLaren, Robert E., Dendrou, Calliope A. et al. · 2024 · Scientific Reports
20. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement
    LaFlamme, Christy W., Rastin, Cassandra, Sengupta, Soham, Pennington, Helen E., Russ-Hall, Sophie J., Schneider, Amy L., Bonkowski, Emily S., Almanza Fuerte, Edith P., Allan, Talia J., Zalusky, Miranda Perez-Galey et al. · 2024 · Nature Communications
21. Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influence on MEF2-dependent transcription
    Minisini, Martina, Di Giorgio, Eros, Kerschbamer, Emanuela, Dalla, Emiliano, Faggiani, Massimo, Franforte, Elisa, Meyer-Almes, Franz-Josef, Ragno, Rino, Antonini, Lorenzo, Mai, Antonello et al. · 2022 · Nucleic Acids Research
22. Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells
    Poisa-Beiro, Laura, Thoma, Judith, Landry, Jonathan, Sauer, Sven, Yamamoto, Akihisa, Eckstein, Volker, Romanov, Natalie, Raffel, Simon, Hoffmann, Georg F., Bork, Peer et al. · 2020 · Scientific Reports
23. A Fibrosis-Independent hepatic transcriptomic signature identifies drivers of disease progression in primary sclerosing cholangitis
    Gindin, Yevgeniy, Chung, Chuhan, Jiang, Zhaoshi, Zhou, Jing Zhu, Xu, Jun, Billin, Andrew N., Myers, Robert P., Goodman, Zachary, Landi, Abdolamir, Houghton, Michael et al. · 2021 · Hepatology
24. TET2-mutant myeloid cells mitigate Alzheimer’s disease progression via CNS infiltration and enhanced phagocytosis in mice
    Matatall, Katie A., Wathan, Trisha K., Nguyen, Minh, Chen, Hu, McDonald, Alexandra, Qi, Guantong, Belk, Julia A., Florez, Marcus A., Le, Duy T., Olarinde, Temitope et al. · 2025 · Cell Stem Cell
25. Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development
    Chakraborty, Shreeta, Wenzlitschke, Nina, Anderson, Matthew J., Eraso, Ariel, Baudic, Manon, Thompson, Joyce J., Evans, Alicia A., Shatford-Adams, Lilly M., Chari, Raj, Awasthi, Parirokh et al. · 2025 · Developmental Cell
26. Complement factor B is critical for sub-RPE deposit accumulation in a model of Doyne honeycomb retinal dystrophy with features of age-related macular degeneration
    Crowley, Maura A, Garland, Donita L, Sellner, Holger, Banks, Angela, Fan, Lin, Rejtar, Tomas, Buchanan, Natasha, Delgado, Omar, Xu, Yong Yao, Jose, Sandra et al. · 2023 · Human Molecular Genetics
27. Using transcriptomics to examine the physiological status of wild-caught walleye (<i>Sander vitreus</i>)
    Jeffrey, Jennifer D., Thorstensen, Matt J., Enders, Eva C., Treberg, Jason R., Jeffries, Ken M. · 2023 · FACETS
28. Chronic Psychological Stress Alters Gene Expression in Rat Colon Epithelial Cells Promoting Chromatin Remodeling, Barrier Dysfunction and Inflammation
    Wiley, John W., Higgins, Gerald A., Hong, Shuangsong · 2022 · PeerJ
29. Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body
    Chia, Minghao, Ng, Amanda Hui Qi, Ravikrishnan, Aarthi, Mohamed Naim, Ahmad Nazri, Wearne, Stephen, Common, John, Nagarajan, Niranjan · 2026 · Nature Biotechnology
30. Rare genetic variants confer a high risk of ADHD and implicate neuronal biology
    Demontis, Ditte, Duan, Jinjie, Hsu, Yu-Han H., Pintacuda, Greta, Grove, Jakob, Nielsen, Trine Tollerup, Thirstrup, Janne, Martorana, Makayla, Botts, Travis, Satterstrom, F. Kyle et al. · 2026 · Nature
31. Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon
    Fefelova, Elena A, Pleshakova, Irina M, Mikhaleva, Elena A, Pirogov, Sergei A, Poltorachenko, Valentin A, Abramov, Yuri A, Romashin, Daniil D, Shatskikh, Aleksei S, Blokh, Roman S, Gvozdev, Vladimir A et al. · 2022 · Nucleic Acids Research
32. A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy
    Townley, Brittany A., Buerer, Luke, Tsao, Ning, Bacolla, Albino, Mansoori, Fadhel, Rusanov, Timur, Clark, Nathaniel E., Goodarzi, Negar, Schmidt, Nicolas, Srivatsan, Sridhar Nonavinkere et al. · 2023 · Molecular Cell
33. Solving for X: Evidence for sex‐specific autism biomarkers across multiple transcriptomic studies
    Lee, Samuel C., Quinn, Thomas P., Lai, Jerry, Kong, Sek Won, Hertz‐Picciotto, Irva, Glatt, Stephen J., Crowley, Tamsyn M., Venkatesh, Svetha, Nguyen, Thin · 2019 · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics
34. Telomeric 8-Oxoguanine Drives Rapid Premature Senescence In The Absence Of Telomere Shortening
    Barnes, Ryan P., de Rosa, Mariarosaria, Thosar, Sanjana A., Detwiler, Ariana C., Roginskaya, Vera, Van Houten, Bennett, Bruchez, Marcel P., Stewart-Ornstein, Jacob, Opresko, Patricia L. · 2021
35. 20-Hydroxyecdysone Boosts Energy Production and Biosynthetic Processes in Non-Transformed Mouse Cells
    Shuvalov, Oleg, Kirdeeva, Yulia, Fefilova, Elizaveta, Daks, Alexandra, Fedorova, Olga, Parfenyev, Sergey, Nazarov, Alexander, Vlasova, Yulia, Krasnov, George S., Barlev, Nick A. · 2024 · Antioxidants
36. PKD1 mutant clones within cirrhotic livers inhibit steatohepatitis without promoting cancer
    Zhu, Min, Wang, Yunguan, Lu, Tianshi, Guo, Jason, Li, Lin, Hsieh, Meng-Hsiung, Gopal, Purva, Han, Yi, Fujiwara, Naoto, Wallace, Darren P. et al. · 2024 · Cell Metabolism
37. Role of natural transformation in the evolution of small cryptic plasmids in <i>Synechocystis</i> sp. <scp>PCC</scp> 6803
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38. Intergenerational transport of double-stranded RNA in C. elegans can limit heritable epigenetic changes
    Shugarts Devanapally, Nathan M, Sathya, Aishwarya, Yi, Andrew L, Chan, Winnie M, Marre, Julia A, Jose, Antony M · 2025 · eLife
39. <i>TDP1</i> splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition
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40. A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation
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41. Study of blood linear RNA nominates <i>CD55</i> and <i>DLD</i> as early-stage biomarkers for Parkinson's disease
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