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For: Schmid MW, Grossniklaus U. Rcount: simple and flexible RNA-Seq read counting. Bioinformatics 2014;31:436-7. [PMID: 25322836 DOI: 10.1093/bioinformatics/btu680] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Morrissey A, Shi J, James DQ, Mahony S. Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome Res 2024;34:937-951. [PMID: 38986578 PMCID: PMC11293539 DOI: 10.1101/gr.278638.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/14/2024] [Indexed: 07/12/2024]
2
Kobiita A, Silva PN, Schmid MW, Stoffel M. FoxM1 coordinates cell division, protein synthesis, and mitochondrial activity in a subset of β cells during acute metabolic stress. Cell Rep 2023;42:112986. [PMID: 37590136 DOI: 10.1016/j.celrep.2023.112986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/06/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023]  Open
3
Roganowicz M, Bär D, Bersaglieri C, Aprigliano R, Santoro R. BAZ2A-RNA mediated association with TOP2A and KDM1A represses genes implicated in prostate cancer. Life Sci Alliance 2023;6:e202301950. [PMID: 37184661 PMCID: PMC10130768 DOI: 10.26508/lsa.202301950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]  Open
4
Deshpande D, Chhugani K, Chang Y, Karlsberg A, Loeffler C, Zhang J, Muszyńska A, Munteanu V, Yang H, Rotman J, Tao L, Balliu B, Tseng E, Eskin E, Zhao F, Mohammadi P, P. Łabaj P, Mangul S. RNA-seq data science: From raw data to effective interpretation. Front Genet 2023;14:997383. [PMID: 36999049 PMCID: PMC10043755 DOI: 10.3389/fgene.2023.997383] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/24/2023] [Indexed: 03/14/2023]  Open
5
Francine P. Systems Biology: New Insight into Antibiotic Resistance. Microorganisms 2022;10:2362. [PMID: 36557614 PMCID: PMC9781975 DOI: 10.3390/microorganisms10122362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]  Open
6
Liu X, Zhao J, Xue L, Zhao T, Ding W, Han Y, Ye H. A comparison of transcriptome analysis methods with reference genome. BMC Genomics 2022;23:232. [PMID: 35337265 PMCID: PMC8957167 DOI: 10.1186/s12864-022-08465-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/08/2022] [Indexed: 11/10/2022]  Open
7
Wang H, Feng X, Muhatai G, Wang L. Expression profile analysis of sheep ovary after superovulation and estrus synchronisation treatment. Vet Med Sci 2022;8:1276-1287. [PMID: 35305293 PMCID: PMC9122410 DOI: 10.1002/vms3.783] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
8
Peña-Hernández R, Aprigliano R, Carina Frommel S, Pietrzak K, Steiger S, Roganowicz M, Lerra L, Bizzarro J, Santoro R. BAZ2A-mediated repression via H3K14ac-marked enhancers promotes prostate cancer stem cells. EMBO Rep 2021;22:e53014. [PMID: 34403195 PMCID: PMC8567280 DOI: 10.15252/embr.202153014] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/09/2022]  Open
9
OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. Nat Protoc 2020;16:728-753. [PMID: 33361798 DOI: 10.1038/s41596-020-00430-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 09/28/2020] [Indexed: 12/20/2022]
10
Dalcher D, Tan JY, Bersaglieri C, Peña‐Hernández R, Vollenweider E, Zeyen S, Schmid MW, Bianchi V, Butz S, Roganowicz M, Kuzyakiv R, Baubec T, Marques AC, Santoro R. BAZ2A safeguards genome architecture of ground-state pluripotent stem cells. EMBO J 2020;39:e105606. [PMID: 33433018 PMCID: PMC7705451 DOI: 10.15252/embj.2020105606] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/30/2022]  Open
11
Eghbalnia HR, Wilfinger WW, Mackey K, Chomczynski P. Coordinated analysis of exon and intron data reveals novel differential gene expression changes. Sci Rep 2020;10:15669. [PMID: 32973253 PMCID: PMC7515875 DOI: 10.1038/s41598-020-72482-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]  Open
12
Nikolaou KC, Vatandaslar H, Meyer C, Schmid MW, Tuschl T, Stoffel M. The RNA-Binding Protein A1CF Regulates Hepatic Fructose and Glycerol Metabolism via Alternative RNA Splicing. Cell Rep 2020;29:283-300.e8. [PMID: 31597092 DOI: 10.1016/j.celrep.2019.08.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/09/2019] [Accepted: 08/29/2019] [Indexed: 01/11/2023]  Open
13
Deschamps-Francoeur G, Simoneau J, Scott MS. Handling multi-mapped reads in RNA-seq. Comput Struct Biotechnol J 2020;18:1569-1576. [PMID: 32637053 PMCID: PMC7330433 DOI: 10.1016/j.csbj.2020.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/06/2020] [Accepted: 06/07/2020] [Indexed: 11/07/2022]  Open
14
Liao Y, Smyth GK, Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res 2019;47:e47. [PMID: 30783653 PMCID: PMC6486549 DOI: 10.1093/nar/gkz114] [Citation(s) in RCA: 1678] [Impact Index Per Article: 279.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 01/02/2019] [Accepted: 02/13/2019] [Indexed: 11/29/2022]  Open
15
Caldelari R, Dogga S, Schmid MW, Franke-Fayard B, Janse CJ, Soldati-Favre D, Heussler V. Transcriptome analysis of Plasmodium berghei during exo-erythrocytic development. Malar J 2019;18:330. [PMID: 31551073 PMCID: PMC6760107 DOI: 10.1186/s12936-019-2968-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022]  Open
16
Krattinger SG, Kang J, Bräunlich S, Boni R, Chauhan H, Selter LL, Robinson MD, Schmid MW, Wiederhold E, Hensel G, Kumlehn J, Sucher J, Martinoia E, Keller B. Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34. THE NEW PHYTOLOGIST 2019;223:853-866. [PMID: 30913300 PMCID: PMC6618152 DOI: 10.1111/nph.15815] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/20/2019] [Indexed: 05/10/2023]
17
Grob S, Grossniklaus U. Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana. Genome Biol 2019;20:120. [PMID: 31186073 PMCID: PMC6560877 DOI: 10.1186/s13059-019-1722-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/22/2019] [Indexed: 01/05/2023]  Open
18
Jin Y, Chen G, Xiao W, Hong H, Xu J, Guo Y, Xiao W, Shi T, Shi L, Tong W, Ning B. Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine. SCIENCE CHINA-LIFE SCIENCES 2019;62:895-904. [PMID: 31114935 DOI: 10.1007/s11427-018-9479-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022]
19
Hou JY, Wu HY, He RQ, Lin P, Dang YW, Chen G. Clinical and prognostic value of chaperonin containing T-complex 1 subunit 3 in hepatocellular carcinoma: A Study based on microarray and RNA-sequencing with 4272 cases. Pathol Res Pract 2018;215:177-194. [PMID: 30473171 DOI: 10.1016/j.prp.2018.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 10/25/2018] [Accepted: 11/06/2018] [Indexed: 12/27/2022]
20
Lippuner C, Ramakrishnan C, Basso WU, Schmid MW, Okoniewski M, Smith NC, Hässig M, Deplazes P, Hehl AB. RNA-Seq analysis during the life cycle of Cryptosporidium parvum reveals significant differential gene expression between proliferating stages in the intestine and infectious sporozoites. Int J Parasitol 2018;48:413-422. [DOI: 10.1016/j.ijpara.2017.10.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 10/21/2017] [Indexed: 10/18/2022]
21
Schmid MW. RNA-Seq Data Analysis Protocol: Combining In-House and Publicly Available Data. Methods Mol Biol 2017;1669:309-335. [PMID: 28936668 DOI: 10.1007/978-1-4939-7286-9_24] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
22
Consiglio A, Mencar C, Grillo G, Marzano F, Caratozzolo MF, Liuni S. A fuzzy method for RNA-Seq differential expression analysis in presence of multireads. BMC Bioinformatics 2016;17:345. [PMID: 28185579 PMCID: PMC5123383 DOI: 10.1186/s12859-016-1195-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
23
Improved Placement of Multi-mapping Small RNAs. G3 (BETHESDA, MD.) 2016. [PMID: 27175019 DOI: 10.1534/g3.116.030452.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
24
Improved Placement of Multi-mapping Small RNAs. G3-GENES GENOMES GENETICS 2016;6:2103-11. [PMID: 27175019 PMCID: PMC4938663 DOI: 10.1534/g3.116.030452] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
25
Schuierer S, Roma G. The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data. Nucleic Acids Res 2016;44:e132. [PMID: 27302131 PMCID: PMC5027495 DOI: 10.1093/nar/gkw538] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 06/04/2016] [Indexed: 01/24/2023]  Open
26
Schmid MW, Schmidt A, Grossniklaus U. The female gametophyte: an emerging model for cell type-specific systems biology in plant development. FRONTIERS IN PLANT SCIENCE 2015;6:907. [PMID: 26579157 PMCID: PMC4630298 DOI: 10.3389/fpls.2015.00907] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/10/2015] [Indexed: 05/03/2023]
27
Spies D, Ciaudo C. Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis. Comput Struct Biotechnol J 2015;13:469-77. [PMID: 26430493 PMCID: PMC4564389 DOI: 10.1016/j.csbj.2015.08.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 12/17/2022]  Open
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