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For: Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, Lancet D, Shmueli O. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 2004;21:650-9. [PMID: 15388519 DOI: 10.1093/bioinformatics/bti042] [Citation(s) in RCA: 803] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
151
Santus L, Sopena-Rios M, García-Pérez R, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Melé M. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. Nat Commun 2023;14:3866. [PMID: 37391481 PMCID: PMC10313701 DOI: 10.1038/s41467-023-39627-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/19/2023] [Indexed: 07/02/2023]  Open
152
Wang W, Bo T, Zhang G, Li J, Ma J, Ma L, Hu G, Tong H, Lv Q, Araujo DJ, Luo D, Chen Y, Wang M, Wang Z, Wang GZ. Noncoding transcripts are linked to brain resting-state activity in non-human primates. Cell Rep 2023;42:112652. [PMID: 37335775 DOI: 10.1016/j.celrep.2023.112652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023]  Open
153
Peng J, Zhao L. The origin and structural evolution of de novo genes in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532420. [PMID: 37425675 PMCID: PMC10326970 DOI: 10.1101/2023.03.13.532420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
154
Xu X, Ma J, Li W, You Y, Jiang Q, Long P, Liu K, Mo T, Jiang J, Wang W, Lei Y, Diao T, Ruan S, Wang X, Guo H, Chen W, Wu T. Polycyclic aromatic hydrocarbons exposure and plasma lncRNA signature: A profile and functional analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023;877:162932. [PMID: 36934921 DOI: 10.1016/j.scitotenv.2023.162932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
155
Esposito R, Lanzós A, Uroda T, Ramnarayanan S, Büchi I, Polidori T, Guillen-Ramirez H, Mihaljevic A, Merlin BM, Mela L, Zoni E, Hovhannisyan L, McCluggage F, Medo M, Basile G, Meise DF, Zwyssig S, Wenger C, Schwarz K, Vancura A, Bosch-Guiteras N, Andrades Á, Tham AM, Roemmele M, Medina PP, Ochsenbein AF, Riether C, Kruithof-de Julio M, Zimmer Y, Medová M, Stroka D, Fox A, Johnson R. Tumour mutations in long noncoding RNAs enhance cell fitness. Nat Commun 2023;14:3342. [PMID: 37291246 PMCID: PMC10250536 DOI: 10.1038/s41467-023-39160-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/01/2023] [Indexed: 06/10/2023]  Open
156
Qian SH, Xiong YL, Chen L, Geng YJ, Tang XM, Chen ZX. Dynamic Spatial-temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:589-600. [PMID: 36031057 PMCID: PMC10787176 DOI: 10.1016/j.gpb.2022.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
157
Roberts M, Josephs EB. Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana. Genetics 2023;224:iyad074. [PMID: 37094602 PMCID: PMC10484170 DOI: 10.1093/genetics/iyad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/06/2023] [Accepted: 04/07/2023] [Indexed: 04/26/2023]  Open
158
Singh A, AT V, Gupta K, Sharma S, Kumar S. Long non-coding RNA and microRNA landscape of two major domesticated cotton species. Comput Struct Biotechnol J 2023;21:3032-3044. [PMID: 37266406 PMCID: PMC10229759 DOI: 10.1016/j.csbj.2023.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023]  Open
159
Yu D, Wu Y, Zhu L, Wang Y, Sheng D, Zhao X, Liang G, Gan L. The landscape of the long non-coding RNAs in developing mouse retinas. BMC Genomics 2023;24:252. [PMID: 37165305 PMCID: PMC10173636 DOI: 10.1186/s12864-023-09354-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023]  Open
160
Zhao Y, Zheng Z, Zhang Z, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of High-Molecular-Mass Hyaluronic Acid is Associated with Subterranean Lifestyle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539764. [PMID: 37215017 PMCID: PMC10197608 DOI: 10.1101/2023.05.08.539764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
161
Cridland JM, Contino CE, Begun DJ. Selection and geography shape male reproductive tract transcriptomes in Drosophila melanogaster. Genetics 2023;224:iyad034. [PMID: 36869688 PMCID: PMC10474930 DOI: 10.1093/genetics/iyad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023]  Open
162
Pan Z, Wang Y, Wang M, Wang Y, Zhu X, Gu S, Zhong C, An L, Shan M, Damas J, Halstead MM, Guan D, Trakooljul N, Wimmers K, Bi Y, Wu S, Delany ME, Bai X, Cheng HH, Sun C, Yang N, Hu X, Lewin HA, Fang L, Zhou H. An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. SCIENCE ADVANCES 2023;9:eade1204. [PMID: 37134160 PMCID: PMC10156120 DOI: 10.1126/sciadv.ade1204] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
163
Guillotin B, Rahni R, Passalacqua M, Mohammed MA, Xu X, Raju SK, Ramírez CO, Jackson D, Groen SC, Gillis J, Birnbaum KD. A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature 2023;617:785-791. [PMID: 37165193 PMCID: PMC10657638 DOI: 10.1038/s41586-023-06053-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
164
Marlétaz F, Timoshevskaya N, Timoshevskiy V, Simakov O, Parey E, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith J, Rokhsar DS. The hagfish genome and the evolution of vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537254. [PMID: 37131617 PMCID: PMC10153176 DOI: 10.1101/2023.04.17.537254] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
165
Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. PLANT PHYSIOLOGY 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
166
Zhao F, Yan Y, Wang Y, Liu Y, Yang R. Splicing complexity as a pivotal feature of alternative exons in mammalian species. BMC Genomics 2023;24:198. [PMID: 37046221 PMCID: PMC10099729 DOI: 10.1186/s12864-023-09247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023]  Open
167
Jones BM, Rubin BER, Dudchenko O, Kingwell CJ, Traniello IM, Wang ZY, Kapheim KM, Wyman ES, Adastra PA, Liu W, Parsons LR, Jackson SR, Goodwin K, Davidson SM, McBride MJ, Webb AE, Omufwoko KS, Van Dorp N, Otárola MF, Pham M, Omer AD, Weisz D, Schraiber J, Villanea F, Wcislo WT, Paxton RJ, Hunt BG, Aiden EL, Kocher SD. Convergent and complementary selection shaped gains and losses of eusociality in sweat bees. Nat Ecol Evol 2023;7:557-569. [PMID: 36941345 PMCID: PMC11610481 DOI: 10.1038/s41559-023-02001-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/18/2023] [Indexed: 03/23/2023]
168
Zeighami Y, Bakken TE, Nickl-Jockschat T, Peterson Z, Jegga AG, Miller JA, Schulkin J, Evans AC, Lein ES, Hawrylycz M. A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases. PLoS Biol 2023;21:e3002058. [PMID: 37079537 PMCID: PMC10118126 DOI: 10.1371/journal.pbio.3002058] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/02/2023] [Indexed: 04/21/2023]  Open
169
Zhang N, Zhang H, Liu Z, Dai Z, Wu W, Zhou R, Li S, Wang Z, Liang X, Wen J, Zhang X, Zhang B, Ouyang S, Zhang J, Luo P, Li X, Cheng Q. An artificial intelligence network-guided signature for predicting outcome and immunotherapy response in lung adenocarcinoma patients based on 26 machine learning algorithms. Cell Prolif 2023;56:e13409. [PMID: 36822595 PMCID: PMC10068958 DOI: 10.1111/cpr.13409] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/27/2022] [Accepted: 01/12/2023] [Indexed: 02/25/2023]  Open
170
Oh MR, Jung SJ, Chae SW, Park BH, Lee SO. Lycium chinense Miller fruit extract lowers liver enzyme levels in subjects with mild hepatic dysfunction: a randomized, double-blind, placebo-controlled clinical trial. Eur J Nutr 2023;62:1415-1425. [PMID: 36629892 DOI: 10.1007/s00394-022-03075-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023]
171
SMRT and Illumina sequencing provide insights into mechanisms of lignin and terpenoids biosynthesis in Pinus massoniana Lamb. Int J Biol Macromol 2023;232:123267. [PMID: 36657535 DOI: 10.1016/j.ijbiomac.2023.123267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
172
Stevanovic M, Kovacevic-Grujicic N, Petrovic I, Drakulic D, Milivojevic M, Mojsin M. Crosstalk between SOX Genes and Long Non-Coding RNAs in Glioblastoma. Int J Mol Sci 2023;24:ijms24076392. [PMID: 37047365 PMCID: PMC10094781 DOI: 10.3390/ijms24076392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023]  Open
173
Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Baker P, Barkan E, Bertagnolli D, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, Dolbeare T, Ellingwood L, Gee J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Jin K, Kroll M, Lathia K, Leon A, Long B, Maltzer Z, Martin N, McCue R, Meyerdierks E, Nguyen TN, Pham T, Rimorin C, Ruiz A, Shapovalova N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Cuevas NV, Wadhwani K, Ward K, Levi B, Farrell C, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith KA, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531121. [PMID: 37034735 PMCID: PMC10081189 DOI: 10.1101/2023.03.06.531121] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
174
Liu Z, Zhang Y, Weng S, Xu H, Han X. Implications of pseudogenes for the prognosis of hepatocellular carcinoma. Clin Transl Med 2023;13:e1195. [PMID: 36750350 PMCID: PMC9905005 DOI: 10.1002/ctm2.1195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023]  Open
175
Li J, Shen J, Wang R, Chen Y, Zhang T, Wang H, Guo C, Qi J. The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution. PLANT COMMUNICATIONS 2023;4:100422. [PMID: 35957520 PMCID: PMC9860166 DOI: 10.1016/j.xplc.2022.100422] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 05/27/2023]
176
Jung SC, Zhou T, Ko EA. Age-dependent expression of ion channel genes in rat. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2023;27:85-94. [PMID: 36575936 PMCID: PMC9806634 DOI: 10.4196/kjpp.2023.27.1.85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 12/29/2022]
177
Tao W, Li R, Li T, Li Z, Li Y, Cui L. The evolutionary patterns, expression profiles, and genetic diversity of expanded genes in barley. FRONTIERS IN PLANT SCIENCE 2023;14:1168124. [PMID: 37180392 PMCID: PMC10171312 DOI: 10.3389/fpls.2023.1168124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/28/2023] [Indexed: 05/16/2023]
178
The sheep miRNAome: Characterization and distribution of miRNAs in 21 tissues. Gene X 2023;851:146998. [DOI: 10.1016/j.gene.2022.146998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]  Open
179
Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence. Nat Ecol Evol 2023;7:155-170. [PMID: 36604553 PMCID: PMC9834058 DOI: 10.1038/s41559-022-01932-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
180
Long X, Charlesworth D, Qi J, Wu R, Chen M, Wang Z, Xu L, Fu H, Zhang X, Chen X, He L, Zheng L, Huang Z, Zhou Q. Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species. Mol Biol Evol 2022;40:6964685. [PMID: 36578180 PMCID: PMC9851323 DOI: 10.1093/molbev/msac279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022]  Open
181
Wu S, Zhang Q, Zhang W, Huang W, Kong Q, Liu Q, Li W, Zou X, Liu CM, Yan S. Linolenic Acid-Derived Oxylipins Inhibit Aflatoxin Biosynthesis in Aspergillus flavus through Activation of Imizoquin Biosynthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022;70:15928-15944. [PMID: 36508213 PMCID: PMC9785051 DOI: 10.1021/acs.jafc.2c06230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
182
Metivier JC, Chain FJJ. Diversity in Expression Biases of Lineage-Specific Genes During Development and Anhydrobiosis Among Tardigrade Species. Evol Bioinform Online 2022;18:11769343221140277. [PMID: 36578471 PMCID: PMC9791283 DOI: 10.1177/11769343221140277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/27/2022] [Indexed: 12/24/2022]  Open
183
Li S, Zhang J, Zhang L, Fang X, Luo J, An H, Zhang X. Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.). FRONTIERS IN PLANT SCIENCE 2022;13:1078085. [PMID: 36582646 PMCID: PMC9792668 DOI: 10.3389/fpls.2022.1078085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
184
Xu R, Martelossi J, Smits M, Iannello M, Peruzza L, Babbucci M, Milan M, Dunham JP, Breton S, Milani L, Nuzhdin SV, Bargelloni L, Passamonti M, Ghiselli F. Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam. Genome Biol Evol 2022;14:6889380. [PMID: 36508337 PMCID: PMC9803972 DOI: 10.1093/gbe/evac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]  Open
185
Lüleci HB, Yılmaz A. Robust and rigorous identification of tissue-specific genes by statistically extending tau score. BioData Min 2022;15:31. [PMID: 36494766 PMCID: PMC9733102 DOI: 10.1186/s13040-022-00315-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022]  Open
186
Ma C, Li C, Ma H, Yu D, Zhang Y, Zhang D, Su T, Wu J, Wang X, Zhang L, Chen CL, Zhang YE. Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum. Genome Biol 2022;23:251. [PMID: 36474250 PMCID: PMC9724437 DOI: 10.1186/s13059-022-02821-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/24/2022] [Indexed: 12/12/2022]  Open
187
Raina P, Guinea R, Chatsirisupachai K, Lopes I, Farooq Z, Guinea C, Solyom CA, de Magalhães JP. GeneFriends: gene co-expression databases and tools for humans and model organisms. Nucleic Acids Res 2022;51:D145-D158. [PMID: 36454018 PMCID: PMC9825523 DOI: 10.1093/nar/gkac1031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 12/05/2022]  Open
188
Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism. Sci Rep 2022;12:20771. [PMID: 36456708 PMCID: PMC9715534 DOI: 10.1038/s41598-022-25132-2] [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: 09/02/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]  Open
189
Zhang H, Zhang N, Wu W, Zhou R, Li S, Wang Z, Dai Z, Zhang L, Liu Z, Zhang J, Luo P, Liu Z, Cheng Q. Machine learning-based tumor-infiltrating immune cell-associated lncRNAs for predicting prognosis and immunotherapy response in patients with glioblastoma. Brief Bioinform 2022;23:bbac386. [PMID: 36136350 DOI: 10.1093/bib/bbac386] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 12/14/2022]  Open
190
Brasó-Vives M, Marlétaz F, Echchiki A, Mantica F, Acemel RD, Gómez-Skarmeta JL, Hartasánchez DA, Le Targa L, Pontarotti P, Tena JJ, Maeso I, Escriva H, Irimia M, Robinson-Rechavi M. Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biol 2022;23:243. [PMID: 36401278 PMCID: PMC9673378 DOI: 10.1186/s13059-022-02808-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022]  Open
191
Qian SH, Chen L, Xiong YL, Chen ZX. Evolution and function of developmentally dynamic pseudogenes in mammals. Genome Biol 2022;23:235. [PMID: 36348461 PMCID: PMC9641868 DOI: 10.1186/s13059-022-02802-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/23/2022] [Indexed: 11/11/2022]  Open
192
Leitão E, Schröder C, Parenti I, Dalle C, Rastetter A, Kühnel T, Kuechler A, Kaya S, Gérard B, Schaefer E, Nava C, Drouot N, Engel C, Piard J, Duban-Bedu B, Villard L, Stegmann APA, Vanhoutte EK, Verdonschot JAJ, Kaiser FJ, Tran Mau-Them F, Scala M, Striano P, Frints SGM, Argilli E, Sherr EH, Elder F, Buratti J, Keren B, Mignot C, Héron D, Mandel JL, Gecz J, Kalscheuer VM, Horsthemke B, Piton A, Depienne C. Systematic analysis and prediction of genes associated with monogenic disorders on human chromosome X. Nat Commun 2022;13:6570. [PMID: 36323681 PMCID: PMC9630267 DOI: 10.1038/s41467-022-34264-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]  Open
193
Huang J, Liu W, Zhang D, Lin B, Li B. TMEM158 expression is negatively regulated by AR signaling and associated with favorite survival outcomes in prostate cancers. Front Oncol 2022;12:1023455. [PMID: 36387246 PMCID: PMC9663988 DOI: 10.3389/fonc.2022.1023455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/18/2022] [Indexed: 08/30/2023]  Open
194
Tang K, Tang J, Zeng J, Shen W, Zou M, Zhang C, Sun Q, Ye X, Li C, Sun C, Liu S, Jiang G, Du X. A network view of human immune system and virus-human interaction. Front Immunol 2022;13:997851. [PMID: 36389817 PMCID: PMC9643829 DOI: 10.3389/fimmu.2022.997851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/11/2022] [Indexed: 11/30/2022]  Open
195
Zhang B, Fei Y, Feng J, Zhu X, Wang R, Xiao H, Zhang H, Huang J. RiceNCexp: a rice non-coding RNA co-expression atlas based on massive RNA-seq and small-RNA seq data. JOURNAL OF EXPERIMENTAL BOTANY 2022;73:6068-6077. [PMID: 35762882 DOI: 10.1093/jxb/erac285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
196
Aparicio-Puerta E, Hirsch P, Schmartz GP, Fehlmann T, Keller V, Engel A, Kern F, Hackenberg M, Keller A. isomiRdb: microRNA expression at isoform resolution. Nucleic Acids Res 2022;51:D179-D185. [PMID: 36243964 PMCID: PMC9825445 DOI: 10.1093/nar/gkac884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/30/2022] [Indexed: 01/29/2023]  Open
197
Transcriptional signatures of wheat inflorescence development. Sci Rep 2022;12:17224. [PMID: 36241895 PMCID: PMC9568521 DOI: 10.1038/s41598-022-21571-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023]  Open
198
Song H, Fu X, Li J, Niu T, Shen J, Wang X, Li Y, Hou Q, Liu A. Phylogenetic analysis and expression profiles of jasmonate ZIM-domain gene family provide insight into abiotic stress resistance in sunflower. FRONTIERS IN PLANT SCIENCE 2022;13:1010404. [PMID: 36275559 PMCID: PMC9580003 DOI: 10.3389/fpls.2022.1010404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
199
Yamamoto R, Chung R, Vazquez JM, Sheng H, Steinberg PL, Ioannidis NM, Sudmant PH. Tissue-specific impacts of aging and genetics on gene expression patterns in humans. Nat Commun 2022;13:5803. [PMID: 36192477 PMCID: PMC9530233 DOI: 10.1038/s41467-022-33509-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 09/21/2022] [Indexed: 11/09/2022]  Open
200
Laloum D, Robinson-Rechavi M. Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level. PLoS Comput Biol 2022;18:e1010399. [PMID: 36095022 PMCID: PMC9518874 DOI: 10.1371/journal.pcbi.1010399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 09/28/2022] [Accepted: 07/17/2022] [Indexed: 11/18/2022]  Open
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