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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)
101
Zhou Z, Zhang J, Zheng X, Pan Z, Zhao F, Gao Y. CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2308115. [PMID: 38308181 PMCID: PMC11005702 DOI: 10.1002/advs.202308115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/03/2024] [Indexed: 02/04/2024]
102
Degalez F, Charles M, Foissac S, Zhou H, Guan D, Fang L, Klopp C, Allain C, Lagoutte L, Lecerf F, Acloque H, Giuffra E, Pitel F, Lagarrigue S. Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Sci Rep 2024;14:6588. [PMID: 38504112 PMCID: PMC10951430 DOI: 10.1038/s41598-024-56705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/09/2024] [Indexed: 03/21/2024]  Open
103
Yang H, Li Q, Stroup EK, Wang S, Ji Z. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features. Nat Commun 2024;15:1932. [PMID: 38431639 PMCID: PMC10908861 DOI: 10.1038/s41467-024-46240-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024]  Open
104
Marlétaz F, Timoshevskaya N, Timoshevskiy VA, Parey E, Simakov O, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith JJ, Rokhsar DS. The hagfish genome and the evolution of vertebrates. Nature 2024;627:811-820. [PMID: 38262590 PMCID: PMC10972751 DOI: 10.1038/s41586-024-07070-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
105
Xu L, Ren Y, Wu J, Cui T, Dong R, Huang C, Feng Z, Zhang T, Yang P, Yuan J, Xu X, Liu J, Wang J, Chen W, Mi D, Irwin DM, Yan Y, Xu L, Yu X, Li G. Evolution and expression patterns of the neo-sex chromosomes of the crested ibis. Nat Commun 2024;15:1670. [PMID: 38395916 PMCID: PMC10891136 DOI: 10.1038/s41467-024-46052-x] [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: 06/21/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024]  Open
106
He Z, Lan Y, Zhou X, Yu B, Zhu T, Yang F, Fu LY, Chao H, Wang J, Feng RX, Zuo S, Lan W, Chen C, Chen M, Zhao X, Hu K, Chen D. Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis. PLANT COMMUNICATIONS 2024;5:100717. [PMID: 37715446 PMCID: PMC10873878 DOI: 10.1016/j.xplc.2023.100717] [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: 04/22/2023] [Revised: 08/14/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
107
Durkin SM, Ballinger MA, Nachman MW. Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice. PLoS Genet 2024;20:e1010892. [PMID: 38306396 PMCID: PMC10866503 DOI: 10.1371/journal.pgen.1010892] [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: 07/31/2023] [Revised: 02/14/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]  Open
108
Peng J, Zhao L. The origin and structural evolution of de novo genes in Drosophila. Nat Commun 2024;15:810. [PMID: 38280868 PMCID: PMC10821953 DOI: 10.1038/s41467-024-45028-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/09/2024] [Indexed: 01/29/2024]  Open
109
Sturgill D, Wang L, Arda HE. PancrESS - a meta-analysis resource for understanding cell-type specific expression in the human pancreas. BMC Genomics 2024;25:76. [PMID: 38238687 PMCID: PMC10797729 DOI: 10.1186/s12864-024-09964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024]  Open
110
Gu X, Wang M, Zhang XO. TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS). Nucleic Acids Res 2024;52:D322-D333. [PMID: 37956335 PMCID: PMC10767810 DOI: 10.1093/nar/gkad1048] [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: 08/13/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]  Open
111
Xu H, Zhang S, Duan Q, Lou M, Ling Y. Comprehensive analyses of 435 goat transcriptomes provides insight into male reproduction. Int J Biol Macromol 2024;255:127942. [PMID: 37979751 DOI: 10.1016/j.ijbiomac.2023.127942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
112
Betti MJ, Aldrich MC, Gamazon ER. Minimum entropy framework identifies a novel class of genomic functional elements and reveals regulatory mechanisms at human disease loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544507. [PMID: 37398170 PMCID: PMC10312628 DOI: 10.1101/2023.06.11.544507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
113
Kozlova A, Sarygina E, Deinichenko K, Radko S, Ptitsyn K, Khmeleva S, Kurbatov L, Spirin P, Prassolov V, Ilgisonis E, Lisitsa A, Ponomarenko E. Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue. BIOLOGY 2023;12:1494. [PMID: 38132320 PMCID: PMC10740679 DOI: 10.3390/biology12121494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
114
Zhao Y, Zheng Z, Zhang Z, Xu Y, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Biashad SA, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle. Nat Commun 2023;14:8054. [PMID: 38052795 PMCID: PMC10698142 DOI: 10.1038/s41467-023-43623-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/15/2023] [Indexed: 12/07/2023]  Open
115
Kurylo C, Guyomar C, Foissac S, Djebali S. TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data. NAR Genom Bioinform 2023;5:lqad089. [PMID: 37850035 PMCID: PMC10578202 DOI: 10.1093/nargab/lqad089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/11/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]  Open
116
Saul F, Scharmann M, Wakatake T, Rajaraman S, Marques A, Freund M, Bringmann G, Channon L, Becker D, Carroll E, Low YW, Lindqvist C, Gilbert KJ, Renner T, Masuda S, Richter M, Vogg G, Shirasu K, Michael TP, Hedrich R, Albert VA, Fukushima K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. NATURE PLANTS 2023;9:2000-2015. [PMID: 37996654 DOI: 10.1038/s41477-023-01562-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
117
Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Aitken M, Baker K, Baker P, Barkan E, Bertagnolli D, Bhandiwad A, Bielstein C, Bishwakarma P, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, DiValentin P, Dolbeare T, Ellingwood L, Fiabane E, Fliss T, Gee J, Gerstenberger J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Hooper M, Huang M, Hupp M, Jin K, Kroll M, Lathia K, Leon A, Li S, Long B, Madigan Z, Malloy J, Malone J, Maltzer Z, Martin N, McCue R, McGinty R, Mei N, Melchor J, Meyerdierks E, Mollenkopf T, Moonsman S, Nguyen TN, Otto S, Pham T, Rimorin C, Ruiz A, Sanchez R, Sawyer L, Shapovalova N, Shepard N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Valera Cuevas N, Vance S, Wadhwani K, Ward K, Levi B, Farrell C, Young R, Staats B, Wang MQM, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith K, Tasic B, Zhuang X, et alYao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Aitken M, Baker K, Baker P, Barkan E, Bertagnolli D, Bhandiwad A, Bielstein C, Bishwakarma P, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, DiValentin P, Dolbeare T, Ellingwood L, Fiabane E, Fliss T, Gee J, Gerstenberger J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Hooper M, Huang M, Hupp M, Jin K, Kroll M, Lathia K, Leon A, Li S, Long B, Madigan Z, Malloy J, Malone J, Maltzer Z, Martin N, McCue R, McGinty R, Mei N, Melchor J, Meyerdierks E, Mollenkopf T, Moonsman S, Nguyen TN, Otto S, Pham T, Rimorin C, Ruiz A, Sanchez R, Sawyer L, Shapovalova N, Shepard N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Valera Cuevas N, Vance S, Wadhwani K, Ward K, Levi B, Farrell C, Young R, Staats B, Wang MQM, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith K, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 2023;624:317-332. [PMID: 38092916 PMCID: PMC10719114 DOI: 10.1038/s41586-023-06812-z] [Show More Authors] [Citation(s) in RCA: 311] [Impact Index Per Article: 155.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
118
Rao L, Cai L, Huang L. Single-cell dynamics of liver development in postnatal pigs. Sci Bull (Beijing) 2023;68:2583-2597. [PMID: 37783617 DOI: 10.1016/j.scib.2023.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/21/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
119
Rodríguez-Montes L, Ovchinnikova S, Yuan X, Studer T, Sarropoulos I, Anders S, Kaessmann H, Cardoso-Moreira M. Sex-biased gene expression across mammalian organ development and evolution. Science 2023;382:eadf1046. [PMID: 37917687 PMCID: PMC7615307 DOI: 10.1126/science.adf1046] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 09/18/2023] [Indexed: 11/04/2023]
120
Nikumbh S, Lenhard B. Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation. PLoS Comput Biol 2023;19:e1011491. [PMID: 37983292 PMCID: PMC10695386 DOI: 10.1371/journal.pcbi.1011491] [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: 04/13/2023] [Revised: 12/04/2023] [Accepted: 09/05/2023] [Indexed: 11/22/2023]  Open
121
Suresh H, Crow M, Jorstad N, Hodge R, Lein E, Dobin A, Bakken T, Gillis J. Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution. Nat Ecol Evol 2023;7:1930-1943. [PMID: 37667001 PMCID: PMC10627823 DOI: 10.1038/s41559-023-02186-7] [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: 02/07/2023] [Accepted: 08/02/2023] [Indexed: 09/06/2023]
122
Patil AB, Kar D, Datta S, Vijay N. Genomic and Transcriptomic Analyses Illuminates Unique Traits of Elusive Night Flowering Jasmine Parijat (Nyctanthes arbor-tristis). PHYSIOLOGIA PLANTARUM 2023;175:e14119. [PMID: 38148217 DOI: 10.1111/ppl.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
123
Almeida-Silva F, Pedrosa-Silva F, Venancio TM. The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023;116:1041-1051. [PMID: 37681739 DOI: 10.1111/tpj.16459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
124
Zhang Y, Guo M, Wang L, Weng S, Xu H, Ren Y, Liu L, Guo C, Cheng Q, Luo P, Zhang J, Han X. A tumor-infiltrating immune cells-related pseudogenes signature based on machine-learning predicts outcomes and immunotherapy responses in ovarian cancer. Cell Signal 2023;111:110879. [PMID: 37659727 DOI: 10.1016/j.cellsig.2023.110879] [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: 06/15/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
125
Liu L, Heidecker M, Depuydt T, Manosalva Perez N, Crespi M, Blein T, Vandepoele K. Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots. PLANT PHYSIOLOGY 2023;193:1933-1953. [PMID: 37345955 DOI: 10.1093/plphys/kiad360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
126
Jorstad NL, Close J, Johansen N, Yanny AM, Barkan ER, Travaglini KJ, Bertagnolli D, Campos J, Casper T, Crichton K, Dee N, Ding SL, Gelfand E, Goldy J, Hirschstein D, Kroll M, Kunst M, Lathia K, Long B, Martin N, McMillen D, Pham T, Rimorin C, Ruiz A, Shapovalova N, Shehata S, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Ward K, Callaway EM, Hof PR, Keene CD, Levi BP, Linnarsson S, Mitra PP, Smith K, Hodge RD, Bakken TE, Lein ES. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. Science 2023;382:eadf6812. [PMID: 37824655 PMCID: PMC11687949 DOI: 10.1126/science.adf6812] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
127
Kai Y, Liu N, Orkin SH, Yuan GC. Identifying quantitatively differential chromosomal compartmentalization changes and their biological significance from Hi-C data using DARIC. BMC Genomics 2023;24:614. [PMID: 37833630 PMCID: PMC10571287 DOI: 10.1186/s12864-023-09675-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023]  Open
128
Modi A, Lopez G, Conkrite KL, Su C, Leung TC, Ramanan S, Manduchi E, Johnson ME, Cheung D, Gadd S, Zhang J, Smith MA, Guidry Auvil JM, Meshinchi S, Perlman EJ, Hunger SP, Maris JM, Wells AD, Grant SF, Diskin SJ. Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors. Cancer Res 2023;83:3462-3477. [PMID: 37584517 PMCID: PMC10787516 DOI: 10.1158/0008-5472.can-22-3186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/07/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
129
Liu Z, Huang YF. Deep multiple-instance learning accurately predicts gene haploinsufficiency and deletion pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555384. [PMID: 37693607 PMCID: PMC10491176 DOI: 10.1101/2023.08.29.555384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
130
Wijfjes Z, van Dalen FJ, Le Gall CM, Verdoes M. Controlling Antigen Fate in Therapeutic Cancer Vaccines by Targeting Dendritic Cell Receptors. Mol Pharm 2023;20:4826-4847. [PMID: 37721387 PMCID: PMC10548474 DOI: 10.1021/acs.molpharmaceut.3c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
131
Lim B, Kim SC, Kim WI, Kim JM. Integrative time-serial networks for genome-wide lncRNA-mRNA interactions reveal interferon-inducible antiviral and T-cell receptor regulations against PRRSV infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023;147:104759. [PMID: 37315774 DOI: 10.1016/j.dci.2023.104759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
132
LaPolice TM, Huang YF. An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data. BMC Bioinformatics 2023;24:347. [PMID: 37723435 PMCID: PMC10506225 DOI: 10.1186/s12859-023-05481-z] [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: 09/13/2022] [Accepted: 09/13/2023] [Indexed: 09/20/2023]  Open
133
Sreedasyam A, Plott C, Hossain MS, Lovell J, Grimwood J, Jenkins J, Daum C, Barry K, Carlson J, Shu S, Phillips J, Amirebrahimi M, Zane M, Wang M, Goodstein D, Haas F, Hiss M, Perroud PF, Jawdy S, Yang Y, Hu R, Johnson J, Kropat J, Gallaher S, Lipzen A, Shakirov E, Weng X, Torres-Jerez I, Weers B, Conde D, Pappas M, Liu L, Muchlinski A, Jiang H, Shyu C, Huang P, Sebastian J, Laiben C, Medlin A, Carey S, Carrell A, Chen JG, Perales M, Swaminathan K, Allona I, Grattapaglia D, Cooper E, Tholl D, Vogel J, Weston DJ, Yang X, Brutnell T, Kellogg E, Baxter I, Udvardi M, Tang Y, Mockler T, Juenger T, Mullet J, Rensing S, Tuskan G, Merchant S, Stacey G, Schmutz J. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Res 2023;51:8383-8401. [PMID: 37526283 PMCID: PMC10484672 DOI: 10.1093/nar/gkad616] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023]  Open
134
Zhou C, Wei X, Xiao Y, Liu S, Wang J. Novel compound heterozygous variants in lectin mannose-binding 2-like gene identified in a Chinese autosomal recessive mental retardation-52 (MRT52) patient with phenotype expansion. Chin Med J (Engl) 2023;136:2107-2109. [PMID: 37667433 PMCID: PMC10476734 DOI: 10.1097/cm9.0000000000002285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Indexed: 09/06/2023]  Open
135
Liu W, Zhu P, Li M, Li Z, Yu Y, Liu G, Du J, Wang X, Yang J, Tian R, Seim I, Kaya A, Li M, Li M, Gladyshev VN, Zhou X. Large-scale across species transcriptomic analysis identifies genetic selection signatures associated with longevity in mammals. EMBO J 2023;42:e112740. [PMID: 37427458 PMCID: PMC10476176 DOI: 10.15252/embj.2022112740] [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: 10/04/2022] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023]  Open
136
Li Y, Mokrani A, Fu H, Shi C, Li Q, Liu S. Development of Nanopore sequencing-based full-length transcriptome database toward functional genome annotation of the Pacific oyster, Crassostrea gigas. Genomics 2023;115:110697. [PMID: 37567397 DOI: 10.1016/j.ygeno.2023.110697] [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: 05/08/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
137
Jain A, Begum T, Ahmad S. Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates. J Mol Biol 2023;435:168208. [PMID: 37479078 DOI: 10.1016/j.jmb.2023.168208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/20/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
138
Li S, Zhang N, Zhang H, Zhou R, Li Z, Yang X, Wu W, Li H, Luo P, Wang Z, Dai Z, Liang X, Wen J, Zhang X, Zhang B, Cheng Q, Zhang Q, Yang Z. Artificial intelligence learning landscape of triple-negative breast cancer uncovers new opportunities for enhancing outcomes and immunotherapy responses. JOURNAL OF BIG DATA 2023;10:132. [DOI: 10.1186/s40537-023-00809-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/07/2023] [Indexed: 01/12/2025]
139
Stevenson DW, Ramakrishnan S, de Santis Alves C, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, Loke S, Rossetto M, McPherson H, Nigris S, Moschin S, Little DP, Katari MS, Varala K, Kolokotronis SO, Ambrose B, Croft LJ, Coruzzi GM, Schatz M, McCombie WR, Martienssen RA. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554647. [PMID: 37662366 PMCID: PMC10473749 DOI: 10.1101/2023.08.24.554647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
140
Cui L, Cheng H, Yang Z, Xia C, Zhang L, Kong X. Comparative Analysis Reveals Different Evolutionary Fates and Biological Functions in Wheat Duplicated Genes (Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2023;12:3021. [PMID: 37687268 PMCID: PMC10489728 DOI: 10.3390/plants12173021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
141
Li J, Wiebenga A, Lipzen A, Ng V, Tejomurthula S, Zhang Y, Grigoriev IV, Peng M, de Vries RP. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi. J Fungi (Basel) 2023;9:860. [PMID: 37623631 PMCID: PMC10455118 DOI: 10.3390/jof9080860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]  Open
142
Li Y, Yang H, Guo J, Yang Y, Yu Q, Guo Y, Zhang C, Wang Z, Zuo P. Uncovering the candidate genes related to sheep body weight using multi-trait genome-wide association analysis. Front Vet Sci 2023;10:1206383. [PMID: 37662987 PMCID: PMC10469697 DOI: 10.3389/fvets.2023.1206383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023]  Open
143
Cervantes S, Kesälahti R, Kumpula TA, Mattila TM, Helanterä H, Pyhäjärvi T. Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory. Mol Biol Evol 2023;40:msad183. [PMID: 37565532 PMCID: PMC10457172 DOI: 10.1093/molbev/msad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023]  Open
144
Kong W, Zhu Q, Zhang Q, Zhu Y, Yang J, Chai K, Lei W, Jiang M, Zhang S, Lin J, Zhang X. 5mC DNA methylation modification-mediated regulation in tissue functional differentiation and important flavor substance synthesis of tea plant (Camellia sinensis L.). HORTICULTURE RESEARCH 2023;10:uhad126. [PMID: 37560013 PMCID: PMC10407603 DOI: 10.1093/hr/uhad126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/05/2023] [Indexed: 08/11/2023]
145
Walker KA, Chen J, Shi L, Yang Y, Fornage M, Zhou L, Schlosser P, Surapaneni A, Grams ME, Duggan MR, Peng Z, Gomez GT, Tin A, Hoogeveen RC, Sullivan KJ, Ganz P, Lindbohm JV, Kivimaki M, Nevado-Holgado AJ, Buckley N, Gottesman RF, Mosley TH, Boerwinkle E, Ballantyne CM, Coresh J. Proteomics analysis of plasma from middle-aged adults identifies protein markers of dementia risk in later life. Sci Transl Med 2023;15:eadf5681. [PMID: 37467317 PMCID: PMC10665113 DOI: 10.1126/scitranslmed.adf5681] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/28/2023] [Indexed: 07/21/2023]
146
Luigi-Sierra MG, Guan D, López-Béjar M, Casas E, Olvera-Maneu S, Gardela J, Palomo MJ, Osuagwuh UI, Ohaneje UL, Mármol-Sánchez E, Amills M. A protein-coding gene expression atlas from the brain of pregnant and non-pregnant goats. Front Genet 2023;14:1114749. [PMID: 37519888 PMCID: PMC10382233 DOI: 10.3389/fgene.2023.1114749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/27/2023] [Indexed: 08/01/2023]  Open
147
Singh AK, Amar I, Ramadasan H, Kappagantula KS, Chavali S. Proteins with amino acid repeats constitute a rapidly evolvable and human-specific essentialome. Cell Rep 2023;42:112811. [PMID: 37453061 DOI: 10.1016/j.celrep.2023.112811] [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: 01/11/2023] [Revised: 05/30/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]  Open
148
Feng T, Pucker B, Kuang T, Song B, Yang Y, Lin N, Zhang H, Moore MJ, Brockington SF, Wang Q, Deng T, Wang H, Sun H. The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation. Commun Biol 2023;6:706. [PMID: 37429977 DOI: 10.1038/s42003-023-05044-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/14/2023] [Indexed: 07/12/2023]  Open
149
Bai J, Lin Y, Zhang J, Chen Z, Wang Y, Li M, Li J. Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages. Int J Mol Sci 2023;24:11076. [PMID: 37446255 DOI: 10.3390/ijms241311076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]  Open
150
Mbebi AJ, Nikoloski Z. Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Comput Biol 2023;19:e1010832. [PMID: 37523414 PMCID: PMC10414675 DOI: 10.1371/journal.pcbi.1010832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/10/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023]  Open
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