• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4612468)   Today's Articles (71)   Subscriber (49385)
For: Levo M, Segal E. In pursuit of design principles of regulatory sequences. Nat Rev Genet 2014;15:453-68. [PMID: 24913666 DOI: 10.1038/nrg3684] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Number Cited by Other Article(s)
1
Li J, Rohs R. Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers. Nucleic Acids Res 2024;52:W7-W12. [PMID: 38801070 PMCID: PMC11223853 DOI: 10.1093/nar/gkae433] [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: 02/26/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]  Open
2
Ali MZ, Guharajan S, Parisutham V, Brewster RC. Regulatory properties of transcription factors with diverse mechanistic function. PLoS Comput Biol 2024;20:e1012194. [PMID: 38857275 PMCID: PMC11192337 DOI: 10.1371/journal.pcbi.1012194] [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: 01/18/2024] [Revised: 06/21/2024] [Accepted: 05/24/2024] [Indexed: 06/12/2024]  Open
3
Hua K, Wu C, Lin C, Chen C. E2F1 promotes cell migration in hepatocellular carcinoma via FNDC3B. FEBS Open Bio 2024;14:687-694. [PMID: 38403291 PMCID: PMC10988749 DOI: 10.1002/2211-5463.13783] [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: 08/10/2023] [Revised: 01/23/2024] [Accepted: 02/16/2024] [Indexed: 02/27/2024]  Open
4
Jin R, He B, Qin Y, Du Z, Cao C, Li J. Unveiling the role of bZIP transcription factors CREB and CEBP in detoxification metabolism of Nilaparvata lugens (Stål). Int J Biol Macromol 2023;253:126576. [PMID: 37648128 DOI: 10.1016/j.ijbiomac.2023.126576] [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: 04/16/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/01/2023]
5
Martyn GE, Montgomery MT, Jones H, Guo K, Doughty BR, Linder J, Chen Z, Cochran K, Lawrence KA, Munson G, Pampari A, Fulco CP, Kelley DR, Lander ES, Kundaje A, Engreitz JM. Rewriting regulatory DNA to dissect and reprogram gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572268. [PMID: 38187584 PMCID: PMC10769263 DOI: 10.1101/2023.12.20.572268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
6
Stellner NI, Rerop ZS, Mehlmer N, Masri M, Ringel M, Brück TB. Expanding the genetic toolbox for Cutaneotrichosporon oleaginosus employing newly identified promoters and a novel antibiotic resistance marker. BMC Biotechnol 2023;23:40. [PMID: 37723521 PMCID: PMC10506223 DOI: 10.1186/s12896-023-00812-7] [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: 06/09/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023]  Open
7
Gosai SJ, Castro RI, Fuentes N, Butts JC, Kales S, Noche RR, Mouri K, Sabeti PC, Reilly SK, Tewhey R. Machine-guided design of synthetic cell type-specific cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552077. [PMID: 37609287 PMCID: PMC10441439 DOI: 10.1101/2023.08.08.552077] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
8
Hartwig T, Banf M, Prietsch GP, Zhu JY, Mora-Ramírez I, Schippers JHM, Snodgrass SJ, Seetharam AS, Huettel B, Kolkman JM, Yang J, Engelhorn J, Wang ZY. Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize. Genome Biol 2023;24:108. [PMID: 37158941 PMCID: PMC10165856 DOI: 10.1186/s13059-023-02909-w] [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: 02/06/2022] [Accepted: 03/23/2023] [Indexed: 05/10/2023]  Open
9
Li M, Yao T, Lin W, Hinckley WE, Galli M, Muchero W, Gallavotti A, Chen JG, Huang SSC. Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors. Nat Commun 2023;14:2600. [PMID: 37147307 PMCID: PMC10163045 DOI: 10.1038/s41467-023-38096-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/15/2023] [Indexed: 05/07/2023]  Open
10
Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK. Diverse logics and grammar encode notochord enhancers. Cell Rep 2023;42:112052. [PMID: 36729834 PMCID: PMC10387507 DOI: 10.1016/j.celrep.2023.112052] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023]  Open
11
Kari H, Bandi SMS, Kumar A, Yella VR. DeePromClass: Delineator for Eukaryotic Core Promoters Employing Deep Neural Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:802-807. [PMID: 35353704 DOI: 10.1109/tcbb.2022.3163418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
12
Liang Y, Xu H, Cheng T, Fu Y, Huang H, Qian W, Wang J, Zhou Y, Qian P, Yin Y, Xu P, Zou W, Chen B. Gene activation guided by nascent RNA-bound transcription factors. Nat Commun 2022;13:7329. [PMID: 36443367 PMCID: PMC9705438 DOI: 10.1038/s41467-022-35041-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022]  Open
13
Patra P, Gao YQ. Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation. J Phys Chem B 2022;126:9187-9206. [PMID: 36322688 DOI: 10.1021/acs.jpcb.2c05749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
14
Fernandez-Lopez R, Ruiz R, del Campo I, Gonzalez-Montes L, Boer D, de la Cruz F, Moncalian G. Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors. Nucleic Acids Res 2022;50:11938-11947. [PMID: 36370103 PMCID: PMC9723621 DOI: 10.1093/nar/gkac1024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]  Open
15
Donohue LK, Guo MG, Zhao Y, Jung N, Bussat RT, Kim DS, Neela PH, Kellman LN, Garcia OS, Meyers RM, Altman RB, Khavari PA. A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation. CELL GENOMICS 2022;2:100191. [PMID: 36742369 PMCID: PMC9894309 DOI: 10.1016/j.xgen.2022.100191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
16
Ghoshdastidar D, Bansal M. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif. Biophys J 2022;121:3987-4000. [PMID: 35978548 PMCID: PMC9674967 DOI: 10.1016/j.bpj.2022.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/02/2022]  Open
17
Yang MG, Ling E, Cowley CJ, Greenberg ME, Vierbuchen T. Characterization of sequence determinants of enhancer function using natural genetic variation. eLife 2022;11:76500. [PMID: 36043696 PMCID: PMC9662815 DOI: 10.7554/elife.76500] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 08/30/2022] [Indexed: 02/04/2023]  Open
18
Barissi S, Sala A, Wieczór M, Battistini F, Orozco M. DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors. Nucleic Acids Res 2022;50:9105-9114. [PMID: 36018808 PMCID: PMC9458447 DOI: 10.1093/nar/gkac708] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/24/2022]  Open
19
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers. Nat Genet 2022;54:613-624. [PMID: 35551305 DOI: 10.1038/s41588-022-01048-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/08/2022] [Indexed: 02/06/2023]
20
Tareen A, Kooshkbaghi M, Posfai A, Ireland WT, McCandlish DM, Kinney JB. MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. Genome Biol 2022;23:98. [PMID: 35428271 PMCID: PMC9011994 DOI: 10.1186/s13059-022-02661-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/24/2022] [Indexed: 12/17/2022]  Open
21
Kim NM, Sinnott RW, Rothschild LN, Sandoval NR. Elucidation of Sequence-Function Relationships for an Improved Biobutanol In Vivo Biosensor in E. coli. Front Bioeng Biotechnol 2022;10:821152. [PMID: 35265600 PMCID: PMC8899819 DOI: 10.3389/fbioe.2022.821152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/17/2022] [Indexed: 11/30/2022]  Open
22
Vanaja A, Yella VR. Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes. ACS OMEGA 2022;7:5657-5669. [PMID: 35224327 PMCID: PMC8867553 DOI: 10.1021/acsomega.1c04603] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/27/2022] [Indexed: 05/02/2023]
23
Wu T, Jiang D, Zou M, Sun W, Wu D, Cui J, Huntress I, Peng X, Li G. Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution. Nucleic Acids Res 2022;50:e5. [PMID: 34634809 PMCID: PMC8754656 DOI: 10.1093/nar/gkab890] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/20/2021] [Accepted: 09/17/2021] [Indexed: 12/30/2022]  Open
24
Ren N, Li B, Liu Q, Yang L, Liu X, Huang Q. Dinucleotide tag-based parallel reporter gene assay method enables efficient identification of regulatory mutations. Biotechnol J 2021;17:e2100341. [PMID: 34894203 DOI: 10.1002/biot.202100341] [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: 07/01/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 11/06/2022]
25
Mauduit D, Taskiran II, Minnoye L, de Waegeneer M, Christiaens V, Hulselmans G, Demeulemeester J, Wouters J, Aerts S. Analysis of long and short enhancers in melanoma cell states. eLife 2021;10:e71735. [PMID: 34874265 PMCID: PMC8691835 DOI: 10.7554/elife.71735] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/06/2021] [Indexed: 12/14/2022]  Open
26
The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nat Genet 2021;53:1564-1576. [PMID: 34650237 PMCID: PMC8763320 DOI: 10.1038/s41588-021-00947-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 09/01/2021] [Indexed: 01/24/2023]
27
Ren N, Li Y, Xiong Y, Li P, Ren Y, Huang Q. Functional Screenings Identify Regulatory Variants Associated with Breast Cancer Susceptibility. Curr Issues Mol Biol 2021;43:1756-1777. [PMID: 34889888 PMCID: PMC8928974 DOI: 10.3390/cimb43030124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022]  Open
28
Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions. Genes (Basel) 2021;12:genes12101571. [PMID: 34680967 PMCID: PMC8536142 DOI: 10.3390/genes12101571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 01/22/2023]  Open
29
Zhang Y, Mo Q, Xue L, Luo J. Evaluation of deep learning approaches for modeling transcription factor sequence specificity. Genomics 2021;113:3774-3781. [PMID: 34534646 DOI: 10.1016/j.ygeno.2021.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/19/2021] [Accepted: 09/11/2021] [Indexed: 11/16/2022]
30
Santiago-Frangos A, Buyukyoruk M, Wiegand T, Krishna P, Wiedenheft B. Distribution and phasing of sequence motifs that facilitate CRISPR adaptation. Curr Biol 2021;31:3515-3524.e6. [PMID: 34174210 PMCID: PMC8552246 DOI: 10.1016/j.cub.2021.05.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/30/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022]
31
Moutsopoulos I, Maischak L, Lauzikaite E, Vasquez Urbina S, Williams E, Drost HG, Mohorianu I. noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise. Nucleic Acids Res 2021;49:e83. [PMID: 34076236 PMCID: PMC8373073 DOI: 10.1093/nar/gkab433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/16/2021] [Accepted: 05/06/2021] [Indexed: 01/22/2023]  Open
32
Ren N, Liu Q, Yan L, Huang Q. Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer Predisposition. Int J Mol Sci 2021;22:8792. [PMID: 34445492 PMCID: PMC8395720 DOI: 10.3390/ijms22168792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023]  Open
33
Savadel SD, Hartwig T, Turpin ZM, Vera DL, Lung PY, Sui X, Blank M, Frommer WB, Dennis JH, Zhang J, Bass HW. The native cistrome and sequence motif families of the maize ear. PLoS Genet 2021;17:e1009689. [PMID: 34383745 PMCID: PMC8360572 DOI: 10.1371/journal.pgen.1009689] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/30/2021] [Indexed: 01/22/2023]  Open
34
Cazier AP, Blazeck J. Advances in promoter engineering: novel applications and predefined transcriptional control. Biotechnol J 2021;16:e2100239. [PMID: 34351706 DOI: 10.1002/biot.202100239] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
35
Saidi A, Hajibarat Z, Hajibarat Z. Phylogeny, gene structure and GATA genes expression in different tissues of solanaceae species. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
36
Ahmed Z, Renart EG, Zeeshan S. Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping. PeerJ 2021;9:e11724. [PMID: 34395068 PMCID: PMC8320519 DOI: 10.7717/peerj.11724] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022]  Open
37
Degtyareva AO, Antontseva EV, Merkulova TI. Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. Int J Mol Sci 2021;22:6454. [PMID: 34208629 PMCID: PMC8235176 DOI: 10.3390/ijms22126454] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022]  Open
38
Zrimec J, Buric F, Kokina M, Garcia V, Zelezniak A. Learning the Regulatory Code of Gene Expression. Front Mol Biosci 2021;8:673363. [PMID: 34179082 PMCID: PMC8223075 DOI: 10.3389/fmolb.2021.673363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022]  Open
39
Peculiarities of Plasmodium falciparum Gene Regulation and Chromatin Structure. Int J Mol Sci 2021;22:ijms22105168. [PMID: 34068393 PMCID: PMC8153576 DOI: 10.3390/ijms22105168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/14/2022]  Open
40
Figla promotes secondary follicle growth in mature mice. Sci Rep 2021;11:9842. [PMID: 33972571 PMCID: PMC8110814 DOI: 10.1038/s41598-021-89052-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/20/2021] [Indexed: 11/09/2022]  Open
41
Zhang D, Lam J, Blobel GA. Engineering three-dimensional genome folding. Nat Genet 2021;53:602-611. [PMID: 33958782 DOI: 10.1038/s41588-021-00860-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/29/2021] [Indexed: 02/02/2023]
42
Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021;22:108. [PMID: 33858480 PMCID: PMC8051032 DOI: 10.1186/s13059-021-02322-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022]  Open
43
Froehlich JJ, Uyar B, Herzog M, Theil K, Glažar P, Akalin A, Rajewsky N. Parallel genetics of regulatory sequences using scalable genome editing in vivo. Cell Rep 2021;35:108988. [PMID: 33852857 DOI: 10.1016/j.celrep.2021.108988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/13/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022]  Open
44
Ruiz Ramírez AV, Flores-Saiffe Farías A, Chávez Álvarez RDC, Prado Montes de Oca E. Predicted regulatory SNPs reveal potential drug targets and novel companion diagnostics in psoriasis. J Transl Autoimmun 2021;4:100096. [PMID: 33898962 PMCID: PMC8060581 DOI: 10.1016/j.jtauto.2021.100096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/27/2021] [Accepted: 03/10/2021] [Indexed: 11/25/2022]  Open
45
Jindal GA, Farley EK. Enhancer grammar in development, evolution, and disease: dependencies and interplay. Dev Cell 2021;56:575-587. [PMID: 33689769 PMCID: PMC8462829 DOI: 10.1016/j.devcel.2021.02.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/19/2022]
46
Fine gene expression regulation by minor sequence variations downstream of the polyadenylation signal. Mol Biol Rep 2021;48:1539-1547. [PMID: 33517473 DOI: 10.1007/s11033-021-06160-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 12/22/2022]
47
Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, Kulakovskiy IV, Kel A, Kolpakov F. GTRD: an integrated view of transcription regulation. Nucleic Acids Res 2021;49:D104-D111. [PMID: 33231677 PMCID: PMC7778956 DOI: 10.1093/nar/gkaa1057] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/18/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]  Open
48
Jana T, Brodsky S, Barkai N. Speed-Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites. Trends Genet 2021;37:421-432. [PMID: 33414013 DOI: 10.1016/j.tig.2020.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022]
49
Paredes O, Romo-Vázquez R, Román-Godínez I, Vélez-Pérez H, Salido-Ruiz RA, Morales JA. Frequency spectra characterization of noncoding human genomic sequences. Genes Genomics 2020;42:1215-1226. [DOI: 10.1007/s13258-020-00980-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/27/2020] [Indexed: 11/28/2022]
50
Bansal R, Hussain S, Chanana UB, Bisht D, Goel I, Muthuswami R. SMARCAL1, the annealing helicase and the transcriptional co-regulator. IUBMB Life 2020;72:2080-2096. [PMID: 32754981 DOI: 10.1002/iub.2354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
PrevPage 1 of 4 1234Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA