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For: Cousminer DL, Wagley Y, Pippin JA, Elhakeem A, Way GP, Pahl MC, McCormack SE, Chesi A, Mitchell JA, Kindler JM, Baird D, Hartley A, Howe L, Kalkwarf HJ, Lappe JM, Lu S, Leonard ME, Johnson ME, Hakonarson H, Gilsanz V, Shepherd JA, Oberfield SE, Greene CS, Kelly A, Lawlor DA, Voight BF, Wells AD, Zemel BS, Hankenson KD, Grant SFA. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual. Genome Biol 2021;22:1. [PMID: 33397451 PMCID: PMC7780623 DOI: 10.1186/s13059-020-02207-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022]  Open
Number Cited by Other Article(s)
1
Hama Faraj GS, Hussen BM, Abdullah SR, Fatih Rasul M, Hajiesmaeili Y, Baniahmad A, Taheri M. Advanced approaches of the use of circRNAs as a replacement for cancer therapy. Noncoding RNA Res 2024;9:811-830. [PMID: 38590433 PMCID: PMC10999493 DOI: 10.1016/j.ncrna.2024.03.012] [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: 12/14/2023] [Revised: 03/18/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024]  Open
2
Wang XS, Chen Y, Zhao YW, Chen MW, Wang H. Assessing the association between a sedentary lifestyle and prevalence of primary osteoporosis: a community-based cross-sectional study among Chinese population. BMJ Open 2024;14:e080243. [PMID: 38834324 PMCID: PMC11163664 DOI: 10.1136/bmjopen-2023-080243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/21/2024] [Indexed: 06/06/2024]  Open
3
Zinati Y, Takiddeen A, Emad A. GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks. Nat Commun 2024;15:4055. [PMID: 38744843 DOI: 10.1038/s41467-024-48516-6] [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] [Accepted: 05/01/2024] [Indexed: 05/16/2024]  Open
4
Kaur G, Pippin JA, Chang S, Redmond J, Chesi A, Wells AD, Maerz T, Grant SFA, Coleman RM, Hankenson KD, Wagley Y. Osteoporosis GWAS-implicated DNM3 locus contextually regulates osteoblastic and chondrogenic fate of mesenchymal stem/progenitor cells through oscillating miR-199a-5p levels. JBMR Plus 2024;8:ziae051. [PMID: 38686038 PMCID: PMC11056323 DOI: 10.1093/jbmrpl/ziae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/15/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024]  Open
5
Kim M, Wang P, Clow PA, Chien I(E, Wang X, Peng J, Chai H, Liu X, Lee B, Ngan CY, Yue F, Milenkovic O, Chuang JH, Wei CL, Casellas R, Cheng AW, Ruan Y. Multifaceted roles of cohesin in regulating transcriptional loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586715. [PMID: 38585764 PMCID: PMC10996690 DOI: 10.1101/2024.03.25.586715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
6
Conery M, Pippin JA, Wagley Y, Trang K, Pahl MC, Villani DA, Favazzo LJ, Ackert-Bicknell CL, Zuscik MJ, Katsevich E, Wells AD, Zemel BS, Voight BF, Hankenson KD, Chesi A, Grant SF. GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585778. [PMID: 38562830 PMCID: PMC10983984 DOI: 10.1101/2024.03.19.585778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
7
Patel R, Menon J, Kumar S, Nóbrega MB, Patel DA, Sakure AA, Vaja MB. Modern day breeding approaches for improvement of castor. Heliyon 2024;10:e27048. [PMID: 38463846 PMCID: PMC10920369 DOI: 10.1016/j.heliyon.2024.e27048] [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: 05/08/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024]  Open
8
Gálvez-Silva M, Arros P, Berríos-Pastén C, Villamil A, Rodas PI, Araya I, Iglesias R, Araya P, Hormazábal JC, Bohle C, Chen Y, Gan YH, Chávez FP, Lagos R, Marcoleta AE. Carbapenem-resistant hypervirulent ST23 Klebsiella pneumoniae with a highly transmissible dual-carbapenemase plasmid in Chile. Biol Res 2024;57:7. [PMID: 38475927 DOI: 10.1186/s40659-024-00485-2] [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: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 03/14/2024]  Open
9
Trang KB, Pahl MC, Pippin JA, Su C, Littleton SH, Sharma P, Kulkarni NN, Ghanem LR, Terry NA, O’Brien JM, Wagley Y, Hankenson KD, Jermusyk A, Hoskins JW, Amundadottir LT, Xu M, Brown KM, Anderson SA, Yang W, Titchenell PM, Seale P, Cook L, Levings MK, Zemel BS, Chesi A, Wells AD, Grant SF. 3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.30.23294092. [PMID: 37693606 PMCID: PMC10491377 DOI: 10.1101/2023.08.30.23294092] [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]
10
Rodrick E, Kindler JM. Bone mass accrual in children. Curr Opin Endocrinol Diabetes Obes 2024;31:53-59. [PMID: 38010050 PMCID: PMC11015822 DOI: 10.1097/med.0000000000000849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
11
Gutierrez-Castillo DE, Barrett E, Roberts R. A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates. Microb Genom 2024;10:001177. [PMID: 38189214 PMCID: PMC10868612 DOI: 10.1099/mgen.0.001177] [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: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024]  Open
12
Sapoval N, Tanevski M, Treangen TJ. KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024;29:506-520. [PMID: 38160303 PMCID: PMC10764071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
13
Drag MH, Debes KP, Franck CS, Flethøj M, Lyhne MK, Møller JE, Ludvigsen TP, Jespersen T, Olsen LH, Kilpeläinen TO. Nanopore sequencing reveals methylation changes associated with obesity in circulating cell-free DNA from Göttingen Minipigs. Epigenetics 2023;18:2199374. [PMID: 37032646 PMCID: PMC10088973 DOI: 10.1080/15592294.2023.2199374] [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: 11/22/2022] [Revised: 01/29/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023]  Open
14
Yan G, Song D, Li JJ. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nat Commun 2023;14:7482. [PMID: 37980428 PMCID: PMC10657386 DOI: 10.1038/s41467-023-43162-w] [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: 05/06/2023] [Accepted: 11/02/2023] [Indexed: 11/20/2023]  Open
15
Hou R, Hon CC, Huang Y. CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data. Nat Commun 2023;14:7240. [PMID: 37945584 PMCID: PMC10636040 DOI: 10.1038/s41467-023-42636-1] [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: 04/14/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]  Open
16
Zhu YJ, Liao ML, Dong YW. Exploring the adaptability of the secondary structure of mRNA to temperature in intertidal snails based on SHAPE experiments. J Exp Biol 2023;226:jeb246544. [PMID: 37767692 DOI: 10.1242/jeb.246544] [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: 08/16/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
17
Lazaros K, Vlamos P, Vrahatis AG. Methods for cell-type annotation on scRNA-seq data: A recent overview. J Bioinform Comput Biol 2023;21:2340002. [PMID: 37743364 DOI: 10.1142/s0219720023400024] [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] [Indexed: 09/26/2023]
18
Kim EY, Kim JE, Chung SH, Park JE, Yoon D, Min HJ, Sung Y, Lee SB, Kim SW, Chang EJ. Concomitant induction of SLIT3 and microRNA-218-2 in macrophages by toll-like receptor 4 activation limits osteoclast commitment. Cell Commun Signal 2023;21:213. [PMID: 37596575 PMCID: PMC10436635 DOI: 10.1186/s12964-023-01226-w] [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: 04/26/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023]  Open
19
Tang Y, Li X, Shi M. LIDER: cell embedding based deep neural network classifier for supervised cell type identification. PeerJ 2023;11:e15862. [PMID: 37601262 PMCID: PMC10439717 DOI: 10.7717/peerj.15862] [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: 04/14/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]  Open
20
Stamp J, DenAdel A, Weinreich D, Crawford L. Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies. G3 (BETHESDA, MD.) 2023;13:jkad118. [PMID: 37243672 PMCID: PMC10484060 DOI: 10.1093/g3journal/jkad118] [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: 01/11/2023] [Revised: 01/11/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
21
Xu X, Qi Z, Han X, Xu A, Geng Z, He X, Ren Y, Duo Z. Predicting anticancer drug sensitivity on distributed data sources using federated deep learning. Heliyon 2023;9:e18615. [PMID: 37593639 PMCID: PMC10427996 DOI: 10.1016/j.heliyon.2023.e18615] [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: 06/16/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023]  Open
22
Magdy Mohamed Abdelaziz Barakat S, Sallehuddin R, Yuhaniz SS, R. Khairuddin RF, Mahmood Y. Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges. PeerJ Comput Sci 2023;9:e1180. [PMID: 37547391 PMCID: PMC10403225 DOI: 10.7717/peerj-cs.1180] [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: 04/07/2022] [Accepted: 04/27/2023] [Indexed: 08/08/2023]
23
Li L, Zheng X, Wang J, Zhang X, He X, Xiong L, Song S, Su J, Diao Y, Yuan Z, Zhang Z, Hu Z. Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids. Nat Commun 2023;14:3930. [PMID: 37402793 DOI: 10.1038/s41467-023-39534-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/16/2023] [Indexed: 07/06/2023]  Open
24
Rundell TB, Brunelli M, Alvi A, Safian G, Capobianco C, Tu W, Subedi S, Fiumera A, Musselman LP. Polygenic adaptation to overnutrition reveals a role for cholinergic signaling in longevity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544888. [PMID: 37398379 PMCID: PMC10312690 DOI: 10.1101/2023.06.14.544888] [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]
25
Kumasaka N, Rostom R, Huang N, Polanski K, Meyer KB, Patel S, Boyd R, Gomez C, Barnett SN, Panousis NI, Schwartzentruber J, Ghoussaini M, Lyons PA, Calero-Nieto FJ, Göttgens B, Barnes JL, Worlock KB, Yoshida M, Nikolić MZ, Stephenson E, Reynolds G, Haniffa M, Marioni JC, Stegle O, Hagai T, Teichmann SA. Mapping interindividual dynamics of innate immune response at single-cell resolution. Nat Genet 2023;55:1066-1075. [PMID: 37308670 PMCID: PMC10260404 DOI: 10.1038/s41588-023-01421-y] [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: 08/28/2021] [Accepted: 04/27/2023] [Indexed: 06/14/2023]
26
Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023;24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
27
Pielawski N, Andersson A, Avenel C, Behanova A, Chelebian E, Klemm A, Nysjö F, Solorzano L, Wählby C. TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data. Heliyon 2023;9:e15306. [PMID: 37131430 PMCID: PMC10149187 DOI: 10.1016/j.heliyon.2023.e15306] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 05/04/2023]  Open
28
Ahlmann-Eltze C, Huber W. Comparison of transformations for single-cell RNA-seq data. Nat Methods 2023;20:665-672. [PMID: 37037999 PMCID: PMC10172138 DOI: 10.1038/s41592-023-01814-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/11/2023] [Indexed: 04/12/2023]
29
Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023;24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
30
Wang D, Hu X, Ye H, Wang Y, Yang Q, Liang X, Wang Z, Zhou Y, Wen M, Yuan X, Zheng X, Ye W, Guo B, Yusuyin M, Russinova E, Zhou Y, Wang K. Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton. Genome Biol 2023;24:49. [PMID: 36918913 PMCID: PMC10012527 DOI: 10.1186/s13059-023-02886-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/26/2023] [Indexed: 03/16/2023]  Open
31
Welsh H, Batalha CMPF, Li W, Mpye KL, Souza-Pinto NC, Naslavsky MS, Parra EJ. A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data. Clin Epigenetics 2023;15:41. [PMID: 36906598 PMCID: PMC10008016 DOI: 10.1186/s13148-023-01459-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: 10/10/2022] [Accepted: 02/24/2023] [Indexed: 03/13/2023]  Open
32
Zhu J, Shang L, Zhou X. SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics. Genome Biol 2023;24:39. [PMID: 36869394 PMCID: PMC9983268 DOI: 10.1186/s13059-023-02879-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023]  Open
33
Yan X, Zheng R, Wu F, Li M. CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity. Bioinformatics 2023;39:7055295. [PMID: 36821425 PMCID: PMC9985174 DOI: 10.1093/bioinformatics/btad099] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/27/2022] [Accepted: 02/22/2023] [Indexed: 02/24/2023]  Open
34
Noya SB, Sehgal A. Variant-to-gene, gene-to-trait: finding new sleep genes through GWAS. Trends Genet 2023;39:338-339. [PMID: 36858881 DOI: 10.1016/j.tig.2023.02.013] [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: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023]
35
Quantifying portable genetic effects and improving cross-ancestry genetic prediction with GWAS summary statistics. Nat Commun 2023;14:832. [PMID: 36788230 PMCID: PMC9929290 DOI: 10.1038/s41467-023-36544-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 02/07/2023] [Indexed: 02/16/2023]  Open
36
Kumar A, Schrader AW, Boroojeny AE, Asadian M, Lee J, Song YJ, Zhao SD, Han HS, Sinha S. Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT). RESEARCH SQUARE 2023:rs.3.rs-2481749. [PMID: 36747718 PMCID: PMC9901031 DOI: 10.21203/rs.3.rs-2481749/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
37
Cohesin controls X chromosome structure remodeling and X-reactivation during mouse iPSC-reprogramming. Proc Natl Acad Sci U S A 2023;120:e2213810120. [PMID: 36669113 PMCID: PMC9942853 DOI: 10.1073/pnas.2213810120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
38
Palermo J, Chesi A, Zimmerman A, Sonti S, Pahl MC, Lasconi C, Brown EB, Pippin JA, Wells AD, Doldur-Balli F, Mazzotti DR, Pack AI, Gehrman PR, Grant SF, Keene AC. Variant-to-gene mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as a regulator of sleep. SCIENCE ADVANCES 2023;9:eabq0844. [PMID: 36608130 PMCID: PMC9821868 DOI: 10.1126/sciadv.abq0844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/05/2022] [Indexed: 05/13/2023]
39
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nat Genet 2023;55:78-88. [PMID: 36624346 PMCID: PMC9840703 DOI: 10.1038/s41588-022-01256-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/01/2022] [Indexed: 01/11/2023]
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Toneyan S, Tang Z, Koo PK. Evaluating deep learning for predicting epigenomic profiles. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00570-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Liu L, Yang Y, Deng Y, Zhang T. Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes. MICROBIOME 2022;10:209. [PMID: 36457010 PMCID: PMC9716684 DOI: 10.1186/s40168-022-01415-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
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An autoactive NB-LRR gene causes Rht13 dwarfism in wheat. Proc Natl Acad Sci U S A 2022;119:e2209875119. [PMID: 36417432 PMCID: PMC9860330 DOI: 10.1073/pnas.2209875119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
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David JK, Maden SK, Wood MA, Thompson RF, Nellore A. Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads. Genome Biol 2022;23:240. [PMID: 36369064 PMCID: PMC9652823 DOI: 10.1186/s13059-022-02789-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]  Open
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DaDalt AA, Bonham CA, Lotze GP, Luiso AA, Vacratsis PO. Src-mediated phosphorylation of the ribosome biogenesis factor hYVH1 affects its localization, promoting partitioning to the 60S ribosomal subunit. J Biol Chem 2022;298:102679. [PMID: 36370849 PMCID: PMC9731860 DOI: 10.1016/j.jbc.2022.102679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022]  Open
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Linder J, Koplik SE, Kundaje A, Seelig G. Deciphering the impact of genetic variation on human polyadenylation using APARENT2. Genome Biol 2022;23:232. [PMID: 36335397 PMCID: PMC9636789 DOI: 10.1186/s13059-022-02799-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/08/2022]  Open
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Hoberecht L, Perampalam P, Lun A, Fortin JP. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies. Nat Commun 2022;13:6568. [PMID: 36323688 PMCID: PMC9630310 DOI: 10.1038/s41467-022-34320-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]  Open
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Hämälä T, Ning W, Kuittinen H, Aryamanesh N, Savolainen O. Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife 2022;11:83115. [PMID: 36306157 PMCID: PMC9616567 DOI: 10.7554/elife.83115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022]  Open
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Rodriguez Gallo MC, Li Q, Mehta D, Uhrig RG. Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation. BMC PLANT BIOLOGY 2022;22:496. [PMID: 36273172 PMCID: PMC9587599 DOI: 10.1186/s12870-022-03870-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/04/2022] [Indexed: 05/24/2023]
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Suh S, Choi EH, Raguram A, Liu DR, Palczewski K. Precision genome editing in the eye. Proc Natl Acad Sci U S A 2022;119:e2210104119. [PMID: 36122230 PMCID: PMC9522375 DOI: 10.1073/pnas.2210104119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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Treppner M, Binder H, Hess M. Interpretable generative deep learning: an illustration with single cell gene expression data. Hum Genet 2022;141:1481-1498. [PMID: 34988661 PMCID: PMC9360114 DOI: 10.1007/s00439-021-02417-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022]
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