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1.
SOX4 Promotes ATOH1-independent Intestinal Secretory Differentiation Toward Tuft and Enteroendocrine Fates.
Gracz AD, Samsa LA, Fordham MJ, Trotier DC, Zwarycz B, Lo YH, Bao K, Starmer J, Raab JR, Shroyer NF, Reinhardt RL, Magness ST.
Gastroenterology. 2018 Jul 25. pii: S0016-5085(18)34811-X. doi: 10.1053/j.gastro.2018.07.023.
2.
Unperturbed expression bias of imprinted genes in schizophrenia.
Gulyas-Kovacs A, Keydar I, Xia E, Fromer M, Hoffman G, Ruderfer D, Sachidanandam R, Chess A.
Nat Commun. 2018 Jul 25;9(1):2914. doi: 10.1038/s41467-018-04960-9.
3.
Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach.
D'Antonio M, Benaglio P, Jakubosky D, Greenwald WW, Matsui H, Donovan MKR, Li H, Smith EN, D'Antonio-Chronowska A, Frazer KA.
Cell Rep. 2018 Jul 24;24(4):883-894. doi: 10.1016/j.celrep.2018.06.091.
4.
Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5.
Lee YJ, Wang Q, Rio DC.
Genes Dev. 2018 Jul 24. doi: 10.1101/gad.316034.118.
5.
Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data.
Assefa AT, De Paepe K, Everaert C, Mestdagh P, Thas O, Vandesompele J.
Genome Biol. 2018 Jul 24;19(1):96. doi: 10.1186/s13059-018-1466-5.
6.
Genes regulated by SATB2 during neurodevelopment contribute to schizophrenia and educational attainment.
Whitton L, Apostolova G, Rieder D, Dechant G, Rea S, Donohoe G, Morris DW.
PLoS Genet. 2018 Jul 24;14(7):e1007515. doi: 10.1371/journal.pgen.1007515.
7.
Angiopoietin-like protein 3 blocks nuclear import of FAK and contributes to sorafenib response.
Bao Y, Yang F, Liu B, Zhao T, Xu Z, Xiong Y, Sun S, Qu L, Wang L.
Br J Cancer. 2018 Jul 23. doi: 10.1038/s41416-018-0189-4.
8.
Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment.
Lauridsen FKB, Jensen TL, Rapin N, Aslan D, Wilhelmson AS, Pundhir S, Rehn M, Paul F, Giladi A, Hasemann MS, Serup P, Amit I, Porse BT.
Cell Rep. 2018 Jul 17;24(3):766-780. doi: 10.1016/j.celrep.2018.06.057.
9.
Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes.
Rheaume BA, Jereen A, Bolisetty M, Sajid MS, Yang Y, Renna K, Sun L, Robson P, Trakhtenberg EF.
Nat Commun. 2018 Jul 17;9(1):2759. doi: 10.1038/s41467-018-05134-3.
10.
MouR controls the expression of the Listeria monocytogenes Agr system and mediates virulence.
Pinheiro J, Lisboa J, Pombinho R, Carvalho F, Carreaux A, Brito C, Pontinen A, Korkeala H, Dos Santos NMS, Morais-Cabral JH, Sousa S, Cabanes D.
Nucleic Acids Res. 2018 Jul 12. doi: 10.1093/nar/gky624.
11.
Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment.
Sarangdhar MA, Chaubey D, Srikakulam N, Pillai B.
Nucleic Acids Res. 2018 Jul 13. doi: 10.1093/nar/gky628.
12.
Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling.
Giraldez MD, Spengler RM, Etheridge A, Godoy PM, Barczak AJ, Srinivasan S, De Hoff PL, Tanriverdi K, Courtright A, Lu S, Khoory J, Rubio R, Baxter D, Driedonks TAP, Buermans HPJ, Nolte-'t Hoen ENM, Jiang H, Wang K, Ghiran I, Wang YE, Van Keuren-Jensen K, Freedman JE, Woodruff PG, Laurent LC, Erle DJ, Galas DJ, Tewari M.
Nat Biotechnol. 2018 Jul 16. doi: 10.1038/nbt.4183.
13.
Overexpression of Rac GTPase activating Protein 1 Contributes to Proliferation of Cancer Cells by Reducing Hippo Signaling to Promote Cytokinesis.
Yang XM, Cao XY, He P, Li J, Feng MX, Zhang YL, Zhang XL, Wang YH, Yang Q, Zhu L, Nie HZ, Jiang SH, Tian GA, Zhang XX, Liu Q, Ji J, Zhu X, Xia Q, Zhang ZG.
Gastroenterology. 2018 Jul 12. pii: S0016-5085(18)34764-4. doi: 10.1053/j.gastro.2018.07.010.
14.
Normal breast-derived epithelial cells with luminal and intrinsic subtype-enriched gene expression document inter-individual differences in their differentiation cascade.
Kumar B, Prasad MS, Bhat-Nakshatri P, Anjanappa M, Kalra M, Marino N, Storniolo AMV, Rao X, Liu S, Wan J, Liu Y, Nakshatri H.
Cancer Res. 2018 Jul 11. pii: canres.0509.2018. doi: 10.1158/0008-5472.CAN-18-0509.
15.
Detection and removal of barcode swapping in single-cell RNA-seq data.
Griffiths JA, Richard AC, Bach K, Lun ATL, Marioni JC.
Nat Commun. 2018 Jul 10;9(1):2667. doi: 10.1038/s41467-018-05083-x.
16.
A temporally dynamic Foxp3 autoregulatory transcriptional circuit controls the effector Treg programme.
Bending D, Paduraru A, Ducker CB, Prieto Martin P, Crompton T, Ono M.
EMBO J. 2018 Jul 10. pii: e99013. doi: 10.15252/embj.201899013.
17.
Genomic and Transcriptomic Analysis Reveals Incremental Disruption of Key Signaling Pathways during Melanoma Evolution.
Shain AH, Joseph NM, Yu R, Benhamida J, Liu S, Prow T, Ruben B, North J, Pincus L, Yeh I, Judson R, Bastian BC.
Cancer Cell. 2018 Jul 9;34(1):45-55.e4. doi: 10.1016/j.ccell.2018.06.005.
18.
Genetic determinants of co-accessible chromatin regions in activated T cells across humans.
Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, De Jager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ, Regev A.
Nat Genet. 2018 Jul 9. doi: 10.1038/s41588-018-0156-2.
19.
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations.
Duren Z, Chen X, Zamanighomi M, Zeng W, Satpathy AT, Chang HY, Wang Y, Wong WH.
Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7723-7728. doi: 10.1073/pnas.1805681115. Epub 2018 Jul 9.
20.
The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978.
Kroger C, MacKenzie KD, Alshabib EY, Kirzinger MWB, Suchan DM, Chao TC, Akulova V, Miranda-CasoLuengo AA, Monzon VA, Conway T, Sivasankaran SK, Hinton JCD, Hokamp K, Cameron ADS.
Nucleic Acids Res. 2018 Jul 9. doi: 10.1093/nar/gky603.
21.
Identification of transcribed protein coding sequence remnants within lincRNAs.
Talyan S, Andrade-Navarro MA, Muro EM.
Nucleic Acids Res. 2018 Jul 9. doi: 10.1093/nar/gky608.
22.
H2A.Z.1 crosstalk with H3K56-acetylation controls gliogenesis through the transcription of folate receptor.
Su L, Xia W, Shen T, Liang Q, Wang W, Li H, Jiao J.
Nucleic Acids Res. 2018 Jul 3. doi: 10.1093/nar/gky585.
23.
Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift.
Okawa S, Salto C, Ravichandran S, Yang S, Toledo EM, Arenas E, Del Sol A.
Nat Commun. 2018 Jul 3;9(1):2595. doi: 10.1038/s41467-018-05016-8.
24.
Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway.
Tang-Huau TL, Gueguen P, Goudot C, Durand M, Bohec M, Baulande S, Pasquier B, Amigorena S, Segura E.
Nat Commun. 2018 Jul 2;9(1):2570. doi: 10.1038/s41467-018-04985-0.
25.
Integrative genomic analysis reveals cancer-associated mutations at diagnosis of CML in patients with high risk disease.
Branford S, Wang P, Yeung DT, Thomson D, Purins A, Wadham C, Shahrin NH, Marum JE, Nataren N, Parker WT, Geoghegan J, Feng J, Shanmuganathan N, Mueller MC, Dietz C, Stangl D, Donaldson Z, Altamura H, Georgievski J, Braley J, Brown A, Hahn C, Walker I, Kim SH, Choi SY, Park SH, Kim DW, White DL, Yong ASM, Ross DM, Scott HS, Schreiber AW, Hughes TP.
Blood. 2018 Jul 2. pii: blood-2018-02-832253. doi: 10.1182/blood-2018-02-832253.
26.
Androgen receptor polyglutamine expansion drives age-dependent quality control defects and muscle dysfunction.
Nath SR, Yu Z, Gipson TA, Marsh GB, Yoshidome E, Robins DM, Todi SV, Housman DE, Lieberman AP.
J Clin Invest. 2018 Jul 23. pii: 99042. doi: 10.1172/JCI99042.
27.
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.
Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood Iii WH, Piao Y, Ogurtsov AY, Utani K, Noskov VN, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V.
Nucleic Acids Res. 2018 Jul 27;46(13):6712-6725. doi: 10.1093/nar/gky442.
28.
PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM.
Kralovicova J, ?evcikova I, Stejskalova E, Obuca M, Hiller M, Stanek D, Vorechovsky I.
Nucleic Acids Res. 2018 Jul 6;46(12):6166-6187. doi: 10.1093/nar/gky389.
29.
Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii.
Lesage KM, Huot L, Mouveaux T, Courjol F, Saliou JM, Gissot M.
Nucleic Acids Res. 2018 Jul 6;46(12):6057-6068. doi: 10.1093/nar/gky373.
30.
SPAR: small RNA-seq portal for analysis of sequencing experiments.
Kuksa PP, Amlie-Wolf A, Katanic ?, Valladares O, Wang LS, Leung YY.
Nucleic Acids Res. 2018 Jul 2;46(W1):W36-W42. doi: 10.1093/nar/gky330.
31.
An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response.
Chang JW, Zhang W, Yeh HS, Park M, Yao C, Shi Y, Kuang R, Yong J.
Nucleic Acids Res. 2018 Jul 6;46(12):5996-6008. doi: 10.1093/nar/gky340.
32.
Global DNA methylation synergistically regulates the nuclear and mitochondrial genomes in glioblastoma cells.
Sun X, Johnson J, St John JC.
Nucleic Acids Res. 2018 Jul 6;46(12):5977-5995. doi: 10.1093/nar/gky339.
33.
Oli2go: an automated multiplex oligonucleotide design tool.
Hendling M, Pabinger S, Peters K, Wolff N, Conzemius R, Bari?ic I.
Nucleic Acids Res. 2018 Jul 2;46(W1):W252-W256. doi: 10.1093/nar/gky319.
34.
Active Host Response to Algal Symbionts in the Sea Slug Elysia chlorotica.
Chan CX, Vaysberg P, Price DC, Pelletreau KN, Rumpho ME, Bhattacharya D.
Mol Biol Evol. 2018 Jul 1;35(7):1706-1711. doi: 10.1093/molbev/msy061.
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