1.
Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia.
Avey D, Sankararaman S, Yim AKY, Barve R, Milbrandt J, Mitra RD.
Cell Rep. 2018 Sep 25;24(13):3619-3629.e4. doi: 10.1016/j.celrep.2018.08.080.
2.
Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing.
Wang P, Chen Y, Yong J, Cui Y, Wang R, Wen L, Qiao J, Tang F.
Cell Rep. 2018 Sep 25;24(13):3554-3567.e3. doi: 10.1016/j.celrep.2018.08.056.
3.
De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis.
Wang S, Mandell JD, Kumar Y, Sun N, Morris MT, Arbelaez J, Nasello C, Dong S, et al.
Cell Rep. 2018 Sep 25;24(13):3441-3454.e12. doi: 10.1016/j.celrep.2018.08.082.
4.
Targeting individual cells by barcode in pooled sequence libraries.
Ranu N, Villani AC, Hacohen N, Blainey PC.
Nucleic Acids Res. 2018 Sep 26. doi: 10.1093/nar/gky856.
5.
Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes.
Pezoldt J, Pasztoi M, Zou M, Wiechers C, Beckstette M, Thierry GR, Vafadarnejad E, Floess S, Arampatzi P, Buettner M, Schweer J, Fleissner D, Vital M, Pieper DH, Basic M, Dersch P, Strowig T, Hornef M, Bleich A, Bode U, Pabst O, Bajénoff M, Saliba AE, Huehn J.
Nat Commun. 2018 Sep 25;9(1):3903. doi: 10.1038/s41467-018-06423-7.
6.
Fine mapping of MHC region in lung cancer highlights independent susceptibility loci by ethnicity.
Ferreiro-Iglesias A, Lesseur C, McKay J, Hung RJ, Han Y, Zong X, Christiani D, Johansson M, et al.
Nat Commun. 2018 Sep 25;9(1):3927. doi: 10.1038/s41467-018-05890-2.
7.
Single-nucleus transcriptomic survey of cell diversity and functional maturation in postnatal mammalian hearts.
Hu P, Liu J, Zhao J, Wilkins BJ, Lupino K, Wu H, Pei L.
Genes Dev. 2018 Sep 25. doi: 10.1101/gad.316802.118.
8.
Pseudogenes provide evolutionary evidence for the competitive endogenous RNA hypothesis.
Glenfield C, McLysaght A.
Mol Biol Evol. 2018 Sep 25. doi: 10.1093/molbev/msy183.
9.
How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.
Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B.
Nucleic Acids Res. 2018 Sep 25. doi: 10.1093/nar/gky836.
10.
Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription.
Qiu J, Dando O, Baxter PS, Hasel P, Heron S, Simpson TI, Hardingham GE.
Nat Protoc. 2018 Sep 24. doi: 10.1038/s41596-018-0029-2.
11.
Hrg1 promotes heme-iron recycling during hemolysis in the zebrafish kidney.
Zhang J, Chambers I, Yun S, Phillips J, Krause M, Hamza I.
PLoS Genet. 2018 Sep 24;14(9):e1007665. doi: 10.1371/journal.pgen.1007665.
12.
The APT complex is involved in non-coding RNA transcription and is distinct from CPF.
Lidschreiber M, Easter AD, Battaglia S, Rodríguez-Molina JB, Casañal A, Carminati M, Baejen C, Grzechnik P, Maier KC, Cramer P, Passmore LA.
Nucleic Acids Res. 2018 Sep 21. doi: 10.1093/nar/gky845.
13.
LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance.
Cunha LD, Yang M, Carter R, Guy C, Harris L, Crawford JC, Quarato G, Boada-Romero E, Kalkavan H, Johnson MDL, Natarajan S, Turnis ME, Finkelstein D, Opferman JT, Gawad C, Green DR.
Cell. 2018 Sep 17. pii: S0092-8674(18)31122-X. doi: 10.1016/j.cell.2018.08.061.
14.
Lung colonization by Aspergillus fumigatus is controlled by ZNF77.
Gago S, Overton NLD, Ben-Ghazzi N, Novak-Frazer L, Read ND, Denning DW, Bowyer P.
Nat Commun. 2018 Sep 20;9(1):3835. doi: 10.1038/s41467-018-06148-7.
15.
Aging alters the epigenetic asymmetry of HSC division.
Florian MC, Klose M, Sacma M, Jablanovic J, Knudson L, Nattamai KJ, Marka G, Vollmer A, Soller K, Sakk V, Cabezas-Wallscheid N, Zheng Y, Mulaw MA, Glauche I, Geiger H.
PLoS Biol. 2018 Sep 20;16(9):e2003389. doi: 10.1371/journal.pbio.2003389.
16.
Differential effects of partial and complete loss of TREM2 on microglial injury response and tauopathy.
Sayed FA, Telpoukhovskaia M, Kodama L, Li Y, Zhou Y, Le D, Hauduc A, Ludwig C, Gao F, Clelland C, Zhan L, Cooper YA, Davalos D, Akassoglou K, Coppola G, Gan L.
Proc Natl Acad Sci U S A. 2018 Sep 19. pii: 201811411. doi: 10.1073/pnas.1811411115.
17.
Reduced CD160 expression contributes to impaired NK cell function and poor clinical outcomes in patients with HCC.
Sun H, Xu J, Huang Q, Huang M, Li K, Qu K, Wen H, Lin R, Zheng M, Wei H, Xiao W, Sun R, Tian Z, Sun C.
Cancer Res. 2018 Sep 19. pii: canres.1049.2018. doi: 10.1158/0008-5472.CAN-18-1049.
18.
Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation.
Werner MS, Sieriebriennikov B, Prabh N, Loschko T, Lanz C, Sommer RJ.
Genome Res. 2018 Sep 19. pii: gr.234872.118. doi: 10.1101/gr.234872.118.
19.
Mannose Alters Gut Microbiome, Prevents Diet-Induced Obesity, and Improves Host Metabolism.
Sharma V, Smolin J, Nayak J, Ayala JE, Scott DA, Peterson SN, Freeze HH.
Cell Rep. 2018 Sep 18;24(12):3087-3098. doi: 10.1016/j.celrep.2018.08.064.
20.
Regulatory cocktail for dopaminergic neurons in a protovertebrate identified by whole-embryo single-cell transcriptomics.
Horie T, Horie R, Chen K, Cao C, Nakagawa M, Kusakabe TG, Satoh N, Sasakura Y, Levine M.
Genes Dev. 2018 Sep 18. doi: 10.1101/gad.317669.118.
21.
Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture.
Grau-Bové X, Ruiz-Trillo I, Irimia M.
Genome Biol. 2018 Sep 17;19(1):135. doi: 10.1186/s13059-018-1499-9.
22.
Use of contraceptive depot medroxyprogesterone acetate is associated with impaired cervicovaginal mucosal integrity.
Zalenskaya IA, Chandra N, Yousefieh N, Fang X, Adedipe OE, Jackson SS, Anderson SM, Mauck CK, Schwartz JL, Thurman AR, Doncel GF.
J Clin Invest. 2018 Sep 17. pii: 120583. doi: 10.1172/JCI120583.
23.
Single Cell and Open Chromatin Analysis Reveals Molecular Origin of Epidermal Cells of the Skin.
Fan X, Wang D, Burgmaier JE, Teng Y, Romano RA, Sinha S, Yi R.
Dev Cell. 2018 Sep 13. pii: S1534-5807(18)30680-4. doi: 10.1016/j.devcel.2018.08.010.
24.
Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop.
Sterne-Weiler T, Weatheritt RJ, Best AJ, Ha KCH, Blencowe BJ.
Mol Cell. 2018 Sep 10. pii: S1097-2765(18)30678-6. doi: 10.1016/j.molcel.2018.08.018.
25.
3' end additions by T7 RNA polymerase are RNA self-templated, distributive and diverse in character-RNA-Seq analyses.
Gholamalipour Y, Karunanayake Mudiyanselage A, Martin CT.
Nucleic Acids Res. 2018 Sep 14. doi: 10.1093/nar/gky796.
26.
Molecular Subtypes of Urothelial Bladder Cancer: Results from a Meta-cohort Analysis of 2411 Tumors.
Tan TZ, Rouanne M, Tan KT, Huang RY, Thiery JP.
Eur Urol. 2018 Sep 10. pii: S0302-2838(18)30619-5. doi: 10.1016/j.eururo.2018.08.027.
27.
ANP32A regulates ATM expression and prevents oxidative stress in cartilage, brain, and bone.
Cornelis FMF, Monteagudo S, Guns LKA, den Hollander W, Nelissen RGHH, Storms L, Peeters T, Jonkers I, Meulenbelt I, Lories RJ.
Sci Transl Med. 2018 Sep 12;10(458). pii: eaar8426. doi: 10.1126/scitranslmed.aar8426.
28.
GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge.
Costa F, Grün D, Backofen R.
Nat Commun. 2018 Sep 11;9(1):3685. doi: 10.1038/s41467-018-05988-7.
29.
Conservation of epigenetic regulation by the MLL3/4 tumour suppressor in planarian pluripotent stem cells.
Mihaylova Y, Abnave P, Kao D, Hughes S, Lai A, Jaber-Hijazi F, Kosaka N, Aboobaker AA.
Nat Commun. 2018 Sep 7;9(1):3633. doi: 10.1038/s41467-018-06092-6.
30.
Gene regulation underlies environmental adaptation in house mice.
Mack KL, Ballinger MA, Phifer-Rixey M, Nachman MW.
Genome Res. 2018 Sep 7. pii: gr.238998.118. doi: 10.1101/gr.238998.118.
31.
Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues.
Birnbaum KD.
Annu Rev Genet. 2018 Sep 7. doi: 10.1146/annurev-genet-120417-031247.
32.
Linking prostate cancer cell AR heterogeneity to distinct castration and enzalutamide responses.
Li Q, Deng Q, Chao HP, Liu X, Lu Y, Lin K, Liu B, Tang GW, Zhang D, Tracz A, Jeter C, Rycaj K, Calhoun-Davis T, Huang J, Rubin MA, Beltran H, Shen J, Chatta G, Puzanov I, Mohler JL, Wang J, Zhao R, Kirk J, Chen X, Tang DG.
Nat Commun. 2018 Sep 6;9(1):3600. doi: 10.1038/s41467-018-06067-7.
33.
Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions.
Wu X, Kabalane H, Kahli M, Petryk N, Laperrousaz B, Jaszczyszyn Y, Drillon G, Nicolini FE, Perot G, Robert A, Fund C, Chibon F, Xia R, Wiels J, Argoul F, Maguer-Satta V, Arneodo A, Audit B, Olivier H.
Nucleic Acids Res. 2018 Sep 5. doi: 10.1093/nar/gky797.
34.
Erratum: 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, Hoff PL, Tanriverdi K, Courtright A, Lu S, Khoory J, Rubio R, Baxter D, Driedonks TAP, Buermans HPJ, Hoen ENMN, Jiang H, Wang K, Ghiran I, Wang YE, Keuren-Jensen KV, Freedman JE, Woodruff PG, Laurent LC, Erle DJ, Galas DJ, Tewari M.
Nat Biotechnol. 2018 Sep 6;36(9):899. doi: 10.1038/nbt0918-899b. No abstract available.
35.
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells.
Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J.
Elife. 2018 Sep 6;7. pii: e36187. doi: 10.7554/eLife.36187.
36.
Macrophages Regulate Schwann Cell Maturation after Nerve Injury.
Stratton JA, Holmes A, Rosin NL, Sinha S, Vohra M, Burma NE, Trang T, Midha R, Biernaskie J.
Cell Rep. 2018 Sep 4;24(10):2561-2572.e6. doi: 10.1016/j.celrep.2018.08.004.
37.
Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq.
Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW.
Nat Commun. 2018 Sep 4;9(1):3588. doi: 10.1038/s41467-018-06052-0.
38.
Elevated Stromal Inflammatory Mediators Promote Prostate Cancer Progression in African American Men.
Gillard M, Javier R, Ji Y, Zheng SL, Xu J, Brendler CB, Crawford SE, Pierce B, Vander Griend DJ, Franco OE.
Cancer Res. 2018 Sep 4. pii: canres.3810.2017. doi: 10.1158/0008-5472.CAN-17-3810.
39.
RNA-Seq of newly diagnosed patients in the PADIMAC study leads to a bortezomib/lenalidomide decision signature.
Chapman MA, Sive J, Ambrose J, Roddie C, Counsell N, Lach A, Abbasian M, Popat R, Cavenagh JD, Oakervee H, Streetly MJ, Schey S, Koh M, Willis F, Virchis AE, Crowe J, Quinn MF, Cook G, Crawley CR, Pratt G, Cook M, Braganza N, Adedayo T, Smith P, Clifton-Hadley L, Owen RG, Sonneveld P, Keats JJ, Herrero J, Yong K.
Blood. 2018 Sep 4. pii: blood-2018-05-849893. doi: 10.1182/blood-2018-05-849893.
40.
Comparing Prognostic Utility of a Single-marker Immunohistochemistry Approach with Commercial Gene Expression Profiling Following Radical Prostatectomy.
Leapman MS, Nguyen HG, Cowan JE, Xue L, Stohr B, Simko J, Cooperberg MR, Carroll PR.
Eur Urol. 2018 Sep 1. pii: S0302-2838(18)30605-5. doi: 10.1016/j.eururo.2018.08.020.
41.
Sputum ANCA in Serum ANCA-Negative Eosinophilic Granulomatosis with Polyangiitis (eGPA).
Mukherjee M, Thomas SR, Radford K, Dvorkin-Gheva A, Davychenko S, Kjarsgaard M, Svenningsen S, Almas S, Felix LC, Stearns J, Li QZ, Khalidi N, Lacy P, Nair P.
Am J Respir Crit Care Med. 2018 Sep 4. doi: 10.1164/rccm.201804-0809OC.
42.
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 Sep 5. pii: S0016-5085(18)34764-4. doi: 10.1053/j.gastro.2018.07.010.
43.
RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF.
Rozenberg JM, Taylor JM, Mack CP.
Nucleic Acids Res. 2018 Sep 19;46(16):8232-8244. doi: 10.1093/nar/gky562.
44.
Casein kinase 2 mediated phosphorylation of Spt6 modulates histone dynamics and regulates spurious transcription.
Gouot E, Bhat W, Rufiange A, Fournier E, Paquet E, Nourani A.
Nucleic Acids Res. 2018 Sep 6;46(15):7612-7630. doi: 10.1093/nar/gky515.
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