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1.
Dissecting the mammary gland one cell at a time.
Cristea S, Polyak K.
Nat Commun. 2018 Jun 26;9(1):2473. doi: 10.1038/s41467-018-04905-2.
2.
Direct cell-cell contact activates SigM to express the ESX-4 secretion system in Mycobacterium smegmatis.
Clark RR, Judd J, Lasek-Nesselquist E, Montgomery SA, Hoffmann JG, Derbyshire KM, Gray TA.
Proc Natl Acad Sci U S A. 2018 Jun 25. pii: 201804227. doi: 10.1073/pnas.1804227115.
3.
Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling.
Burl RB, Ramseyer VD, Rondini EA, Pique-Regi R, Lee YH, Granneman JG.
Cell Metab. 2018 Jun 9. pii: S1550-4131(18)30332-2. doi: 10.1016/j.cmet.2018.05.025.
4.
Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming.
Zhao T, Fu Y, Zhu J, Liu Y, Zhang Q, Yi Z, Chen S, Jiao Z, Xu X, Xu J, Duo S, Bai Y, Tang C, Li C, Deng H.
Cell Stem Cell. 2018 Jun 12. pii: S1934-5909(18)30280-7. doi: 10.1016/j.stem.2018.05.025.
5.
Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.
Harmanci A, Gerstein M.
Nat Commun. 2018 Jun 22;9(1):2453. doi: 10.1038/s41467-018-04875-5.
6.
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 Jun 21. doi: 10.1093/nar/gky562.
7.
Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations.
Pellagatti A, Armstrong RN, Steeples V, Sharma E, Repapi E, Singh S, Sanchi A, Radujkovic A, Horn P, Dolatshad H, Roy S, Broxholme J, Lockstone H, Taylor S, Giagounidis A, Vyas P, Schuh A, Hamblin A, Papaemmanuil E, Killick S, Malcovati L, Hennrich ML, Gavin AC, Ho AD, Luft T, Hellstrom-Lindberg E, Cazzola M, Smith CWJ, Smith S, Boultwood J.
Blood. 2018 Jun 21. pii: blood-2018-04-843771. doi: 10.1182/blood-2018-04-843771.
8.
Salmonella Activation of STAT3 Signaling by SarA Effector Promotes Intracellular Replication and Production of IL-10.
Jaslow SL, Gibbs KD, Fricke WF, Wang L, Pittman KJ, Mammel MK, Thaden JT, Fowler VG Jr, Hammer GE, Elfenbein JR, Ko DC.
Cell Rep. 2018 Jun 19;23(12):3525-3536. doi: 10.1016/j.celrep.2018.05.072.
9.
Reporters to mark and eliminate basal or luminal epithelial cells in culture and in vivo.
Sonzogni O, Haynes J, Seifried LA, Kamel YM, Huang K, BeGora MD, Yeung FA, Robert-Tissot C, Heng YJ, Yuan X, Wulf GM, Kron KJ, Wagenblast E, Lupien M, Kislinger T, Hannon GJ, Muthuswamy SK.
PLoS Biol. 2018 Jun 20;16(6):e2004049. doi: 10.1371/journal.pbio.2004049.
10.
A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection.
Singhania A, Verma R, Graham CM, Lee J, Tran T, Richardson M, Lecine P, Leissner P, Berry MPR, Wilkinson RJ, Kaiser K, Rodrigue M, Woltmann G, Haldar P, O'Garra A.
Nat Commun. 2018 Jun 19;9(1):2308. doi: 10.1038/s41467-018-04579-w.
11.
Computational characterization of suppressive immune microenvironments in glioblastoma.
Luoto S, Hermelo I, Vuorinen EM, Hannus P, Kesseli J, Nykter M, Granberg KJ.
Cancer Res. 2018 Jun 19. pii: canres.3714.2017. doi: 10.1158/0008-5472.CAN-17-3714.
12.
DDX3 activates CBC-eIF3-mediated translation of uORF-containing oncogenic mRNAs to promote metastasis in HNSCC.
Chen HH, Yu HI, Yang MH, Tarn WY.
Cancer Res. 2018 Jun 19. pii: canres.0282.2018. doi: 10.1158/0008-5472.CAN-18-0282.
13.
dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments.
Petukhov V, Guo J, Baryawno N, Severe N, Scadden DT, Samsonova MG, Kharchenko PV.
Genome Biol. 2018 Jun 19;19(1):78. doi: 10.1186/s13059-018-1449-6.
14.
Regulation of Epithelial Plasticity Determines Metastatic Organotropism in Pancreatic Cancer.
Reichert M, Bakir B, Moreira L, Pitarresi JR, Feldmann K, Simon L, Suzuki K, Maddipati R, Rhim AD, Schlitter AM, Kriegsmann M, Weichert W, Wirth M, Schuck K, Schneider G, Saur D, Reynolds AB, Klein-Szanto AJ, Pehlivanoglu B, Memis B, Adsay NV, Rustgi AK.
Dev Cell. 2018 Jun 18;45(6):696-711.e8. doi: 10.1016/j.devcel.2018.05.025.
15.
Predictive Biomarkers for Endocrine Therapy: Retrospective Study in Tamoxifen and Exemestane Adjuvant Multinational (TEAM) Trial.
Roseweir AK, Bennett L, Dickson A, Cheng K, Quintayo MA, Bayani J, McMillan DC, Horgan PG, van de Velde CJH, Seynaeve C, Hasenburg A, Kieback DG, Markopoulos C, Dirix LY, Rea DW, Mallon EA, Bartlett JMS, Edwards J.
J Natl Cancer Inst. 2018 Jun 1;110(6):616-627. doi: 10.1093/jnci/djx255.
16.
A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the LAZY1-dependent Asymmetric Distribution of Auxin.
Zhang N, Yu H, Yu H, Cai Y, Huang L, Xu C, Xiong G, Meng X, Wang J, Chen H, Liu G, Jing Y, Yuan Y, Liang Y, Li S, Smith SM, Li J, Wang Y.
Plant Cell. 2018 Jun 18. pii: tpc.00063.2018. doi: 10.1105/tpc.18.00063.
17.
A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain.
Davie K, Janssens J, Koldere D, De Waegeneer M, Pech U, Kreft Ł, Aibar S, Makhzami S, Christiaens V, Bravo Gonzalez-Blas C, Poovathingal S, Hulselmans G, Spanier KI, Moerman T, Vanspauwen B, Geurs S, Voet T, Lammertyn J, Thienpont B, Liu S, Konstantinides N, Fiers M, Verstreken P, Aerts S.
Cell. 2018 Jun 9. pii: S0092-8674(18)30720-7. doi: 10.1016/j.cell.2018.05.057.
18.
Selection and Application of Tissue microRNAs for Non-endoscopic Diagnosis of Barrett's Esophagus.
Li X, Kleeman S, Coburn SB, Fumagalli C, Perner J, Jammula S, Pfeiffer RM, Orzolek L, Hao H, Taylor PR, Miremadi A, Galeano-Dalmau N, Lao-Sirieix P, Tennyson M, MacRae S, Cook MB, Fitzgerald RC.
Gastroenterology. 2018 Jun 12. pii: S0016-5085(18)34643-2. doi: 10.1053/j.gastro.2018.05.050.
19.
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 Jun 14. doi: 10.1093/nar/gky515.
20.
Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes.
Barshad G, Blumberg A, Cohen T, Mishmar D.
Genome Res. 2018 Jun 14. doi: 10.1101/gr.226324.117.
21.
SOX9 has distinct regulatory roles in alternative splicing and transcription.
Girardot M, Bayet E, Maurin J, Fort P, Roux P, Raynaud P.
Nucleic Acids Res. 2018 Jun 13. doi: 10.1093/nar/gky553.
22.
EWS/ETS-driven Ewing Sarcoma requires BET bromodomain proteins.
Gollavilli PN, Pawar A, Wilder-Romans K, Ramakrishnan N, Engelke CG, Dommeti VL, Krishnamurthy PM, Nallasivam A, Apel IJ, Xu T, Qin Z, Feng FY, Asangani IA.
Cancer Res. 2018 Jun 13. pii: canres.0484.2018. doi: 10.1158/0008-5472.CAN-18-0484.
23.
Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.
Fan J, Lee HO, Lee S, Ryu DE, Lee S, Xue C, Kim SJ, Kim K, Barkas N, Park PJ, Park WY, Kharchenko PV.
Genome Res. 2018 Jun 13. doi: 10.1101/gr.228080.117.
24.
Ambient Pollution Related Reprogramming of the Human Small Airway Epithelial Transcriptome.
O'Beirne SL, Shenoy SA, Salit J, Strulovici-Barel Y, Kaner RJ, Visvanathan S, Fine JS, Mezey JG, Crystal RG.
Am J Respir Crit Care Med. 2018 Jun 13. doi: 10.1164/rccm.201712-2526OC.
25.
Ca2+-binding protein NECAB2 facilitates inflammatory pain hypersensitivity.
Zhang MD, Su J, Adori C, Cinquina V, Malenczyk K, Girach F, Peng C, Ernfors P, Low P, Borgius L, Kiehn O, Watanabe M, Uhlen M, Mitsios N, Mulder J, Harkany T, Hokfelt T.
J Clin Invest. 2018 Jun 12. pii: 120913. doi: 10.1172/JCI120913.
26.
Genetics of alternative splicing evolution during sunflower domestication.
Smith CCR, Tittes S, Mendieta JP, Collier-Zans E, Rowe HC, Rieseberg LH, Kane NC.
Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6768-6773. doi: 10.1073/pnas.1803361115. Epub 2018 Jun 11.
27.
A Single-Cell Transcriptomic Atlas of Thymus Organogenesis Resolves Cell Types and Developmental Maturation.
Kernfeld EM, Genga RMJ, Neherin K, Magaletta ME, Xu P, Maehr R.
Immunity. 2018 Jun 19;48(6):1258-1270.e6. doi: 10.1016/j.immuni.2018.04.015. Epub 2018 Jun 5.
28.
Toxins that Trash Translation.
Buskirk AR.
Mol Cell. 2018 Jun 7;70(5):759-760. doi: 10.1016/j.molcel.2018.05.027. Epub 2018 Jun 7.
29.
Histone Variant H2A.Z is Required for the Maintenance of Smooth Muscle Cell Identity as Revealed by Single-Cell Transcriptomics.
Yao F, Yu P, Li Y, Yuan X, Li Z, Zhang T, Liu F, Wang Y, Wang Y, Li D, Ma B, Shu C, Kong W, Zhou B, Wang L.
Circulation. 2018 Jun 5. pii: CIRCULATIONAHA.117.033114. doi: 10.1161/CIRCULATIONAHA.117.033114.
30.
Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response.
Gerrick ER, Barbier T, Chase MR, Xu R, Francois J, Lin VH, Szucs MJ, Rock JM, Ahmad R, Tjaden B, Livny J, Fortune SM.
Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6464-6469. doi: 10.1073/pnas.1718003115. Epub 2018 Jun 5.
31.
Oncogenic properties of NEAT1 in prostate cancer cells depend on the CDC5L-AGRN transcriptional regulation circuit.
Li X, Wang X, Song W, Xu H, Huang R, Wang Y, Zhao W, Xiao Z, Yang X.
Cancer Res. 2018 Jun 5. pii: canres.0688.2018. doi: 10.1158/0008-5472.CAN-18-0688.
32.
SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology.
Abdelmoez MN, Iida K, Oguchi Y, Nishikii H, Yokokawa R, Kotera H, Uemura S, Santiago JG, Shintaku H.
Genome Biol. 2018 Jun 6;19(1):66. doi: 10.1186/s13059-018-1446-9.
33.
Comprehensive comparative analysis of 5'-end RNA-sequencing methods.
Adiconis X, Haber AL, Simmons SK, Levy Moonshine A, Ji Z, Busby MA, Shi X, Jacques J, Lancaster MA, Pan JQ, Regev A, Levin JZ.
Nat Methods. 2018 Jun 4. doi: 10.1038/s41592-018-0014-2.
34.
Striking circadian neuron diversity and cycling of Drosophila alternative splicing.
Wang Q, Abruzzi KC, Rosbash M, Rio DC.
Elife. 2018 Jun 4;7. pii: e35618. doi: 10.7554/eLife.35618.
35.
Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides.
Zhang S, Samocha KE, Rivas MA, Karczewski KJ, Daly E, Schmandt B, Neale BM, MacArthur DG, Daly MJ.
Genome Res. 2018 Jun 1. doi: 10.1101/gr.231902.117.
36.
The fractured landscape of RNA-seq alignment: the default in our STARs.
Ballouz S, Dobin A, Gingeras TR, Gillis J.
Nucleic Acids Res. 2018 Jun 1;46(10):5125-5138. doi: 10.1093/nar/gky325.
37.
Tn5Prime, a Tn5 based 5' capture method for single cell RNA-seq.
Cole C, Byrne A, Beaudin AE, Forsberg EC, Vollmers C.
Nucleic Acids Res. 2018 Jun 1;46(10):e62. doi: 10.1093/nar/gky182.
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