Monthly Letter

1. Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression.
Padeken J, Zeller P, Towbin B, Katic I, Kalck V, Methot SP, Gasser SM. Genes Dev. 2019 Feb 25. doi: 10.1101/gad.322495.118.

2. hESC-Derived Thalamic Organoids Form Reciprocal Projections When Fused with Cortical Organoids.
Xiang Y, Tanaka Y, Cakir B, Patterson B, Kim KY, Sun P, Kang YJ, Zhong M, Liu X, Patra P, Lee SH, Weissman SM, Park IH. Cell Stem Cell. 2019 Feb 14. pii: S1934-5909(18)30605-2. doi: 10.1016/j.stem.2018.12.015.

3. De novo gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization.
Levitin HM, Yuan J, Cheng YL, Ruiz FJ, Bush EC, Bruce JN, Canoll P, Iavarone A, Lasorella A, Blei DM, Sims PA. Mol Syst Biol. 2019 Feb 22;15(2):e8557. doi: 10.15252/msb.20188557.

4. Extreme slow growth as alternative strategy to survive deep starvation in bacteria.
Gray DA, Dugar G, Gamba P, Strahl H, Jonker MJ, Hamoen LW. Nat Commun. 2019 Feb 21;10(1):890. doi: 10.1038/s41467-019-08719-8.

5. T cell clonal expansions in ileal Crohn's disease are associated with smoking behaviour and postoperative recurrence.
Allez M, Auzolle C, Ngollo M, Bottois H, Chardiny V, Corraliza AM, Salas A, Perez K, Stefanescu C, Nancey S, Buisson A, Pariente B, Fumery M, Sokol H, Tréton X, Barnich N, Seksik P, Le Bourhis L; REMIND Study Group. Gut. 2019 Feb 12. pii: gutjnl-2018-317878. doi: 10.1136/gutjnl-2018-317878.

6. Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells.
Sharma S, Wang J, Alqassim E, Portwood S, Cortes Gomez E, Maguire O, Basse PH, Wang ES, Segal BH, Baysal BE. Genome Biol. 2019 Feb 21;20(1):37. doi: 10.1186/s13059-019-1651-1.

7. Global transcriptional regulation of innate immunity by ATF-7 in C. elegans.
Fletcher M, Tillman EJ, Butty VL, Levine SS, Kim DH. PLoS Genet. 2019 Feb 21;15(2):e1007830. doi: 10.1371/journal.pgen.1007830.

8. Long noncoding RNA MALAT1 releases epigenetic silencing of HIV-1 replication by displacing the polycomb repressive complex 2 from binding to the LTR promoter.
Qu D, Sun WW, Li L, Ma L, Sun L, Jin X, Li T, Hou W, Wang JH. Nucleic Acids Res. 2019 Feb 21. pii: gkz117. doi: 10.1093/nar/gkz117.

9. lnCAR: a comprehensive resource for lncRNAs from Cancer Arrays.
Zheng Y, Xu Q, Liu M, Hu H, Xie Y, Zuo Z, Ren J. Cancer Res. 2019 Feb 20. pii: canres.2169.2018. doi: 10.1158/0008-5472.CAN-18-2169.

10. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads.
Liao Y, Smyth GK, Shi W. Nucleic Acids Res. 2019 Feb 20. pii: gkz114. doi: 10.1093/nar/gkz114.

11. A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.
Wang D, Eraslan B, Wieland T, Hallström B, Hopf T, Zolg DP, Zecha J, Asplund A, Li LH, Meng C, Frejno M, Schmidt T, Schnatbaum K, Wilhelm M, Ponten F, Uhlen M, Gagneur J, Hahne H, Kuster B. Mol Syst Biol. 2019 Feb 18;15(2):e8503. doi: 10.15252/msb.20188503.

12. Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq.
Guo L, Lin L, Wang X, Gao M, Cao S, Mai Y, Wu F, Kuang J, Liu H, Yang J, Chu S, Song H, Li D, Liu Y, Wu K, Liu J, Wang J, Pan G, Hutchins AP, Liu J, Pei D, Chen J. Mol Cell. 2019 Feb 21;73(4):815-829.e7. doi: 10.1016/j.molcel.2019.01.042. Epub 2019 Feb 13.

13. Integrated analysis of multiple receptor tyrosine kinases identifies Axl as a therapeutic target and mediator of resistance to sorafenib in hepatocellular carcinoma.
Pinato DJ, Brown MW, Trousil S, Aboagye EO, Beaumont J, Zhang H, Coley HM, Mauri FA, Sharma R. Br J Cancer. 2019 Feb 15. doi: 10.1038/s41416-018-0373-6.

14. Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen.
Depledge DP, Srinivas KP, Sadaoka T, Bready D, Mori Y, Placantonakis DG, Mohr I, Wilson AC. Nat Commun. 2019 Feb 14;10(1):754. doi: 10.1038/s41467-019-08734-9.

15. Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma.
Silvestris DA, Picardi E, Cesarini V, Fosso B, Mangraviti N, Massimi L, Martini M, Pesole G, Locatelli F, Gallo A. Genome Biol. 2019 Feb 13;20(1):33. doi: 10.1186/s13059-019-1647-x.

16. PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.
Tyler SR, Rotti PG, Sun X, Yi Y, Xie W, Winter MC, Flamme-Wiese MJ, Tucker BA, Mullins RF, Norris AW, Engelhardt JF. Cell Rep. 2019 Feb 12;26(7):1951-1964.e8. doi: 10.1016/j.celrep.2019.01.063.

17. Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart.
Cui Y, Zheng Y, Liu X, Yan L, Fan X, Yong J, Hu Y, Dong J, Li Q, Wu X, Gao S, Li J, Wen L, Qiao J, Tang F. Cell Rep. 2019 Feb 12;26(7):1934-1950.e5. doi: 10.1016/j.celrep.2019.01.079.

18. Cold sensing by NaV1.8-positive and NaV1.8-negative sensory neurons.
Luiz AP, MacDonald DI, Santana-Varela S, Millet Q, Sikandar S, Wood JN, Emery EC. Proc Natl Acad Sci U S A. 2019 Feb 12. pii: 201814545. doi: 10.1073/pnas.1814545116.

19. Acidification of tumor at stromal boundaries drives transcriptome alterations associated with aggressive phenotypes.
Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. Cancer Res. 2019 Feb 12. pii: canres.1604.2018. doi: 10.1158/0008-5472.CAN-18-1604.

20. Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy.
Gide TN, Quek C, Menzies AM, Tasker AT, Shang P, Holst J, Madore J, Lim SY, Velickovic R, Wongchenko M, Yan Y, Lo S, Carlino MS, Guminski A, Saw RPM, Pang A, McGuire HM, Palendira U, Thompson JF, Rizos H, Silva IPD, Batten M, Scolyer RA, Long GV, Wilmott JS. Cancer Cell. 2019 Feb 11;35(2):238-255.e6. doi: 10.1016/j.ccell.2019.01.003.

21. CPPred: coding potential prediction based on the global description of RNA sequence.
Tong X, Liu S. Nucleic Acids Res. 2019 Feb 11. doi: 10.1093/nar/gkz087.

22. Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data.
Linderman GC, Rachh M, Hoskins JG, Steinerberger S, Kluger Y. Nat Methods. 2019 Feb 11. doi: 10.1038/s41592-018-0308-4.

23. Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions.
Gutierrez-Arcelus M, Teslovich N, Mola AR, Polidoro RB, Nathan A, Kim H, Hannes S, Slowikowski K, Watts GFM, Korsunsky I, Brenner MB, Raychaudhuri S, Brennan PJ. Nat Commun. 2019 Feb 8;10(1):687. doi: 10.1038/s41467-019-08604-4.

24. Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution.
Yu XX, Qiu WL, Yang L, Zhang Y, He MY, Li LC, Xu CR. EMBO J. 2019 Feb 8. pii: e100164. doi: 10.15252/embj.2018100164.

25. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562.
Zhou B, Ho SS, Greer SU, Zhu X, Bell JM, Arthur JG, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney MS, Haraksingh RR, Song G, Ji HP, Perrin D, Wong WH, Abyzov A, Urban AE. Genome Res. 2019 Feb 8. doi: 10.1101/gr.234948.118.

26. Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation.
Miragaia RJ, Gomes T, Chomka A, Jardine L, Riedel A, Hegazy AN, Whibley N, Tucci A, Chen X, Lindeman I, Emerton G, Krausgruber T, Shields J, Haniffa M, Powrie F, Teichmann SA. Immunity. 2019 Feb 19;50(2):493-504.e7. doi: 10.1016/j.immuni.2019.01.001. Epub 2019 Feb 5.

27. Widespread and Functional RNA Circularization in Localized Prostate Cancer.
Chen S, Huang V, Xu X, Livingstone J, Soares F, Jeon J, Zeng Y, Hua JT, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua MLK, Heisler LE, Foucal A, Fox NS, Fraser M, Bhandari V, Shiah YJ, Guan J, Li J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Liu S, Feng F, Wu X, Shao YW, Komor MA, Sahinalp C, Collins C, Hoogstrate Y, de Jong M, Fijneman RJA, Fei T, Jenster G, van der Kwast T, Bristow RG, Boutros PC, He HH. Cell. 2019 Feb 7;176(4):831-843.e22. doi: 10.1016/j.cell.2019.01.025.

28. A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene.
Hecker M, Boxberger N, Illner N, Fitzner B, Schröder I, Winkelmann A, Dudesek A, Meister S, Koczan D, Lorenz P, Thiesen HJ, Zettl UK. PLoS Genet. 2019 Feb 7;15(2):e1007961. doi: 10.1371/journal.pgen.1007961. eCollection 2019 Feb.

29. RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types.
Monaco G, Lee B, Xu W, Mustafah S, Hwang YY, Carré C, Burdin N, Visan L, Ceccarelli M, Poidinger M, Zippelius A, Pedro de Magalhães J, Larbi A. Cell Rep. 2019 Feb 5;26(6):1627-1640.e7. doi: 10.1016/j.celrep.2019.01.041.

30. A Designed Small Molecule Inhibitor of a Non-Coding RNA Sensitizes HER2 Negative Cancers to Herceptin.
Costales MG, Hoch DG, Abegg D, Childs-Disney JL, Velagapudi SP, Adibekian A, Disney MD. J Am Chem Soc. 2019 Feb 20;141(7):2960-2974. doi: 10.1021/jacs.8b10558. Epub 2019 Feb 6.

31. Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data.
Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP. Nat Commun. 2019 Feb 4;10(1):646. doi: 10.1038/s41467-019-08614-2.

32. Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs.
Yan Z, Huang N, Wu W, Chen W, Jiang Y, Chen J, Huang X, Wen X, Xu J, Jin Q, Zhang K, Chen Z, Chien S, Zhong S. Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3328-3337. doi: 10.1073/pnas.1819788116. Epub 2019 Feb 4.

33. HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses.
Langer S, Hammer C, Hopfensperger K, Klein L, Hotter D, De Jesus PD, Herbert KM, Pache L, Smith N, van der Merwe JA, Chanda SK, Fellay J, Kirchhoff F, Sauter D. Elife. 2019 Feb 5;8. pii: e41930. doi: 10.7554/eLife.41930.

34. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.
Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD. Nat Protoc. 2019 Feb;14(2):482-517. doi: 10.1038/s41596-018-0103-9.

35. Long noncoding RNA NEXN-AS1 mitigates atherosclerosis by regulating the actin-binding protein NEXN.
Hu YW, Guo FX, Xu YJ, Li P, Lu ZF, McVey DG, Zheng L, Wang Q, Ye JH, Kang CM, Wu SG, Zhao JJ, Ma X, Yang Z, Fang FC, Qiu YR, Xu BM, Xiao L, Wu Q, Wu LM, Ding L, Webb TR, Samani NJ, Ye S. J Clin Invest. 2019 Feb 4. pii: 98230. doi: 10.1172/JCI98230.

36. RhoE Fine-Tunes Inflammatory Response in Myocardial Infarction.
Dai Y, Song J, Li W, Yang T, Yue X, Lin X, Yang X, Luo W, Guo J, Wang X, Lai S, Andrade KC, Chang J. Circulation. 2019 Feb 26;139(9):1185-1198. doi: 10.1161/CIRCULATIONAHA.118.033700.