Monthly Letter

1. High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions.
Aprianto R, Slager J, Holsappel S, Veening JW. Nucleic Acids Res. 2018 Aug 27. doi: 10.1093/nar/gky750.

2. Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3' End RNA-Seq.
Schmid M, Tudek A, Jensen TH. Cell Rep. 2018 Aug 28;24(9):2468-2478.e4. doi: 10.1016/j.celrep.2018.07.104.

3. Lysine benzoylation is a histone mark regulated by SIRT2.
Huang H, Zhang D, Wang Y, Perez-Neut M, Han Z, Zheng YG, Hao Q, Zhao Y. Nat Commun. 2018 Aug 28;9(1):3374. doi: 10.1038/s41467-018-05567-w.

4. Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos.
Liu D, Wang X, He D, Sun C, He X, Yan L, Li Y, Han JJ, Zheng P. Genome Res. 2018 Aug 28. pii: gr.233437.117. doi: 10.1101/gr.233437.117.

5. Screening for genes that regulate the differentiation of human megakaryocytic lineage cells.
Zhu F, Feng M, Sinha R, Seita J, Mori Y, Weissman IL. Proc Natl Acad Sci U S A. 2018 Aug 27. pii: 201805434. doi: 10.1073/pnas.1805434115.

6. Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases.
Michlmayr D, Pak TR, Rahman AH, Amir ED, Kim EY, Kim-Schulze S, Suprun M, Stewart MG, Thomas GP, Balmaseda A, Wang L, Zhu J, Suaréz-Fariñas M, Wolinsky SM, Kasarskis A, Harris E. Mol Syst Biol. 2018 Aug 27;14(8):e7862. doi: 10.15252/msb.20177862.

7. A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq.
Green CD, Ma Q, Manske GL, Shami AN, Zheng X, Marini S, Moritz L, Sultan C, Gurczynski SJ, Moore BB, Tallquist MD, Li JZ, Hammoud SS. Dev Cell. 2018 Aug 21. pii: S1534-5807(18)30636-1. doi: 10.1016/j.devcel.2018.07.025.

8. Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?
Crow M, Gillis J. Trends Genet. 2018 Aug 23. pii: S0168-9525(18)30128-8. doi: 10.1016/j.tig.2018.07.007.

9. Association Between Expression Level of PD1 by Tumor-Infiltrating CD8+ T Cells and Features of Hepatocellular Carcinoma.
Kim HD, Song GW, Park S, Jung MK, Kim MH, Kang HJ, Yoo C, Yi K, Kim KH, Eo S, Moon DB, Hong SM, Ju YS, Shin EC, Hwang S, Park SH. Gastroenterology. 2018 Aug 23. pii: S0016-5085(18)34897-2. doi: 10.1053/j.gastro.2018.08.030.

10. Elevated H3K79 homocysteinylation causes abnormal gene expression during neural development and subsequent neural tube defects.
Zhang Q, Bai B, Mei X, Wan C, Cao H, Dan Li, Wang S, Zhang M, Wang Z, Wu J, Wang H, Huo J, Ding G, Zhao J, Xie Q, Wang L, Qiu Z, Zhao S, Zhang T. Nat Commun. 2018 Aug 24;9(1):3436. doi: 10.1038/s41467-018-05451-7.

11. CSTF2-induced shortening of the RAC1 3'UTR promotes the pathogenesis of urothelial carcinoma of the bladder.
Chen X, Zhang J, Luo JH, Wu S, Yuan G, Ma NF, Feng Y, Cai M, Chen R, Lu J, Jiang L, Chen JW, Jin XH, Liu H, Chen W, Guan XY, Kang T, Zhou FJ, Xie D. Cancer Res. 2018 Aug 24. pii: canres.0822.2018. doi: 10.1158/0008-5472.CAN-18-0822.

12. Prognostic Value of a Long Non-coding RNA Signature in Localized Clear Cell Renal Cell Carcinoma.
Qu L, Wang ZL, Chen Q, Li YM, He HW, Hsieh JJ, Xue S, Wu ZJ, Liu B, Tang H, Xu XF, Xu F, Wang J, Bao Y, Wang AB, Wang D, Yi XM, Zhou ZK, Shi CJ, Zhong K, Sheng ZC, Zhou YL, Jiang J, Chu XY, He J, Ge JP, Zhang ZY, Zhou WQ, Chen C, Yang JH, Sun YH, Wang LH. Eur Urol. 2018 Aug 21. pii: S0302-2838(18)30554-2. doi: 10.1016/j.eururo.2018.07.032.

13. Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma.
Smith CC, Beckermann KE, Bortone DS, de Cubas AA, Bixby LM, Lee SJ, Panda A, Ganesan S, Bhanot G, Wallen EM, Milowsky MI, Kim WY, Rathmell WK, Swanstrom R, Parker JS, Serody JS, Selitsky SR, Vincent BG. J Clin Invest. 2018 Aug 23. pii: 121476. doi: 10.1172/JCI121476.

14. Epigenetic reprogramming with antisense oligonucleotides enhances the effectiveness of androgen receptor inhibition in castration-resistant prostate cancer.
Xiao L, Tien JC, Vo J, Tan M, Parolia A, Zhang Y, Wang L, Qiao Y, Shukla S, Wang X, Zheng H, Su F, Jing X, Luo E, Delekta A, Juckette KM, Xu A, Cao X, Alva AS, Kim Y, Macleod AR, Chinnaiyan AM. Cancer Res. 2018 Aug 22. pii: canres.0941.2018. doi: 10.1158/0008-5472.CAN-18-0941.

15. Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity.
Campbell KM, Lin T, Zolkind P, Barnell EK, Skidmore ZL, Winkler AE, Law JH, Mardis ER, Wartman LD, Adkins DR, Chernock RD, Griffith M, Uppaluri R, Griffith OL. Cell Rep. 2018 Aug 21;24(8):2167-2178. doi: 10.1016/j.celrep.2018.07.058.

16. Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome.
Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Huestis MA, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE, Jaffe AE. Mol Psychiatry. 2018 Aug 21. doi: 10.1038/s41380-018-0223-1.

17. Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells.
Wimmers F, Subedi N, van Buuringen N, Heister D, Vivié J, Beeren-Reinieren I, Woestenenk R, Dolstra H, Piruska A, Jacobs JFM, van Oudenaarden A, Figdor CG, Huck WTS, de Vries IJM, Tel J. Nat Commun. 2018 Aug 20;9(1):3317. doi: 10.1038/s41467-018-05784-3.

18. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response.
Jiang P, Gu S, Pan D, Fu J, Sahu A, Hu X, Li Z, Traugh N, Bu X, Li B, Liu J, Freeman GJ, Brown MA, Wucherpfennig KW, Liu XS. Nat Med. 2018 Aug 20. doi: 10.1038/s41591-018-0136-1.

19. Material microenvironmental properties couple to induce distinct transcriptional programs in mammalian stem cells.
Darnell M, O'Neil A, Mao A, Gu L, Rubin LL, Mooney DJ. Proc Natl Acad Sci U S A. 2018 Aug 17. pii: 201802568. doi: 10.1073/pnas.1802568115.

20. A radiomics approach to assess tumour-infiltrating CD8 cells and response to anti-PD-1 or anti-PD-L1 immunotherapy: an imaging biomarker, retrospective multicohort study.
Sun R, Limkin EJ, Vakalopoulou M, Dercle L, Champiat S, Han SR, Verlingue L, Brandao D, Lancia A, Ammari S, Hollebecque A, Scoazec JY, Marabelle A, Massard C, Soria JC, Robert C, Paragios N, Deutsch E, Ferté C. Lancet Oncol. 2018 Aug 14. pii: S1470-2045(18)30413-3. doi: 10.1016/S1470-2045(18)30413-3.

21. ErbB3 targeting enhances the effects of MEK inhibitor in wild-type BRAF/NRAS melanoma.
Capparelli C, Purwin TJ, Heilman SA, Chervoneva I, McCue PA, Berger AC, Davies MA, Gershenwald JE, Krepler C, Aplin AE. Cancer Res. 2018 Aug 16. pii: canres.1001.2018. doi: 10.1158/0008-5472.CAN-18-1001.

22. In vivo cleavage rules and target repertoire of RNase III in Escherichia coli.
Altuvia Y, Bar A, Reiss N, Karavani E, Argaman L, Margalit H. Nucleic Acids Res. 2018 Aug 3. doi: 10.1093/nar/gky684.

23. Serum Biomarker Signature-Based Liquid Biopsy for Diagnosis of Early-Stage Pancreatic Cancer.
Mellby LD, Nyberg AP, Johansen JS, Wingren C, Nordestgaard BG, Bojesen SE, Mitchell BL, Sheppard BC, Sears RC, Borrebaeck CAK. J Clin Oncol. 2018 Aug 14:JCO2017776658. doi: 10.1200/JCO.2017.77.6658.

24. Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations.
Raman AT, Pohodich AE, Wan YW, Yalamanchili HK, Lowry WE, Zoghbi HY, Liu Z. Nat Commun. 2018 Aug 13;9(1):3225. doi: 10.1038/s41467-018-05627-1.

25. JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns.
Wang Q, Rio DC. Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8181-E8190. doi: 10.1073/pnas.1806018115. Epub 2018 Aug 13.

26. North American ATLL has a distinct mutational and transcriptional profile and responds to epigenetic therapies.
Shah UA, Chung EY, Giricz O, Pradhan K, Kataoka K, Gordon-Mitchell S, Bhagat TD, Mai Y, Wei Y, Ishida E, Choudhary GS, Joseph A, Rice R, Gitego N, Parrish C, Bartenstein M, Goel S, Mantzaris I, Shastri A, Derman O, Binder A, Gritsman K, Kornblum N, Braunschweig I, Bhagat C, Hall J, Graber A, Ratner L, Wang Y, Ogawa S, Verma A, Ye BH, Janakiram M. Blood. 2018 Aug 13. pii: blood-2018-01-824607. doi: 10.1182/blood-2018-01-824607.

27. Combined Inactivation of TP53 and MIR34A Promotes Colorectal Cancer Development and Progression in Mice via Increasing Levels of IL6R and PAI1.
Öner MG, Rokavec M, Kaller M, Bouznad N, Horst D, Kirchner T, Hermeking H. Gastroenterology. 2018 Aug 9. pii: S0016-5085(18)34868-6. doi: 10.1053/j.gastro.2018.08.011.

28. Immune Cell and Stromal Signature Associated with Progression-free Survival of Patients with Resected Pancreatic Ductal Adenocarcinoma.
Mahajan UM, Langhoff E, Goni E, Costello E, Greenhalf W, Halloran C, Ormanns S, Kruger S, Boeck S, Ribback S, Beyer G, Dombroswki F, Weiss FU, Neoptolemos JP, Werner J, D'Haese JG, Bazhin A, Peterhansl J, Pichlmeier S, Büchler MW, Kleeff J, Ganeh P, Sendler M, Palmer DH, Kohlmann T, Rad R, Regel I, Lerch MM, Mayerle J. Gastroenterology. 2018 Aug 6. pii: S0016-5085(18)34838-8. doi: 10.1053/j.gastro.2018.08.009.

29. Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer.
Lei JT, Shao J, Zhang J, Iglesia M, Chan DW, Cao J, Anurag M, Singh P, He X, Kosaka Y, Matsunuma R, Crowder R, Hoog J, Phommaly C, Goncalves R, Ramalho S, Peres RMR, Punturi N, Schmidt C, Bartram A, Jou E, Devarakonda V, Holloway KR, Lai WV, Hampton O, Rogers A, Tobias E, Parikh PA, Davies SR, Li S, Ma CX, Suman VJ, Hunt KK, Watson MA, Hoadley KA, Thompson EA, Chen X, Kavuri SM, Creighton CJ, Maher CA, Perou CM, Haricharan S, Ellis MJ. Cell Rep. 2018 Aug 7;24(6):1434-1444.e7. doi: 10.1016/j.celrep.2018.07.009.

30. RNA editing of Filamin A pre-mRNA regulates vascular contraction and diastolic blood pressure.
Jain M, Mann TD, Stulić M, Rao SP, Kirsch A, Pullirsch D, Strobl X, Rath C, Reissig L, Moreth K, Klein-Rodewald T, Bekeredjian R, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Pablik E, Cimatti L, Martin D, Zinnanti J, Graier WF, Sibilia M, Frank S, Levanon EY, Jantsch MF. EMBO J. 2018 Aug 7. pii: e94813. doi: 10.15252/embj.201694813.

31. A novel environment-evoked transcriptional signature predicts reactivity in single dentate granule neurons.
Jaeger BN, Linker SB, Parylak SL, Barron JJ, Gallina IS, Saavedra CD, Fitzpatrick C, Lim CK, Schafer ST, Lacar B, Jessberger S, Gage FH. Nat Commun. 2018 Aug 6;9(1):3084. doi: 10.1038/s41467-018-05418-8.

32. Mitotic progression, arrest, exit or death relies on centromere structural integrity, rather than de novo transcription.
Novais-Cruz M, Alba Abad M, van IJcken WF, Galjart N, Jeyaprakash AA, Maiato H, Ferrás C. Elife. 2018 Aug 6;7. pii: e36898. doi: 10.7554/eLife.36898.

33. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.
Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C; Cancer Genome Atlas Research Network, Rätsch G. Cancer Cell. 2018 Aug 13;34(2):211-224.e6. doi: 10.1016/j.ccell.2018.07.001. Epub 2018 Aug 2.

34. Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.
Marques S, van Bruggen D, Vanichkina DP, Floriddia EM, Munguba H, Väremo L, Giacomello S, Falcão AM, Meijer M, Björklund ÅK, Hjerling-Leffler J, Taft RJ, Castelo-Branco G. Dev Cell. 2018 Aug 20;46(4):504-517.e7. doi: 10.1016/j.devcel.2018.07.005. Epub 2018 Aug 2.

35. Sensory Neuron Diversity in the Inner Ear Is Shaped by Activity.
Shrestha BR, Chia C, Wu L, Kujawa SG, Liberman MC, Goodrich LV. Cell. 2018 Aug 23;174(5):1229-1246.e17. doi: 10.1016/j.cell.2018.07.007. Epub 2018 Aug 2.

36. Tumor genetic analysis from single-cell RNA-seq data.
Nawy T. Nat Methods. 2018 Aug;15(8):571. doi: 10.1038/s41592-018-0089-9. No abstract available.

37. BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq.
Lindeman I, Emerton G, Mamanova L, Snir O, Polanski K, Qiao SW, Sollid LM, Teichmann SA, Stubbington MJT. Nat Methods. 2018 Aug;15(8):563-565. doi: 10.1038/s41592-018-0082-3. No abstract available.

38. Author Correction: Hypothalamic stem cells control ageing speed partly through exosomal miRNAs.
Zhang Y, Kim MS, Jia B, Yan J, Zuniga-Hertz JP, Han C, Cai D. Nature. 2018 Aug;560(7719):E33. doi: 10.1038/s41586-018-0303-z.

39. BCseq: accurate single cell RNA-seq quantification with bias correction.
Chen L, Zheng S. Nucleic Acids Res. 2018 Aug 21;46(14):e82. doi: 10.1093/nar/gky308.