Monthly Letter

1. iDog: an integrated resource for domestic dogs and wild canids.
Tang B, Zhou Q, Dong L, Li W, Zhang X, Lan L, Zhai S, Xiao J, Zhang Z, Bao Y, Zhang YP, Wang GD, Zhao W. Nucleic Acids Res. 2018 Oct 29. doi: 10.1093/nar/gky1041.

2. Host suppression of quorum sensing during catheter-associated urinary tract infections.
Cole SJ, Hall CL, Schniederberend M, Farrow Iii JM, Goodson JR, Pesci EC, Kazmierczak BI, Lee VT. Nat Commun. 2018 Oct 25;9(1):4436. doi: 10.1038/s41467-018-06882-y.

3. ArrayExpress update - from bulk to single-cell expression data.
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. Nucleic Acids Res. 2018 Oct 24. doi: 10.1093/nar/gky964.

4. Aberrant splicing in B-cell acute lymphoblastic leukemia.
Black KL, Naqvi AS, Asnani M, Hayer KE, Yang SY, Gillespie E, Bagashev A, Pillai V, Tasian SK, Gazzara MR, Carroll M, Taylor D, Lynch KW, Barash Y, Thomas-Tikhonenko A. Nucleic Acids Res. 2018 Oct 24. doi: 10.1093/nar/gky946.

5. DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data.
Kodama Y, Mashima J, Kosuge T, Ogasawara O. Nucleic Acids Res. 2018 Oct 24. doi: 10.1093/nar/gky1002.

6. 15 years of GDR: New data and functionality in the Genome Database for Rosaceae.
Jung S, Lee T, Cheng CH, Buble K, Zheng P, Yu J, Humann J, Ficklin SP, Gasic K, Scott K, Frank M, Ru S, Hough H, Evans K, Peace C, Olmstead M, DeVetter LW, McFerson J, Coe M, Wegrzyn JL, Staton ME, Abbott AG, Main D. Nucleic Acids Res. 2018 Oct 24. doi: 10.1093/nar/gky1000.

7. Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae.
Winter DJ, Ganley ARD, Young CA, Liachko I, Schardl CL, Dupont PY, Berry D, Ram A, Scott B, Cox MP. PLoS Genet. 2018 Oct 24;14(10):e1007467. doi: 10.1371/journal.pgen.1007467.

8. Epigenetic intersection of BDNF Val66Met genotype with premenstrual dysphoric disorder transcriptome in a cross-species model of estradiol add-back.
Marrocco J, Einhorn NR, Petty GH, Li H, Dubey N, Hoffman J, Berman KF, Goldman D, Lee FS, Schmidt PJ, McEwen BS. Mol Psychiatry. 2018 Oct 24. doi: 10.1038/s41380-018-0274-3.

9. CD49b defines functionally mature Treg cells that survey skin and vascular tissues.
Fan X, Moltedo B, Mendoza A, Davydov AN, Faire MB, Mazutis L, Sharma R, Pe'er D, Chudakov DM, Rudensky AY. J Exp Med. 2018 Oct 24. pii: jem.20181442. doi: 10.1084/jem.20181442.

10. Ranking noncanonical 5' splice site usage by genome-wide RNA-seq analysis and splicing reporter assays.
Erkelenz S, Theiss S, Kaisers W, Ptok J, Walotka L, Müller L, Hillebrand F, Brillen AL, Sladek M, Schaal H. Genome Res. 2018 Oct 24. pii: gr.235861.118. doi: 10.1101/gr.235861.118.

11. Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution.
Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S, Fassett MS, Golovato J, Gray M, Ghadially R, Liao W, Perez White BE, Mauro TM, Mully T, Kim EA, Sbitany H, Neuhaus IM, Grekin RC, Yu SS, Gray JW, Purdom E, Paus R, Vaske CJ, Benz SC, Song JS, Cho RJ. Cell Rep. 2018 Oct 23;25(4):871-883. doi: 10.1016/j.celrep.2018.09.006.

12. Regulatory Evolution Drives Evasion of Host Inflammasomes by Salmonella Typhimurium.
Ilyas B, Mulder DT, Little DJ, Elhenawy W, Banda MM, Pérez-Morales D, Tsai CN, Chau NYE, Bustamante VH, Coombes BK. Cell Rep. 2018 Oct 23;25(4):825-832.e5. doi: 10.1016/j.celrep.2018.09.078.

13. Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine.
Kiefer L, Schofield JA, Simon MD. J Am Chem Soc. 2018 Oct 24. doi: 10.1021/jacs.8b08554.

14. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.
Salmén F, Ståhl PL, Mollbrink A, Navarro JF, Vickovic S, Frisén J, Lundeberg J. Nat Protoc. 2018 Oct 23. doi: 10.1038/s41596-018-0045-2.

15. Epigenetics in eating disorders: a systematic review.
Hübel C, Marzi SJ, Breen G, Bulik CM. Mol Psychiatry. 2018 Oct 23. doi: 10.1038/s41380-018-0254-7.

16. Synthetic Neoepitopes of the Transglutaminase-Deamidated Gliadin Complex as Biomarkers for Diagnosing and Monitoring Celiac Disease.
Choung RS, Rostamkolaei SK, Ju JM, Marietta EV, Van Dyke CT, Rajasekaran JJ, Jayaraman V, Wang T, Bei K, Rajasekaran KE, Krishna K, Krishnamurthy HK, Murray JA. Gastroenterology. 2018 Oct 17. pii: S0016-5085(18)35156-4. doi: 10.1053/j.gastro.2018.10.025.

17. SeqOthello: querying RNA-seq experiments at scale.
Yu Y, Liu J, Liu X, Zhang Y, Magner E, Lehnert E, Qian C, Liu J. Genome Biol. 2018 Oct 19;19(1):167. doi: 10.1186/s13059-018-1535-9.

18. DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery.
Ye C, Ho DJ, Neri M, Yang C, Kulkarni T, Randhawa R, Henault M, Mostacci N, Farmer P, Renner S, Ihry R, Mansur L, Keller CG, McAllister G, Hild M, Jenkins J, Kaykas A. Nat Commun. 2018 Oct 17;9(1):4307. doi: 10.1038/s41467-018-06500-x.

19. Holo-Seq: single-cell sequencing of holo-transcriptome.
Xiao Z, Cheng G, Jiao Y, Pan C, Li R, Jia D, Zhu J, Wu C, Zheng M, Jia J. Genome Biol. 2018 Oct 17;19(1):163. doi: 10.1186/s13059-018-1553-7.

20. Defective Mitochondrial Cardiolipin Remodeling Dampens HIF-1α Expression in Hypoxia.
Chowdhury A, Aich A, Jain G, Wozny K, Lüchtenborg C, Hartmann M, Bernhard O, Balleiniger M, Alfar EA, Zieseniss A, Toischer K, Guan K, Rizzoli SO, Brügger B, Fischer A, Katschinski DM, Rehling P, Dudek J. Cell Rep. 2018 Oct 16;25(3):561-570.e6. doi: 10.1016/j.celrep.2018.09.057.

21. SHQ1 regulation of RNA splicing is required for T-lymphoblastic leukemia cell survival.
Su H, Hu J, Huang L, Yang Y, Thenoz M, Kuchmiy A, Hu Y, Li P, Feng H, Zhou Y, Taghon T, Van Vlierberghe P, Qing G, Chen Z, Liu H. Nat Commun. 2018 Oct 15;9(1):4281. doi: 10.1038/s41467-018-06523-4.

22. Single cell RNA-seq reveals profound transcriptional similarity between Barrett's oesophagus and oesophageal submucosal glands.
Owen RP, White MJ, Severson DT, Braden B, Bailey A, Goldin R, Wang LM, Ruiz-Puig C, Maynard ND, Green A, Piazza P, Buck D, Middleton MR, Ponting CP, Schuster-Böckler B, Lu X. Nat Commun. 2018 Oct 15;9(1):4261. doi: 10.1038/s41467-018-06796-9.

23. Circulating glioma cells exhibit stem cell-like properties.
Liu T, Xu H, Huang M, Ma W, Saxena D, Lustig RA, Alonso-Basanta M, Zhang Z, O Rourke DM, Zhang L, Gong Y, Kao GD, Dorsey JF, Fan Y. Cancer Res. 2018 Oct 15. pii: canres.0650.2018. doi: 10.1158/0008-5472.CAN-18-0650.

24. CDT2-controlled cell cycle reentry regulates the pathogenesis of Alzheimer's disease.
Huang F, Wang M, Liu R, Wang JZ, Schadt E, Haroutunian V, Katsel P, Zhang B, Wang X. Alzheimers Dement. 2018 Oct 12. pii: S1552-5260(18)33522-2. doi: 10.1016/j.jalz.2018.08.013.

25. Genome-wide identification of genic and intergenic neuronal DNA regions bound by Tau protein under physiological and stress conditions.
Benhelli-Mokrani H, Mansuroglu Z, Chauderlier A, Albaud B, Gentien D, Sommer S, Schirmer C, Laqueuvre L, Josse T, Buée L, Lefebvre B, Galas MC, Souès S, Bonnefoy E. Nucleic Acids Res. 2018 Oct 13. doi: 10.1093/nar/gky929.

26. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops.
Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, K Reddy U, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. Nucleic Acids Res. 2018 Oct 13. doi: 10.1093/nar/gky944.

27. Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.
Gupta I, Collier PG, Haase B, Mahfouz A, Joglekar A, Floyd T, Koopmans F, Barres B, Smit AB, Sloan SA, Luo W, Fedrigo O, Ross ME, Tilgner HU. Nat Biotechnol. 2018 Oct 15. doi: 10.1038/nbt.4259.

28. Species and cell-type properties of classically defined human and rodent neurons and glia.
Xu X, Stoyanova EI, Lemiesz AE, Xing J, Mash DC, Heintz N. Elife. 2018 Oct 15;7. pii: e37551. doi: 10.7554/eLife.37551.

29. Profilin-1 deficiency leads to SMAD3 upregulation and impaired 3D outgrowth of breast cancer cells.
Chakraborty S, Jiang C, Gau D, Oddo M, Ding Z, Vollmer L, Joy M, Schiemann W, Stolz DB, Vogt A, Ghosh S, Roy P. Br J Cancer. 2018 Oct 15. doi: 10.1038/s41416-018-0284-6.

30. Neonatal Tbr1 Dosage Controls Cortical Layer 6 Connectivity.
Fazel Darbandi S, Robinson Schwartz SE, Qi Q, Catta-Preta R, Pai EL, Mandell JD, Everitt A, Rubin A, Krasnoff RA, Katzman S, Tastad D, Nord AS, Willsey AJ, Chen B, State MW, Sohal VS, Rubenstein JLR. Neuron. 2018 Oct 11. pii: S0896-6273(18)30829-8. doi: 10.1016/j.neuron.2018.09.027.

31. SWI/SNF component ARID1A restrains pancreatic neoplasia formation.
Wang SC, Nassour I, Xiao S, Zhang S, Luo X, Lee J, Li L, Sun X, Nguyen LH, Chuang JC, Peng L, Daigle S, Shen J, Zhu H. Gut. 2018 Oct 12. pii: gutjnl-2017-315490. doi: 10.1136/gutjnl-2017-315490.

32. Central Dicer-miR-103/107 controls developmental switch of POMC progenitors into NPY neurons and impacts glucose homeostasis.
Croizier S, Park S, Maillard J, Bouret SG. Elife. 2018 Oct 12;7. pii: e40429. doi: 10.7554/eLife.40429.

33. RPA1 binding to NRF2 switches ARE-dependent transcriptional activation to ARE-NRE-dependent repression.
Liu P, Rojo de la Vega M, Sammani S, Mascarenhas JB, Kerins M, Dodson M, Sun X, Wang T, Ooi A, Garcia JGN, Zhang DD. Proc Natl Acad Sci U S A. 2018 Oct 11. pii: 201812125. doi: 10.1073/pnas.1812125115.

34. XBP1s activation can globally remodel N-glycan structure distribution patterns.
Wong MY, Chen K, Antonopoulos A, Kasper BT, Dewal MB, Taylor RJ, Whittaker CA, Hein PP, Dell A, Genereux JC, Haslam SM, Mahal LK, Shoulders MD. Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):E10089-E10098. doi: 10.1073/pnas.1805425115. Epub 2018 Oct 10.

35. Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling.
Alyagor I, Berkun V, Keren-Shaul H, Marmor-Kollet N, David E, Mayseless O, Issman-Zecharya N, Amit I, Schuldiner O. Dev Cell. 2018 Oct 8;47(1):38-52.e6. doi: 10.1016/j.devcel.2018.09.013.

36. Gα12 ablation exacerbates liver steatosis and obesity by suppressing USP22/SIRT1-regulated mitochondrial respiration.
Kim TH, Yang YM, Han CY, Koo JH, Oh H, Kim SS, You BH, Choi YH, Park TS, Lee CH, Kurose H, Noureddin M, Seki E, Wan YY, Choi CS, Kim SG. J Clin Invest. 2018 Oct 9. pii: 97831. doi: 10.1172/JCI97831.

37. A comprehensive overview of genomic imprinting in breast and its deregulation in cancer.
Goovaerts T, Steyaert S, Vandenbussche CA, Galle J, Thas O, Van Criekinge W, De Meyer T. Nat Commun. 2018 Oct 8;9(1):4120. doi: 10.1038/s41467-018-06566-7.

38. Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.
Friedman CE, Nguyen Q, Lukowski SW, Helfer A, Chiu HS, Miklas J, Levy S, Suo S, Han JJ, Osteil P, Peng G, Jing N, Baillie GJ, Senabouth A, Christ AN, Bruxner TJ, Murry CE, Wong ES, Ding J, Wang Y, Hudson J, Ruohola-Baker H, Bar-Joseph Z, Tam PPL, Powell JE, Palpant NJ. Cell Stem Cell. 2018 Oct 4;23(4):586-598.e8. doi: 10.1016/j.stem.2018.09.009.

39. RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq.
Svensson V, Pachter L. Mol Cell. 2018 Oct 4;72(1):7-9. doi: 10.1016/j.molcel.2018.09.026.

40. Human genetic variation in GLS2 is associated with development of complicated Staphylococcus aureus bacteremia.
Scott WK, Medie FM, Ruffin F, Sharma-Kuinkel BK, Cyr DD, Guo S, Dykxhoorn DM, Skov RL, Bruun NE, Dahl A, Lerche CJ, Petersen A, Larsen AR, Lauridsen TK, Johansen HK, Ullum H, Sørensen E, Hassager C, Bundgaard H, Schønheyder HC, Torp-Pedersen C, Østergaard LB, Arpi M, Rosenvinge F, Erikstrup LT, Chehri M, Søgaard P, Andersen PS, Fowler VG Jr. PLoS Genet. 2018 Oct 5;14(10):e1007667. doi: 10.1371/journal.pgen.1007667. eCollection 2018 Oct.

41. Kallikrein-related peptidases 4, 5, 6 and 7 regulate tumour-associated factors in serous ovarian cancer.
Wang P, Magdolen V, Seidl C, Dorn J, Drecoll E, Kotzsch M, Yang F, Schmitt M, Schilling O, Rockstroh A, Clements JA, Loessner D. Br J Cancer. 2018 Oct;119(7):823-831. doi: 10.1038/s41416-018-0260-1. Epub 2018 Oct 5.

42. High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.
Mihailovic MK, Vazquez-Anderson J, Li Y, Fry V, Vimalathas P, Herrera D, Lease RA, Powell WB, Contreras LM. Nat Commun. 2018 Oct 4;9(1):4084. doi: 10.1038/s41467-018-06207-z.

43. A novel long noncoding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1.
Zhang E, He X, Zhang C, Su J, Lu X, Si X, Chen J, Yin D, Han L, De W. Genome Biol. 2018 Oct 4;19(1):154. doi: 10.1186/s13059-018-1523-0.

44. Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies.
Deane-Coe PE, Chu ET, Slavney A, Boyko AR, Sams AJ. PLoS Genet. 2018 Oct 4;14(10):e1007648. doi: 10.1371/journal.pgen.1007648. eCollection 2018 Oct.

45. Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency.
Bradley T, Ferrari G, Haynes BF, Margolis DM, Browne EP. Cell Rep. 2018 Oct 2;25(1):107-117.e3. doi: 10.1016/j.celrep.2018.09.020.

46. psichomics: graphical application for alternative splicing quantification and analysis.
Saraiva-Agostinho N, Barbosa-Morais NL. Nucleic Acids Res. 2018 Oct 2. doi: 10.1093/nar/gky888.

47. Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism.
Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Cancer Res. 2018 Oct 1;78(19):5538-5547. doi: 10.1158/0008-5472.CAN-18-0454.

48. 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 Oct;13(10):2176-2199. doi: 10.1038/s41596-018-0029-2.

49. 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 Oct 12;46(18):9253-9263. doi: 10.1093/nar/gky796.

50. 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, Pöntinen A, Korkeala H, Dos Santos NMS, Morais-Cabral JH, Sousa S, Cabanes D. Nucleic Acids Res. 2018 Oct 12;46(18):9338-9352. doi: 10.1093/nar/gky624.

51. Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment.
Sarangdhar MA, Chaubey D, Srikakulam N, Pillai B. Nucleic Acids Res. 2018 Oct 12;46(18):9726-9735. doi: 10.1093/nar/gky628.

52. The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978.
Kröger 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 Oct 12;46(18):9684-9698. doi: 10.1093/nar/gky603.