Monthly Letter

1. Identification and Application of Gene Expression Signatures Associated with Lifespan Extension.
Tyshkovskiy A, Bozaykut P, Borodinova AA, Gerashchenko MV, Ables GP, Garratt M, Khaitovich P, Clish CB, Miller RA, Gladyshev VN. Cell Metab. 2019 Jul 19. pii: S1550-4131(19)30372-9. doi: 10.1016/j.cmet.2019.06.018.

2. Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation.
Nagashima H, Mahlakõiv T, Shih HY, Davis FP, Meylan F, Huang Y, Harrison OJ, Yao C, Mikami Y, Urban JF Jr, Caron KM, Belkaid Y, Kanno Y, Artis D, O'Shea JJ. Immunity. 2019 Jul 16. pii: S1074-7613(19)30279-1. doi: 10.1016/j.immuni.2019.06.009.

3. Haploinsufficiency of the Notch Ligand DLL1 Causes Variable Neurodevelopmental Disorders.
Fischer-Zirnsak B, Segebrecht L, Schubach M, Charles P, Alderman E, Brown K, Cadieux-Dion M, Cartwright T, Chen Y, Costin C, Fehr S, Fitzgerald KM, Fleming E, Foss K, Ha T, Hildebrand G, Horn D, Liu S, Marco EJ, McDonald M, McWalter K, Race S, Rush ET, Si Y, Saunders C, Slavotinek A, Stockler-Ipsiroglu S, Telegrafi A, Thiffault I, Torti E, Tsai AC, Wang X, Zafar M, Keren B, Kornak U, Boerkoel CF, Mirzaa G, Ehmke N. Am J Hum Genet. 2019 Jul 19. pii: S0002-9297(19)30265-4. doi: 10.1016/j.ajhg.2019.07.002.

4. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.
Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, Sud M, Andrews E, Velonias G, Haber AL, Jagadeesh K, Vickovic S, Yao J, Stevens C, Dionne D, Nguyen LT, Villani AC, Hofree M, Creasey EA, Huang H, Rozenblatt-Rosen O, Garber JJ, Khalili H, Desch AN, Daly MJ, Ananthakrishnan AN, Shalek AK, Xavier RJ, Regev A. Cell. 2019 Jul 25;178(3):714-730.e22. doi: 10.1016/j.cell.2019.06.029.

5. RNA sequencing: the teenage years.
Stark R, Grzelak M, Hadfield J. Nat Rev Genet. 2019 Jul 24. doi: 10.1038/s41576-019-0150-2.

6. FMRP Modulates Neural Differentiation through m6A-Dependent mRNA Nuclear Export.
Edens BM, Vissers C, Su J, Arumugam S, Xu Z, Shi H, Miller N, Rojas Ringeling F, Ming GL, He C, Song H, Ma YC. Cell Rep. 2019 Jul 23;28(4):845-854.e5. doi: 10.1016/j.celrep.2019.06.072.

7. Methodology and theoretical basis of forward genetic screening for sleep/wakefulness in mice.
Miyoshi C, Kim SJ, Ezaki T, Ikkyu A, Hotta-Hirashima N, Kanno S, Kakizaki M, Yamada M, Wakana S, Yanagisawa M, Funato H. Proc Natl Acad Sci U S A. 2019 Jul 23. pii: 201906774. doi: 10.1073/pnas.1906774116.

8. Differential variation analysis enables detection of tumor heterogeneity using single-cell RNA-sequencing data.
Davis-Marcisak EF, Sherman TD, Orugunta P, Stein-O'Brien GL, Puram SV, Roussos Torres ET, Hopkins AC, Jaffee EM, Favorov AV, Afsari B, Goff LA, Fertig EJ. Cancer Res. 2019 Jul 23. pii: canres.3882.2018. doi: 10.1158/0008-5472.CAN-18-3882.

9. Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells.
Bossel Ben-Moshe N, Hen-Avivi S, Levitin N, Yehezkel D, Oosting M, Joosten LAB, Netea MG, Avraham R. Nat Commun. 2019 Jul 22;10(1):3266. doi: 10.1038/s41467-019-11257-y.

10. Acute social isolation alters neurogenomic state in songbird forebrain.
George JM, Bell ZW, Condliffe D, Dohrer K, Abaurrea T, Spencer K, Leitão A, Gahr M, Hurd PJ, Clayton DF. Proc Natl Acad Sci U S A. 2019 Jul 22. pii: 201820841. doi: 10.1073/pnas.1820841116.

11. Selective Targeting of Myoblast Fusogenic Signaling and Differentiation-Arrest Antagonizes Rhabdomyosarcoma Cells.
Granados VA, Avirneni-Vadlamudi U, Dalal P, Scarborough SR, Galindo KA, Mahajan P, Galindo RL. Cancer Res. 2019 Jul 22. pii: canres.2096.2018. doi: 10.1158/0008-5472.CAN-18-2096.

12. Long non-coding RNA FAM225A promotes nasopharyngeal carcinoma tumorigenesis and metastasis by acting as ceRNA to sponge miR-590-3p/miR-1275 and upregulate ITGB3.
Zheng ZQ, Li ZX, Zhou GQ, Lin L, Zhang LL, Lv JW, Huang XD, Liu RQ, Chen F, He XJ, Kou J, Zhang J, Wen X, Li YQ, Ma J, Liu N, Sun Y. Cancer Res. 2019 Jul 22. pii: canres.0799.2019. doi: 10.1158/0008-5472.CAN-19-0799.

13. BCDIN3D regulates tRNAHis 3' fragment processing.
Reinsborough CW, Ipas H, Abell NS, Nottingham RM, Yao J, Devanathan SK, Shelton SB, Lambowitz AM, Xhemalçe B. PLoS Genet. 2019 Jul 22;15(7):e1008273. doi: 10.1371/journal.pgen.1008273.

14. De Novo Missense Variants in WDR37 Cause a Severe Multisystemic Syndrome.
Reis LM, Sorokina EA, Thompson S, Muheisen S, Velinov M, Zamora C, Aylsworth AS, Semina EV. Am J Hum Genet. 2019 Jul 9. pii: S0002-9297(19)30240-X. doi: 10.1016/j.ajhg.2019.06.015.

15. Ultra-Rare Genetic Variation in the Epilepsies: A Whole-Exome Sequencing Study of 17,606 Individuals.
Epi25 Collaborative. Electronic address: s.berkovic@unimelb.edu.au; Epi25 Collaborative. Am J Hum Genet. 2019 Jul 16. pii: S0002-9297(19)30207-1. doi: 10.1016/j.ajhg.2019.05.020.

16. Genetic mapping of cell type specificity for complex traits.
Watanabe K, Umićević Mirkov M, de Leeuw CA, van den Heuvel MP, Posthuma D. Nat Commun. 2019 Jul 19;10(1):3222. doi: 10.1038/s41467-019-11181-1.

17. The flowering hormone florigen accelerates secondary cell wall biogenesis to harmonize vascular maturation with reproductive development.
Shalit-Kaneh A, Eviatar-Ribak T, Horev G, Suss N, Aloni R, Eshed Y, Lifschitz E. Proc Natl Acad Sci U S A. 2019 Jul 19. pii: 201906405. doi: 10.1073/pnas.1906405116.

18. Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates.
Eres IE, Luo K, Hsiao CJ, Blake LE, Gilad Y. PLoS Genet. 2019 Jul 19;15(7):e1008278. doi: 10.1371/journal.pgen.1008278.

19. Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets.
Newell F, Kong Y, Wilmott JS, Johansson PA, Ferguson PM, Cui C, Li Z, Kazakoff SH, Burke H, Dodds TJ, Patch AM, Nones K, Tembe V, Shang P, van der Weyden L, Wong K, Holmes O, Lo S, Leonard C, Wood S, Xu Q, Rawson RV, Mukhopadhyay P, Dummer R, Levesque MP, Jönsson G, Wang X, Yeh I, Wu H, Joseph N, Bastian BC, Long GV, Spillane AJ, Shannon KF, Thompson JF, Saw RPM, Adams DJ, Si L, Pearson JV, Hayward NK, Waddell N, Mann GJ, Guo J, Scolyer RA. Nat Commun. 2019 Jul 18;10(1):3163. doi: 10.1038/s41467-019-11107-x.

20. Genomic signatures reveal DNA damage response deficiency in colorectal cancer brain metastases.
Sun J, Wang C, Zhang Y, Xu L, Fang W, Zhu Y, Zheng Y, Chen X, Xie X, Hu X, Hu W, Zheng J, Li P, Yu J, Mei Z, Cai X, Wang B, Hu Z, Shu Y, Shen H, Gu Y. Nat Commun. 2019 Jul 18;10(1):3190. doi: 10.1038/s41467-019-10987-3.

21. The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5' structure element.
Romilly C, Deindl S, Wagner EGH. Proc Natl Acad Sci U S A. 2019 Jul 18. pii: 201904309. doi: 10.1073/pnas.1904309116.

22. The Rho-family GTPase OsRac1 controls rice grain size and yield by regulating cell division.
Zhang Y, Xiong Y, Liu R, Xue HW, Yang Z. Proc Natl Acad Sci U S A. 2019 Jul 18. pii: 201902321. doi: 10.1073/pnas.1902321116.

23. Speciation in Howea palms occurred in sympatry, was preceded by ancestral admixture, and was associated with edaphic and phenological adaptation.
Osborne OG, Ciezarek A, Wilson T, Crayn D, Hutton I, Baker WJ, Turnbull CGN, Savolainen V. Mol Biol Evol. 2019 Jul 18. pii: msz166. doi: 10.1093/molbev/msz166.

24. NASC-seq monitors RNA synthesis in single cells.
Hendriks GJ, Jung LA, Larsson AJM, Lidschreiber M, Andersson Forsman O, Lidschreiber K, Cramer P, Sandberg R. Nat Commun. 2019 Jul 17;10(1):3138. doi: 10.1038/s41467-019-11028-9.

25. BRCA2 abrogation triggers innate immune responses potentiated by treatment with PARP inhibitors.
Reisländer T, Lombardi EP, Groelly FJ, Miar A, Porru M, Di Vito S, Wright B, Lockstone H, Biroccio A, Harris A, Londoño-Vallejo A, Tarsounas M. Nat Commun. 2019 Jul 17;10(1):3143. doi: 10.1038/s41467-019-11048-5.

26. Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing.
Zhang S, Wang Y, Jia L, Wen X, Zhonghua D, Wang C, Hao Y, Yu D, Zhou L, Chen N, Chen J, Chen H, Zhang H, Celik I, Gulsoy G, Luo J, Qin B, Cui X, Liu Z, Zhang S, Esteban MA, Ay F, Li W, Xu W, Chen R, Hoffman AR, Hu J, Cui J. Genome Res. 2019 Jul 17. pii: gr.244996.118. doi: 10.1101/gr.244996.118.

27. CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data.
Wegmann R, Neri M, Schuierer S, Bilican B, Hartkopf H, Nigsch F, Mapa F, Waldt A, Cuttat R, Salick MR, Raymond J, Kaykas A, Roma G, Keller CG. Genome Biol. 2019 Jul 17;20(1):142. doi: 10.1186/s13059-019-1739-7.

28. Mouse Watch: A Cautionary Tale.
Dikiy S, Rudensky AY. Immunity. 2019 Jul 16;51(1):10-12. doi: 10.1016/j.immuni.2019.06.019.

29. The genomic landscape of Epstein-Barr virus-associated pulmonary lymphoepithelioma-like carcinoma.
Hong S, Liu D, Luo S, Fang W, Zhan J, Fu S, Zhang Y, Wu X, Zhou H, Chen X, Chen G, Zhang Z, Zheng Q, Li X, Chen J, Liu X, Lei M, Ye C, Wang J, Yang H, Xu X, Zhu S, Yang Y, Zhao Y, Zhou N, Zhao H, Huang Y, Zhang L, Wu K, Zhang L. Nat Commun. 2019 Jul 16;10(1):3108. doi: 10.1038/s41467-019-10902-w.

30. High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes.
Singh M, Al-Eryani G, Carswell S, Ferguson JM, Blackburn J, Barton K, Roden D, Luciani F, Giang Phan T, Junankar S, Jackson K, Goodnow CC, Smith MA, Swarbrick A. Nat Commun. 2019 Jul 16;10(1):3120. doi: 10.1038/s41467-019-11049-4.

31. TNF-alpha driven inflammation and mitochondrial dysfunction define the platelet hyperreactivity of aging.
Davizon-Castillo P, McMahon B, Aguila S, Bark D, Ashworth K, Allawzi A, Campbell RA, Montenont E, Nemkov T, D'Alessandro A, Clendenen N, Shih L, Sanders NA, Higa K, Cox A, Padilla-Romo Z, Hernandez G, Wartchow E, Trahan GD, Nozik-Grayck E, Jones K, Pietras E, DeGregori J, Rondina MT, Di Paola J. Blood. 2019 Jul 16. pii: blood.2019000200. doi: 10.1182/blood.2019000200.

32. Joint analysis of heterogeneous single-cell RNA-seq dataset collections.
Barkas N, Petukhov V, Nikolaeva D, Lozinsky Y, Demharter S, Khodosevich K, Kharchenko PV. Nat Methods. 2019 Jul 15. doi: 10.1038/s41592-019-0466-z.

33. Diagnosis, prognosis, and treatment of leukodystrophies.
van der Knaap MS, Schiffmann R, Mochel F, Wolf NI. Lancet Neurol. 2019 Jul 12. pii: S1474-4422(19)30143-7. doi: 10.1016/S1474-4422(19)30143-7.

34. Molecular dissection of the oncogenic role of ETS1 in the mesenchymal subtypes of head and neck squamous cell carcinoma.
Gluck C, Glathar A, Tsompana M, Nowak N, Garrett-Sinha LA, Buck MJ, Sinha S. PLoS Genet. 2019 Jul 15;15(7):e1008250. doi: 10.1371/journal.pgen.1008250. eCollection 2019 Jul.

35. Visualization and analysis of RNA-Seq assembly graphs.
Nazarie FW, Shih B, Angus T, Barnett MW, Chen SH, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M, Dongen SV, Enright AJ, Freeman TC. Nucleic Acids Res. 2019 Jul 15. pii: gkz599. doi: 10.1093/nar/gkz599.

36. Generation of Human PSC-Derived Kidney Organoids with Patterned Nephron Segments and a De Novo Vascular Network.
Low JH, Li P, Chew EGY, Zhou B, Suzuki K, Zhang T, Lian MM, Liu M, Aizawa E, Rodriguez Esteban C, Yong KSM, Chen Q, Campistol JM, Fang M, Khor CC, Foo JN, Izpisua Belmonte JC, Xia Y. Cell Stem Cell. 2019 Jul 2. pii: S1934-5909(19)30273-5. doi: 10.1016/j.stem.2019.06.009.

37. Brain somatic mutations observed in Alzheimer's disease associated with aging and dysregulation of tau phosphorylation.
Park JS, Lee J, Jung ES, Kim MH, Kim IB, Son H, Kim S, Kim S, Park YM, Mook-Jung I, Yu SJ, Lee JH. Nat Commun. 2019 Jul 12;10(1):3090. doi: 10.1038/s41467-019-11000-7.

38. Loss of Setd2 promotes Kras-induced acinar-to-ductal metaplasia and epithelia-mesenchymal transition during pancreatic carcinogenesis.
Niu N, Lu P, Yang Y, He R, Zhang L, Shi J, Wu J, Yang M, Zhang ZG, Wang LW, Gao WQ, Habtezion A, Xiao GG, Sun Y, Li L, Xue J. Gut. 2019 Jul 11. pii: gutjnl-2019-318362. doi: 10.1136/gutjnl-2019-318362.

39. Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges.
Suvà ML, Tirosh I. Mol Cell. 2019 Jul 11;75(1):7-12. doi: 10.1016/j.molcel.2019.05.003. Review.

40. Spectrin-based membrane skeleton supports ciliogenesis.
Jia R, Li D, Li M, Chai Y, Liu Y, Xie Z, Shao W, Xie C, Li L, Huang X, Chen L, Li W, Ou G. PLoS Biol. 2019 Jul 12;17(7):e3000369. doi: 10.1371/journal.pbio.3000369. eCollection 2019 Jul.

41. Pathogenic TSR1 Gene Variants in Patients With Spontaneous Coronary Artery Dissection.
Grond-Ginsbach C, Böckler D, Newton-Cheh C. J Am Coll Cardiol. 2019 Jul 16;74(2):177-178. doi: 10.1016/j.jacc.2019.06.005. No abstract available.

42. Association of TSR1 Variants and Spontaneous Coronary Artery Dissection.
Sun Y, Chen Y, Li Y, Li Z, Li C, Yu T, Xiao L, Yu B, Zhao H, Tao M, Jiang J, Yan J, Wang Y, Zeng H, Shen X, Zhou Y, Jin L, Song W, Dou K, Wang DW. J Am Coll Cardiol. 2019 Jul 16;74(2):167-176. doi: 10.1016/j.jacc.2019.04.062.

43. scSLAM-seq reveals core features of transcription dynamics in single cells.
Erhard F, Baptista MAP, Krammer T, Hennig T, Lange M, Arampatzi P, Jürges CS, Theis FJ, Saliba AE, Dölken L. Nature. 2019 Jul;571(7765):419-423. doi: 10.1038/s41586-019-1369-y. Epub 2019 Jul 10.

44. Paternal-age-related de novo mutations and risk for five disorders.
Taylor JL, Debost JPG, Morton SU, Wigdor EM, Heyne HO, Lal D, Howrigan DP, Bloemendal A, Larsen JT, Kosmicki JA, Weiner DJ, Homsy J, Seidman JG, Seidman CE, Agerbo E, McGrath JJ, Mortensen PB, Petersen L, Daly MJ, Robinson EB. Nat Commun. 2019 Jul 10;10(1):3043. doi: 10.1038/s41467-019-11039-6.

45. Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma.
Mottok A, Hung SS, Chavez EA, Woolcock B, Telenius A, Chong LC, Meissner B, Nakamura H, Rushton C, Viganò E, Sarkozy C, Gascoyne RD, Connors JM, Ben Neriah S, Mungall A, Marra MA, Siebert R, Scott DW, Savage KJ, Steidl C. Blood. 2019 Jul 10. pii: blood.2019001126. doi: 10.1182/blood.2019001126.

46. Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.
Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J, Gómez-H L, Julià E, Moutinho C, Aiese Cigliano R, Sanseverino W, Fornas O, Pendás AM, Heyn H, Waters PD, Marti-Renom MA, Ruiz-Herrera A. Cell Rep. 2019 Jul 9;28(2):352-367.e9. doi: 10.1016/j.celrep.2019.06.037.

47. Mapping Distinct Bone Marrow Niche Populations and Their Differentiation Paths.
Wolock SL, Krishnan I, Tenen DE, Matkins V, Camacho V, Patel S, Agarwal P, Bhatia R, Tenen DG, Klein AM, Welner RS. Cell Rep. 2019 Jul 9;28(2):302-311.e5. doi: 10.1016/j.celrep.2019.06.031.

48. Defective AMH signaling disrupts GnRH neuron development and function and contributes to hypogonadotropic hypogonadism.
Malone SA, Papadakis GE, Messina A, Mimouni NEH, Trova S, Imbernon M, Allet C, Cimino I, Acierno J, Cassatella D, Xu C, Quinton R, Szinnai G, Pigny P, Alonso-Cotchico L, Masgrau L, Maréchal JD, Prevot V, Pitteloud N, Giacobini P. Elife. 2019 Jul 10;8. pii: e47198. doi: 10.7554/eLife.47198.

49. The Role of APAL/ST8SIA6-AS1 lncRNA in PLK1 Activation and Mitotic Catastrophe of Tumor Cells.
Luo ML, Li J, Shen L, Chu J, Guo Q, Liang G, Wu W, Chen J, Chen R, Song E. J Natl Cancer Inst. 2019 Jul 9. pii: djz134. doi: 10.1093/jnci/djz134.

50. Molecular portrait of high alpha-fetoprotein in hepatocellular carcinoma: implications for biomarker-driven clinical trials.
Montal R, Andreu-Oller C, Bassaganyas L, Esteban-Fabró R, Moran S, Montironi C, Moeini A, Pinyol R, Peix J, Cabellos L, Villanueva A, Sia D, Mazzaferro V, Esteller M, Llovet JM. Br J Cancer. 2019 Jul 9. doi: 10.1038/s41416-019-0513-7.

51. Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins.
Chothani S, Schäfer S, Adami E, Viswanathan S, Widjaja AA, Langley SR, Tan J, Wang M, Quaife NM, Pua CJ, D'Agostino G, Shekeran SG, George BL, Lim S, Cao EY, van Heesch S, Witte F, Felkin LE, Christodoulou EG, Dong J, Blachut S, Patone G, Barton PJR, Hubner N, Cook SA, Rackham OJL. Circulation. 2019 Jul 9. doi: 10.1161/CIRCULATIONAHA.119.039596.

52. Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq.
Kotliar D, Veres A, Nagy MA, Tabrizi S, Hodis E, Melton DA, Sabeti PC. Elife. 2019 Jul 8;8. pii: e43803. doi: 10.7554/eLife.43803.

53. Accurate estimation of cell-type composition from gene expression data.
Tsoucas D, Dong R, Chen H, Zhu Q, Guo G, Yuan GC. Nat Commun. 2019 Jul 5;10(1):2975. doi: 10.1038/s41467-019-10802-z.

54. Upper tract urothelial carcinoma has a luminal-papillary T-cell depleted contexture and activated FGFR3 signaling.
Robinson BD, Vlachostergios PJ, Bhinder B, Liu W, Li K, Moss TJ, Bareja R, Park K, Tavassoli P, Cyrta J, Tagawa ST, Nanus DM, Beltran H, Molina AM, Khani F, Miguel Mosquera J, Xylinas E, Shariat SF, Scherr DS, Rubin MA, Lerner SP, Matin SF, Elemento O, Faltas BM. Nat Commun. 2019 Jul 5;10(1):2977. doi: 10.1038/s41467-019-10873-y.

55. Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast.
Buchmuller BC, Herbst K, Meurer M, Kirrmaier D, Sass E, Levy ED, Knop M. Nat Commun. 2019 Jul 4;10(1):2960. doi: 10.1038/s41467-019-10816-7.

56. Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming.
Stone NR, Gifford CA, Thomas R, Pratt KJB, Samse-Knapp K, Mohamed TMA, Radzinsky EM, Schricker A, Ye L, Yu P, van Bemmel JG, Ivey KN, Pollard KS, Srivastava D. Cell Stem Cell. 2019 Jul 3;25(1):87-102.e9. doi: 10.1016/j.stem.2019.06.012.

57. An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa.
Huang H, Shao X, Xie Y, Wang T, Zhang Y, Wang X, Deng X. Nat Commun. 2019 Jul 3;10(1):2931. doi: 10.1038/s41467-019-10778-w.

58. Deep evolutionary origin of limb and fin regeneration.
Darnet S, Dragalzew AC, Amaral DB, Sousa JF, Thompson AW, Cass AN, Lorena J, Pires ES, Costa CM, Sousa MP, Fröbisch NB, Oliveira G, Schneider PN, Davis MC, Braasch I, Schneider I. Proc Natl Acad Sci U S A. 2019 Jul 23;116(30):15106-15115. doi: 10.1073/pnas.1900475116. Epub 2019 Jul 3.

59. Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis.
Hu Y, Wang X, Hu B, Mao Y, Chen Y, Yan L, Yong J, Dong J, Wei Y, Wang W, Wen L, Qiao J, Tang F. PLoS Biol. 2019 Jul 3;17(7):e3000365. doi: 10.1371/journal.pbio.3000365. eCollection 2019 Jul.

60. RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.
Morf J, Wingett SW, Farabella I, Cairns J, Furlan-Magaril M, Jiménez-García LF, Liu X, Craig FF, Walker S, Segonds-Pichon A, Andrews S, Marti-Renom MA, Fraser P. Nat Biotechnol. 2019 Jul;37(7):793-802. doi: 10.1038/s41587-019-0166-3. Epub 2019 Jul 1.

61. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics.
Gaublomme JT, Li B, McCabe C, Knecht A, Yang Y, Drokhlyansky E, Van Wittenberghe N, Waldman J, Dionne D, Nguyen L, De Jager PL, Yeung B, Zhao X, Habib N, Rozenblatt-Rosen O, Regev A. Nat Commun. 2019 Jul 2;10(1):2907. doi: 10.1038/s41467-019-10756-2.

62. Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments.
Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, Alečković M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister SS, Polyak K. Nat Cell Biol. 2019 Jul;21(7):879-888. doi: 10.1038/s41556-019-0346-x. Epub 2019 Jul 1.

63. Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice.
Fang Y, Chen L, Lin K, Feng Y, Zhang P, Pan X, Sanders J, Wu Y, Wang XE, Su Z, Chen C, Wei H, Zhang W. Genome Res. 2019 Jul 1. doi: 10.1101/gr.246009.118.

64. Conserved NPPB+ Border Zone Switches from MEF2 to AP-1 Driven Gene Program.
van Duijvenboden K, de Bakker DEM, Man JCK, Janssen R, Günthel M, Hill MC, Hooijkaas IB, van der Made I, van der Kraak PH, Vink A, Creemers EE, Martin JF, Barnett P, Bakkers J, Christoffels VM. Circulation. 2019 Jul 1. doi: 10.1161/CIRCULATIONAHA.118.038944.

65. Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization.
Zhang L, Zhang S. Nucleic Acids Res. 2019 Jul 26;47(13):6606-6617. doi: 10.1093/nar/gkz488.

66. Thermoregulation via Temperature-Dependent PGD2 Production in Mouse Preoptic Area.
Wang TA, Teo CF, Åkerblom M, Chen C, Tynan-La Fontaine M, Greiner VJ, Diaz A, McManus MT, Jan YN, Jan LY. Neuron. 2019 Jul 17;103(2):309-322.e7. doi: 10.1016/j.neuron.2019.04.035. Epub 2019 May 28. Erratum in: Neuron. 2019 Jul 17;103(2):349.

67. RNAmod: an integrated system for the annotation of mRNA modifications.
Liu Q, Gregory RI. Nucleic Acids Res. 2019 Jul 2;47(W1):W548-W555. doi: 10.1093/nar/gkz479.

68. Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome.
Hwang S, Lee N, Jeong Y, Lee Y, Kim W, Cho S, Palsson BO, Cho BK. Nucleic Acids Res. 2019 Jul 9;47(12):6114-6129. doi: 10.1093/nar/gkz471.

69. sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.
Aparicio-Puerta E, Lebrón R, Rueda A, Gómez-Martín C, Giannoukakos S, Jaspez D, Medina JM, Zubkovic A, Jurak I, Fromm B, Marchal JA, Oliver J, Hackenberg M. Nucleic Acids Res. 2019 Jul 2;47(W1):W530-W535. doi: 10.1093/nar/gkz415.

70. ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma'ayan A. Nucleic Acids Res. 2019 Jul 2;47(W1):W212-W224. doi: 10.1093/nar/gkz446.

71. Geneshot: search engine for ranking genes from arbitrary text queries.
Lachmann A, Schilder BM, Wojciechowicz ML, Torre D, Kuleshov MV, Keenan AB, Ma'ayan A. Nucleic Acids Res. 2019 Jul 2;47(W1):W571-W577. doi: 10.1093/nar/gkz393.

72. GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis.
Tang Z, Kang B, Li C, Chen T, Zhang Z. Nucleic Acids Res. 2019 Jul 2;47(W1):W556-W560. doi: 10.1093/nar/gkz430.

73. MutationDistiller: user-driven identification of pathogenic DNA variants.
Hombach D, Schuelke M, Knierim E, Ehmke N, Schwarz JM, Fischer-Zirnsak B, Seelow D. Nucleic Acids Res. 2019 Jul 2;47(W1):W114-W120. doi: 10.1093/nar/gkz330.

74. The RNA workbench 2.0: next generation RNA data analysis.
Fallmann J, Videm P, Bagnacani A, Batut B, Doyle MA, Klingstrom T, Eggenhofer F, Stadler PF, Backofen R, Grüning B. Nucleic Acids Res. 2019 Jul 2;47(W1):W511-W515. doi: 10.1093/nar/gkz353.

75. modEnrichr: a suite of gene set enrichment analysis tools for model organisms.
Kuleshov MV, Diaz JEL, Flamholz ZN, Keenan AB, Lachmann A, Wojciechowicz ML, Cagan RL, Ma'ayan A. Nucleic Acids Res. 2019 Jul 2;47(W1):W183-W190. doi: 10.1093/nar/gkz347.

76. CPGAVAS2, an integrated plastome sequence annotator and analyzer.
Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L, Liu C. Nucleic Acids Res. 2019 Jul 2;47(W1):W65-W73. doi: 10.1093/nar/gkz345.

77. Gene Expression Does Not Support the Developmental Hourglass Model in Three Animals with Spiralian Development.
Wu L, Ferger KE, Lambert JD. Mol Biol Evol. 2019 Jul 1;36(7):1373-1383. doi: 10.1093/molbev/msz065.