Monthly Letter

1. Splicing factor SRSF1 promotes gliomagenesis via oncogenic splice-switching of MYO1B.
Zhou X, Wang R, Li X, Yu L, Hua D, Sun C, Shi C, Luo W, Rao C, Jiang Z, Feng Y, Wang Q, Yu S. J Clin Invest. 2018 Nov 27. pii: 120279. doi: 10.1172/JCI120279.

2. Identification and prioritization of gene sets associated with schizophrenia risk by co-expression network analysis in human brain.
Radulescu E, Jaffe AE, Straub RE, Chen Q, Shin JH, Hyde TM, Kleinman JE, Weinberger DR. Mol Psychiatry. 2018 Nov 26. doi: 10.1038/s41380-018-0304-1.

3. Retrograde BMP signaling activates neuronal gene expression through widespread deployment of a conserved BMP-responsive cis-regulatory activation element.
Vuilleumier R, Lian T, Flibotte S, Khan ZN, Fuchs A, Pyrowolakis G, Allan DW. Nucleic Acids Res. 2018 Nov 22. doi: 10.1093/nar/gky1135.

4. Transcriptome Landscape of Human Folliculogenesis Reveals Oocyte and Granulosa Cell Interactions.
Zhang Y, Yan Z, Qin Q, Nisenblat V, Chang HM, Yu Y, Wang T, Lu C, Yang M, Yang S, Yao Y, Zhu X, Xia X, Dang Y, Ren Y, Yuan P, Li R, Liu P, Guo H, Han J, He H, Zhang K, Wang Y, Wu Y, Li M, Qiao J, Yan J, Yan L. Mol Cell. 2018 Nov 15. pii: S1097-2765(18)30889-X. doi: 10.1016/j.molcel.2018.10.029.

5. Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems.
Zhang X, Li T, Liu F, Chen Y, Yao J, Li Z, Huang Y, Wang J. Mol Cell. 2018 Nov 16. pii: S1097-2765(18)30880-3. doi: 10.1016/j.molcel.2018.10.020.

6. Quantitative Clonal Analysis and Single-Cell Transcriptomics Reveal Division Kinetics, Hierarchy, and Fate of Oral Epithelial Progenitor Cells.
Jones KB, Furukawa S, Marangoni P, Ma H, Pinkard H, D'Urso R, Zilionis R, Klein AM, Klein OD. Cell Stem Cell. 2018 Nov 7. pii: S1934-5909(18)30496-X. doi: 10.1016/j.stem.2018.10.015.

7. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.
Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. Cancer Cell. 2018 Nov 14. pii: S1535-6108(18)30480-X. doi: 10.1016/j.ccell.2018.10.014.

8. Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes.
Hammond TR, Dufort C, Dissing-Olesen L, Giera S, Young A, Wysoker A, Walker AJ, Gergits F, Segel M, Nemesh J, Marsh SE, Saunders A, Macosko E, Ginhoux F, Chen J, Franklin RJM, Piao X, McCarroll SA, Stevens B. Immunity. 2018 Nov 21. pii: S1074-7613(18)30485-0. doi: 10.1016/j.immuni.2018.11.004.

9. Comparative expression profiling reveals widespread coordinated evolution of gene expression across eukaryotes.
Martin T, Fraser HB. Nat Commun. 2018 Nov 23;9(1):4963. doi: 10.1038/s41467-018-07436-y.

10. Publisher Correction: Single-cell RNA-seq reveals cell type-specific transcriptional signatures at the maternal-foetal interface during pregnancy.
Nelson AC, Mould AW, Bikoff EK, Robertson EJ. Nat Commun. 2018 Nov 19;9:16219. doi: 10.1038/ncomms16219.

11. Integrative epigenetic taxonomy of primary prostate cancer.
Stelloo S, Nevedomskaya E, Kim Y, Schuurman K, Valle-Encinas E, Lobo J, Krijgsman O, Peeper DS, Chang SL, Feng FY, Wessels LFA, Henrique R, Jerónimo C, Bergman AM, Zwart W. Nat Commun. 2018 Nov 21;9(1):4900. doi: 10.1038/s41467-018-07270-2.

12. Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis.
Churko JM, Garg P, Treutlein B, Venkatasubramanian M, Wu H, Lee J, Wessells QN, Chen SY, Chen WY, Chetal K, Mantalas G, Neff N, Jabart E, Sharma A, Nolan GP, Salomonis N, Wu JC. Nat Commun. 2018 Nov 21;9(1):4906. doi: 10.1038/s41467-018-07333-4.

13. Corn ChIPs and RNA-seq: Researchers Dip into Advanced Tools and Resources to Examine bZIP Transcription Factor Function in the Maize Endosperm.
Mach J. Plant Cell. 2018 Nov 21. pii: tpc.00882.2018. doi: 10.1105/tpc.18.00882.

14. Seq-ing out the Killers of Mice and Men.
Peng V, Cella M. Immunity. 2018 Nov 20;49(5):793-795. doi: 10.1016/j.immuni.2018.11.007.

15. COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference.
Obayashi T, Kagaya Y, Aoki Y, Tadaka S, Kinoshita K. Nucleic Acids Res. 2018 Nov 20. doi: 10.1093/nar/gky1155.

16. Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage.
Poirion O, Zhu X, Ching T, Garmire LX. Nat Commun. 2018 Nov 20;9(1):4892. doi: 10.1038/s41467-018-07170-5.

17. Bridging the Gap between Connectome and Transcriptome.
Fornito A, Arnatkevičiūtė A, Fulcher BD. Trends Cogn Sci. 2018 Nov 16. pii: S1364-6613(18)30253-5. doi: 10.1016/j.tics.2018.10.005.

18. Activation of autophagy, observed in liver tissues from patients with Wilson disease and from Atp7b-deficient animals, protects hepatocytes from copper-induced apoptosis.
Polishchuk EV, Merolla A, Lichtmannegger J, Romano A, Indrieri A, Ilyechova EY, Concilli M, De Cegli R, Crispino R, Mariniello M, Petruzzelli R, Ranucci G, Iorio R, Pietrocola F, Einer C, Borchard S, Zibert A, Schmidt HH, Di Schiavi E, Puchkova LV, Franco B, Kroemer G, Zischka H, Polishchuk RS. Gastroenterology. 2018 Nov 16. pii: S0016-5085(18)35280-6. doi: 10.1053/j.gastro.2018.11.032.

19. Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement.
Jia G, Preussner J, Chen X, Guenther S, Yuan X, Yekelchyk M, Kuenne C, Looso M, Zhou Y, Teichmann S, Braun T. Nat Commun. 2018 Nov 19;9(1):4877. doi: 10.1038/s41467-018-07307-6.

20. Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics.
Wu H, Uchimura K, Donnelly EL, Kirita Y, Morris SA, Humphreys BD. Cell Stem Cell. 2018 Nov 1. pii: S1934-5909(18)30491-0. doi: 10.1016/j.stem.2018.10.010.

21. Preclinical Models for Studying NASH-Driven HCC: How Useful Are They?
Febbraio MA, Reibe S, Shalapour S, Ooi GJ, Watt MJ, Karin M. Cell Metab. 2018 Nov 9. pii: S1550-4131(18)30644-2. doi: 10.1016/j.cmet.2018.10.012.

22. Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function.
Shifrut E, Carnevale J, Tobin V, Roth TL, Woo JM, Bui CT, Li PJ, Diolaiti ME, Ashworth A, Marson A. Cell. 2018 Nov 13. pii: S0092-8674(18)31333-3. doi: 10.1016/j.cell.2018.10.024.

23. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection.
Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL, Regev A, Behrens T, Hacohen N. Genome Res. 2018 Nov 16. doi: 10.1101/gr.240390.118.

24. Long Non-coding RNA GMAN, Upregulated in Gastric Cancer Tissues, is Associated with Metastasis in Patients and Promotes Translation of Ephrin A1 by Competitively Binding GMAN-AS.
Zhuo W, Liu Y, Li S, Guo D, Sun Q, Jin J, Rao X, Li M, Sun M, Jiang M, Xu Y, Teng L, Jin Y, Si J, Liu W, Kang Y, Zhou T. Gastroenterology. 2018 Nov 13. pii: S0016-5085(18)35268-5. doi: 10.1053/j.gastro.2018.10.054.

25. A web server for comparative analysis of single-cell RNA-seq data.
Alavi A, Ruffalo M, Parvangada A, Huang Z, Bar-Joseph Z. Nat Commun. 2018 Nov 13;9(1):4768. doi: 10.1038/s41467-018-07165-2.

26. H3K36 trimethylation mediated by SETD2 regulates the fate of bone marrow mesenchymal stem cells.
Wang L, Niu N, Li L, Shao R, Ouyang H, Zou W. PLoS Biol. 2018 Nov 13;16(11):e2006522. doi: 10.1371/journal.pbio.2006522. eCollection 2018 Nov.

27. SOX9 expression decreases survival of patients with intrahepatic cholangiocarcinoma by conferring chemoresistance.
Yuan X, Li J, Coulouarn C, Lin T, Sulpice L, Bergeat D, De La Torre C, Liebe R, Gretz N, Ebert MPA, Dooley S, Weng HL. Br J Cancer. 2018 Nov 13. doi: 10.1038/s41416-018-0338-9.

28. Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.
Nazaryan-Petersen L, Eisfeldt J, Pettersson M, Lundin J, Nilsson D, Wincent J, Lieden A, Lovmar L, Ottosson J, Gacic J, Mäkitie O, Nordgren A, Vezzi F, Wirta V, Käller M, Hjortshøj TD, Jespersgaard C, Houssari R, Pignata L, Bak M, Tommerup N, Lundberg ES, Tümer Z, Lindstrand A. PLoS Genet. 2018 Nov 12;14(11):e1007780. doi: 10.1371/journal.pgen.1007780. eCollection 2018 Nov.

29. Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases.
Vallania F, Tam A, Lofgren S, Schaffert S, Azad TD, Bongen E, Haynes W, Alsup M, Alonso M, Davis M, Engleman E, Khatri P. Nat Commun. 2018 Nov 9;9(1):4735. doi: 10.1038/s41467-018-07242-6.

30. Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance.
Su Z, Tang Y, Ritchey LE, Tack DC, Zhu M, Bevilacqua PC, Assmann SM. Proc Natl Acad Sci U S A. 2018 Nov 9. pii: 201807988. doi: 10.1073/pnas.1807988115.

31. Reply to "Evaluation of immune repertoire inference methods from RNA-seq data".
Bolotin DA, Poslavsky S, Davydov AN, Chudakov DM. Nat Biotechnol. 2018 Nov 9;36(11):1035-1036. doi: 10.1038/nbt.4296. No abstract available.

32. Evaluation of immune repertoire inference methods from RNA-seq data.
Hu X, Zhang J, Liu JS, Li B, Liu XS. Nat Biotechnol. 2018 Nov 9;36(11):1034. doi: 10.1038/nbt.4294. No abstract available

33. T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1.
Zhu H, Zhang L, Wu Y, Dong B, Guo W, Wang M, Yang L, Fan X, Tang Y, Liu N, Lei X, Wu H. Elife. 2018 Nov 9;7. pii: e38314. doi: 10.7554/eLife.38314.

34. FusionGDB: fusion gene annotation DataBase.
Kim P, Zhou X. Nucleic Acids Res. 2018 Nov 8. doi: 10.1093/nar/gky1067.

35. Stemformatics: visualize and download curated stem cell data.
Choi J, Pacheco CM, Mosbergen R, Korn O, Chen T, Nagpal I, Englart S, Angel PW, Wells CA. Nucleic Acids Res. 2018 Nov 8. doi: 10.1093/nar/gky1064.

36. Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.
Lizio M, Abugessaisa I, Noguchi S, Kondo A, Hasegawa A, Hon CC, de Hoon M, Severin J, Oki S, Hayashizaki Y, Carninci P, Kasukawa T, Kawaji H. Nucleic Acids Res. 2018 Nov 8. doi: 10.1093/nar/gky1099.

37. Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers.
Gao Y, Wang P, Wang Y, Ma X, Zhi H, Zhou D, Li X, Fang Y, Shen W, Xu Y, Shang S, Wang L, Wang L, Ning S, Li X. Nucleic Acids Res. 2018 Nov 8. doi: 10.1093/nar/gky1096.

38. MaizeGDB 2018: the maize multi-genome genetics and genomics database.
Portwood JL 2nd, Woodhouse MR, Cannon EK, Gardiner JM, Harper LC, Schaeffer ML, Walsh JR, Sen TZ, Cho KT, Schott DA, Braun BL, Dietze M, Dunfee B, Elsik CG, Manchanda N, Coe E, Sachs M, Stinard P, Tolbert J, Zimmerman S, Andorf CM. Nucleic Acids Res. 2018 Nov 8. doi: 10.1093/nar/gky1046.

39. Simulation-based benchmarking of isoform quantification in single-cell RNA-seq.
Westoby J, Herrera MS, Ferguson-Smith AC, Hemberg M. Genome Biol. 2018 Nov 7;19(1):191. doi: 10.1186/s13059-018-1571-5.

40. Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics.
Kumar MP, Du J, Lagoudas G, Jiao Y, Sawyer A, Drummond DC, Lauffenburger DA, Raue A. Cell Rep. 2018 Nov 6;25(6):1458-1468.e4. doi: 10.1016/j.celrep.2018.10.047.

41. Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas.
Suo S, Zhu Q, Saadatpour A, Fei L, Guo G, Yuan GC. Cell Rep. 2018 Nov 6;25(6):1436-1445.e3. doi: 10.1016/j.celrep.2018.10.045.

42. SoxB1 Activity Regulates Sensory Neuron Regeneration, Maintenance, and Function in Planarians.
Ross KG, Molinaro AM, Romero C, Dockter B, Cable KL, Gonzalez K, Zhang S, Collins ES, Pearson BJ, Zayas RM. Dev Cell. 2018 Nov 5;47(3):331-347.e5. doi: 10.1016/j.devcel.2018.10.014.

43. Multidimensional Assessment of the Host Response in Mechanically Ventilated Patients with Suspected Pneumonia.
Walter JM, Ren Z, Yacoub T, Reyfman PA, Shah RD, Abdala-Valencia H, Nam K, Morgan VK, Anekalla KR, Joshi N, McQuattie-Pimentel AC, Chen CI, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Aillon RP, Watanabe S, Williams KJN, Lu Z, Paonessa J, Hountras P, Breganio M, Borkowski N, Donnelly HK, Allen JP, Amaral LA, Bharat A, Misharin AV, Bagheri N, Hauser AR, Budinger GRS, Wunderink RG. Am J Respir Crit Care Med. 2018 Nov 6. doi: 10.1164/rccm.201804-0650OC.

44. Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans.
Choi J, Baldwin TM, Wong M, Bolden JE, Fairfax KA, Lucas EC, Cole R, Biben C, Morgan C, Ramsay KA, Ng AP, Kauppi M, Corcoran LM, Shi W, Wilson N, Wilson MJ, Alexander WS, Hilton DJ, de Graaf CA. Nucleic Acids Res. 2018 Nov 5. doi: 10.1093/nar/gky1020.

45. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.
Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ. Cell. 2018 Nov 15;175(5):1307-1320.e22. doi: 10.1016/j.cell.2018.10.008. Epub 2018 Nov 1.

46. Prognostic effect of whole chromosomal aberration signatures in standard-risk, non-WNT/non-SHH medulloblastoma: a retrospective, molecular analysis of the HIT-SIOP PNET 4 trial.
Goschzik T, Schwalbe EC, Hicks D, Smith A, Zur Muehlen A, Figarella-Branger D, Doz F, Rutkowski S, Lannering B, Pietsch T, Clifford SC. Lancet Oncol. 2018 Nov 1. pii: S1470-2045(18)30532-1. doi: 10.1016/S1470-2045(18)30532-1.

47. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N. Cell. 2018 Nov 1;175(4):998-1013.e20. doi: 10.1016/j.cell.2018.10.038.

48. Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic.
Combs PA, Fraser HB. PLoS Genet. 2018 Nov 1;14(11):e1007631. doi: 10.1371/journal.pgen.1007631. eCollection 2018 Nov.

49. VISTA expressed in tumour cells regulates T cell function.
Mulati K, Hamanishi J, Matsumura N, Chamoto K, Mise N, Abiko K, Baba T, Yamaguchi K, Horikawa N, Murakami R, Taki M, Budiman K, Zeng X, Hosoe Y, Azuma M, Konishi I, Mandai M. Br J Cancer. 2018 Nov 9. doi: 10.1038/s41416-018-0313-5.

50. 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 Nov;13(11):2501-2534. doi: 10.1038/s41596-018-0045-2.

51. 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 Nov 12. pii: 97831. doi: 10.1172/JCI97831.

52. How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.
Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B. Nucleic Acids Res. 2018 Nov 2;46(19):10514-10529. doi: 10.1093/nar/gky836.

53. Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions.
Wu X, Kabalane H, Kahli M, Petryk N, Laperrousaz B, Jaszczyszyn Y, Drillon G, Nicolini FE, Perot G, Robert A, Fund C, Chibon F, Xia R, Wiels J, Argoul F, Maguer-Satta V, Arneodo A, Audit B, Hyrien O. Nucleic Acids Res. 2018 Nov 2;46(19):10157-10172. doi: 10.1093/nar/gky797.

54. Dual Gene Repertoires for Larval and Adult Shells Reveal Molecules Essential for Molluscan Shell Formation.
Zhao R, Takeuchi T, Luo YJ, Ishikawa A, Kobayashi T, Koyanagi R, Villar-Briones A, Yamada L, Sawada H, Iwanaga S, Nagai K, Satoh N, Endo K. Mol Biol Evol. 2018 Nov 1;35(11):2751-2761. doi: 10.1093/molbev/msy172.

55. 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 Nov 2;46(19):9990-10006. doi: 10.1093/nar/gky750.

56. 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 Nov 2;46(19):10380-10394. doi: 10.1093/nar/gky684.