Monthly Letter

2. Decoding myofibroblast origins in human kidney fibrosis.
Kuppe C et al. Nature. 2021 Jan;589(7841):281-286. doi: 10.1038/s41586-020-2941-1. Epub 2020 Nov 11.

3. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.
Andrews TS et al. Nat Protoc. 2021 Jan;16(1):1-9. doi: 10.1038/s41596-020-00409-w. Epub 2020 Dec 7.

4. YAP1 mediates gastric adenocarcinoma peritoneal metastases that are attenuated by YAP1 inhibition.
Ajani JA et al. Gut. 2021 Jan;70(1):55-66. doi: 10.1136/gutjnl-2019-319748. Epub 2020 Apr 27.

5. Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential.
Huang S et al. Cell. 2021 Jan 21;184(2):441-459.e25. doi: 10.1016/j.cell.2020.11.028. Epub 2020 Dec 16.

6. Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK(+) CD8(+) T Cells as Conserved Hallmark of Inflammaging.
Mogilenko DA et al. Immunity. 2021 Jan 12;54(1):99-115.e12. doi: 10.1016/j.immuni.2020.11.005. Epub 2020 Dec 2.

7. Cell-Type-Specific Immune Dysregulation in Severely Ill COVID-19 Patients.
Yao C et al. Cell Rep. 2021 Jan 5;34(1):108590. doi: 10.1016/j.celrep.2020.108590. Epub 2020 Dec 16.

8. Targeting clinical epigenetic reprogramming for chemoprevention of metabolic and viral hepatocellular carcinoma.
Jühling F et al. Gut. 2021 Jan;70(1):157-169. doi: 10.1136/gutjnl-2019-318918. Epub 2020 Mar 26.

9. Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.
Ding Y et al. Blood. 2021 Jan 14;137(2):190-202. doi: 10.1182/blood.2020005219.

10. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia.
Grant RA et al. Nature. 2021 Jan 11. doi: 10.1038/s41586-020-03148-w. Online ahead of print.

11. Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade.
Sehgal K et al. J Clin Invest. 2021 Jan 19;131(2):e135038. doi: 10.1172/JCI135038.

12. Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma.
Wang R et al. Nat Med. 2021 Jan;27(1):141-151. doi: 10.1038/s41591-020-1125-8. Epub 2021 Jan 4.

13. Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery.
Xu X et al. Dev Cell. 2021 Jan 4:S1534-5807(20)31021-2. doi: 10.1016/j.devcel.2020.12.015. Online ahead of print.

14. Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.
Shao W et al. Genome Res. 2021 Jan;31(1):88-100. doi: 10.1101/gr.265173.120. Epub 2020 Dec 21.

15. VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide.
Leppek K et al. Cell Rep. 2021 Jan 19;34(3):108629. doi: 10.1016/j.celrep.2020.108629.

16. Cancer-Related Mutations Are Not Enriched in Naive Human Pluripotent Stem Cells.
Stirparo GG et al. Cell Stem Cell. 2021 Jan 7;28(1):164-169.e2. doi: 10.1016/j.stem.2020.11.014. Epub 2020 Dec 14.

17. PINA 3.0: mining cancer interactome.
Du Y et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1351-D1357. doi: 10.1093/nar/gkaa1075.

18. T Cell Development: Old Tales Retold By Single-Cell RNA Sequencing.
Liu C et al. Trends Immunol. 2021 Jan 11:S1471-4906(20)30285-4. doi: 10.1016/j.it.2020.12.004. Online ahead of print.

19. Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy.
Somasundaram R et al. Nat Commun. 2021 Jan 12;12(1):346. doi: 10.1038/s41467-020-20600-7.

20. Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing.
Murdock DR et al. J Clin Invest. 2021 Jan 4;131(1):e141500. doi: 10.1172/JCI141500.

21. Aging Atlas: a multi-omics database for aging biology.
Aging Atlas Consortium et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D825-D830. doi: 10.1093/nar/gkaa894.

22. Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data.
Gao Y et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1251-D1258. doi: 10.1093/nar/gkaa1006.

23. Identifying genome-wide off-target sites of CRISPR RNA-guided nucleases and deaminases with Digenome-seq.
Kim D et al. Nat Protoc. 2021 Jan 18. doi: 10.1038/s41596-020-00453-6. Online ahead of print.

24. MeDAS: a Metazoan Developmental Alternative Splicing database.
Li Z et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D144-D150. doi: 10.1093/nar/gkaa886.

25. The mouse Gene Expression Database (GXD): 2021 update.
Baldarelli RM et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D924-D931. doi: 10.1093/nar/gkaa914.

26. RJunBase: a database of RNA splice junctions in human normal and cancerous tissues.
Li Q et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D201-D211. doi: 10.1093/nar/gkaa1056.

27. Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines.
SoRelle ED et al. Elife. 2021 Jan 27;10:e62586. doi: 10.7554/eLife.62586. Online ahead of print.

28. isoCirc catalogs full-length circular RNA isoforms in human transcriptomes.
Xin R et al. Nat Commun. 2021 Jan 12;12(1):266. doi: 10.1038/s41467-020-20459-8.

29. MdERDL6-mediated glucose efflux to the cytosol promotes sugar accumulation in the vacuole through up-regulating TSTs in apple and tomato.
Zhu L et al. Proc Natl Acad Sci U S A. 2021 Jan 5;118(1):e2022788118. doi: 10.1073/pnas.2022788118. Epub 2020 Dec 21.

30. A cell atlas of the chick retina based on single-cell transcriptomics.
Yamagata M et al. Elife. 2021 Jan 4;10:e63907. doi: 10.7554/eLife.63907.

31. Thymidylate synthase drives the phenotypes of epithelial-to-mesenchymal transition in non-small cell lung cancer.
Siddiqui MA et al. Br J Cancer. 2021 Jan;124(1):281-289. doi: 10.1038/s41416-020-01095-x. Epub 2020 Oct 7.

32. Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis.
Reimer KA et al. Mol Cell. 2021 Jan 12:S1097-2765(20)30937-0. doi: 10.1016/j.molcel.2020.12.018. Online ahead of print.

33. GTRD: an integrated view of transcription regulation.
Kolmykov S et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D104-D111. doi: 10.1093/nar/gkaa1057.

34. Transcriptome alterations in myotonic dystrophy frontal cortex.
Otero BA et al. Cell Rep. 2021 Jan 19;34(3):108634. doi: 10.1016/j.celrep.2020.108634.

35. PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs.
Jin J et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1489-D1495. doi: 10.1093/nar/gkaa910.

36. RASP: an atlas of transcriptome-wide RNA secondary structure probing data.
Li P et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D183-D191. doi: 10.1093/nar/gkaa880.

37. Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 in lung epithelium.
Schuler BA et al. J Clin Invest. 2021 Jan 4;131(1):e140766. doi: 10.1172/JCI140766.

38. Global computational alignment of tumor and cell line transcriptional profiles.
Warren A et al. Nat Commun. 2021 Jan 4;12(1):22. doi: 10.1038/s41467-020-20294-x.

39. Single-cell transcriptome profiling of the vaginal wall in women with severe anterior vaginal prolapse.
Li Y et al. Nat Commun. 2021 Jan 4;12(1):87. doi: 10.1038/s41467-020-20358-y.

40. HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets.
Hounkpe BW et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D947-D955. doi: 10.1093/nar/gkaa609.

41. SCISSOR: a framework for identifying structural changes in RNA transcripts.
Choi HY et al. Nat Commun. 2021 Jan 12;12(1):286. doi: 10.1038/s41467-020-20593-3.

42. Transcriptional and morphological profiling of parvalbumin interneuron subpopulations in the mouse hippocampus.
Que L et al. Nat Commun. 2021 Jan 4;12(1):108. doi: 10.1038/s41467-020-20328-4.

43. TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment.
Sun D et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1420-D1430. doi: 10.1093/nar/gkaa1020.

44. Runx2-Twist1 interaction coordinates cranial neural crest guidance of soft palate myogenesis.
Han X et al. Elife. 2021 Jan 22;10:e62387. doi: 10.7554/eLife.62387.

45. LncSEA: a platform for long non-coding RNA related sets and enrichment analysis.
Chen J et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D969-D980. doi: 10.1093/nar/gkaa806.

46. Detection of aberrant gene expression events in RNA sequencing data.
Yépez VA et al. Nat Protoc. 2021 Jan 18. doi: 10.1038/s41596-020-00462-5. Online ahead of print.

47. SC2disease: a manually curated database of single-cell transcriptome for human diseases.
Zhao T et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1413-D1419. doi: 10.1093/nar/gkaa838.

48. Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data.
Lu T et al. Cell Rep. 2021 Jan 5;34(1):108589. doi: 10.1016/j.celrep.2020.108589.

49. MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development.
Parada GE et al. Genome Biol. 2021 Jan 22;22(1):43. doi: 10.1186/s13059-020-02246-2.

50. Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing.
Gao Y et al. Genome Biol. 2021 Jan 7;22(1):22. doi: 10.1186/s13059-020-02241-7.

51. Detection of aberrant splicing events in RNA-seq data using FRASER.
Mertes C et al. Nat Commun. 2021 Jan 22;12(1):529. doi: 10.1038/s41467-020-20573-7.

52. Multi-domain translation between single-cell imaging and sequencing data using autoencoders.
Yang KD et al. Nat Commun. 2021 Jan 4;12(1):31. doi: 10.1038/s41467-020-20249-2.

53. Congenital heart disease risk loci identified by genome-wide association study in European patients.
Lahm H et al. J Clin Invest. 2021 Jan 19;131(2):e141837. doi: 10.1172/JCI141837.

54. Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells.
Bunis DG et al. Cell Rep. 2021 Jan 5;34(1):108573. doi: 10.1016/j.celrep.2020.108573.

55. CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method.
Hahn O et al. Nucleic Acids Res. 2021 Jan 25;49(2):e11. doi: 10.1093/nar/gkaa1127.

56. The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus.
Karimi MM et al. Nat Commun. 2021 Jan 4;12(1):99. doi: 10.1038/s41467-020-20306-w.

57. PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.
Yue Z et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D589-D599. doi: 10.1093/nar/gkaa1094.

58. Optimized design of antisense oligomers for targeted rRNA depletion.
Phelps WA et al. Nucleic Acids Res. 2021 Jan 11;49(1):e5. doi: 10.1093/nar/gkaa1072.

59. PI3K-driven HER2 expression is a potential therapeutic target in colorectal cancer stem cells.
Mangiapane LR et al. Gut. 2021 Jan 12:gutjnl-2020-323553. doi: 10.1136/gutjnl-2020-323553. Online ahead of print.

60. GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions.
Fang L et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D97-D103. doi: 10.1093/nar/gkaa995.

61. Identification of lysine isobutyrylation as a new histone modification mark.
Zhu Z et al. Nucleic Acids Res. 2021 Jan 11;49(1):177-189. doi: 10.1093/nar/gkaa1176.

62. Dll1(+) quiescent tumor stem cells drive chemoresistance in breast cancer through NF-κB survival pathway.
Kumar S et al. Nat Commun. 2021 Jan 18;12(1):432. doi: 10.1038/s41467-020-20664-5.

63. Apobec1 complementation factor overexpression promotes hepatic steatosis, fibrosis, and hepatocellular cancer.
Blanc V et al. J Clin Invest. 2021 Jan 4;131(1):e138699. doi: 10.1172/JCI138699.

64. Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation.
Noureen N et al. Nat Commun. 2021 Jan 8;12(1):139. doi: 10.1038/s41467-020-20474-9.

65. tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species.
Zuo Y et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1038-D1045. doi: 10.1093/nar/gkaa888.

66. LegumeIP V3: from models to crops-an integrative gene discovery platform for translational genomics in legumes.
Dai X et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1472-D1479. doi: 10.1093/nar/gkaa976.

67. Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.
Yu AM et al. Mol Cell. 2021 Jan 13:S1097-2765(20)30936-9. doi: 10.1016/j.molcel.2020.12.017. Online ahead of print.

68. Aberrant regulation of a poison exon caused by a non-coding variant in a mouse model of Scn1a-associated epileptic encephalopathy.
Voskobiynyk Y et al. PLoS Genet. 2021 Jan 7;17(1):e1009195. doi: 10.1371/journal.pgen.1009195. eCollection 2021 Jan.

69. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.
Bastian FB et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D831-D847. doi: 10.1093/nar/gkaa793.

70. The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline.
Janosevic D et al. Elife. 2021 Jan 15;10:e62270. doi: 10.7554/eLife.62270.

71. Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping.
Adams PP et al. Elife. 2021 Jan 18;10:e62438. doi: 10.7554/eLife.62438.

72. Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress.
Lehman BJ et al. PLoS Genet. 2021 Jan 7;17(1):e1009277. doi: 10.1371/journal.pgen.1009277. eCollection 2021 Jan.

73. The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2.
Chow RD et al. Nat Commun. 2021 Jan 4;12(1):4. doi: 10.1038/s41467-020-20323-9.

74. Early T follicular helper cell activity accelerates hepatitis C virus-specific B cell expansion.
Salinas E et al. J Clin Invest. 2021 Jan 19;131(2):e140590. doi: 10.1172/JCI140590.

75. Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression.
Kong NR et al. Cell Rep. 2021 Jan 5;34(1):108574. doi: 10.1016/j.celrep.2020.108574.

76. Oncogenic HPV promotes the expression of the long noncoding RNA lnc-FANCI-2 through E7 and YY1.
Liu H et al. Proc Natl Acad Sci U S A. 2021 Jan 19;118(3):e2014195118. doi: 10.1073/pnas.2014195118.

77. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes.
Gao R et al. Nat Biotechnol. 2021 Jan 18. doi: 10.1038/s41587-020-00795-2. Online ahead of print.

78. Disrupted spermatogenesis in a metabolic syndrome model: the role of vitamin A metabolism in the gut-testis axis.
Zhang T et al. Gut. 2021 Jan 27:gutjnl-2020-323347. doi: 10.1136/gutjnl-2020-323347. Online ahead of print.

79. Unraveling the Genetic Basis for the Rapid Diversification of Male Genitalia between Drosophila Species.
Hagen JFD et al. Mol Biol Evol. 2021 Jan 23;38(2):437-448. doi: 10.1093/molbev/msaa232.

80. Hyperglycemia cooperates with Tet2 heterozygosity to induce leukemia driven by proinflammatory cytokine-induced lncRNA Morrbid.
Cai Z et al. J Clin Invest. 2021 Jan 4;131(1):e140707. doi: 10.1172/JCI140707.

81. Greater epithelial ridge cells are the principal organoid-forming progenitors of the mouse cochlea.
Kubota M et al. Cell Rep. 2021 Jan 19;34(3):108646. doi: 10.1016/j.celrep.2020.108646.

82. Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer.
Huang KK et al. Genome Biol. 2021 Jan 22;22(1):44. doi: 10.1186/s13059-021-02261-x.

83. scMC learns biological variation through the alignment of multiple single-cell genomics datasets.
Zhang L et al. Genome Biol. 2021 Jan 4;22(1):10. doi: 10.1186/s13059-020-02238-2.

84. The BMP signaling gradient is interpreted through concentration thresholds in dorsal-ventral axial patterning.
Greenfeld H et al. PLoS Biol. 2021 Jan 22;19(1):e3001059. doi: 10.1371/journal.pbio.3001059. Online ahead of print.

85. Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma.
Jerby-Arnon L et al. Nat Med. 2021 Jan 25. doi: 10.1038/s41591-020-01212-6. Online ahead of print.

86. E7386, a selective inhibitor of the interaction between β-catenin and CBP, exerts antitumor activity in tumor models with activated canonical Wnt signaling.
Yamada K et al. Cancer Res. 2021 Jan 6:canres.0782.2020. doi: 10.1158/0008-5472.CAN-20-0782. Online ahead of print.

1. Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome.
Semick SA et al. Mol Psychiatry. 2020 Dec;25(12):3267-3277. doi: 10.1038/s41380-018-0223-1. Epub 2018 Aug 21.

87. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression.
Hou G et al. Nat Commun. 2021 Jan 8;12(1):135. doi: 10.1038/s41467-020-20460-1.

88. Tailoring the resolution of single-cell RNA sequencing for primary cytotoxic T cells.
Kanev K et al. Nat Commun. 2021 Jan 25;12(1):569. doi: 10.1038/s41467-020-20751-7.

89. Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model.
Hung YH et al. Nucleic Acids Res. 2021 Jan 25;49(2):726-744. doi: 10.1093/nar/gkaa1204.

90. Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network.
Balarezo-Cisneros LN et al. PLoS Genet. 2021 Jan 25;17(1):e1008761. doi: 10.1371/journal.pgen.1008761. Online ahead of print.