Monthly Letter

1. Zooming into Cellular and Molecular Heterogeneity of Pulmonary Hypertension: What More Single-cell Omics Can Offer.
Chelladurai P et al. Am J Respir Crit Care Med. 2020 Nov 10. doi: 10.1164/rccm.202010-3889ED. Online ahead of print.

2. Autosomal Clonal Monoallelic Expression: Natural or Artifactual?.
Rv P et al. Trends Genet. 2020 Nov 21:S0168-9525(20)30303-6. doi: 10.1016/j.tig.2020.10.011. Online ahead of print.

3. Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis.
Alencar GF et al. Circulation. 2020 Nov 24;142(21):2045-2059. doi: 10.1161/CIRCULATIONAHA.120.046672. Epub 2020 Jul 17.

4. Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity.
Kinker GS et al. Nat Genet. 2020 Nov;52(11):1208-1218. doi: 10.1038/s41588-020-00726-6. Epub 2020 Oct 30.

5. Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.
Ma S et al. Cell. 2020 Nov 12;183(4):1103-1116.e20. doi: 10.1016/j.cell.2020.09.056. Epub 2020 Oct 23.

6. CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity.
Lazzarotto CR et al. Nat Biotechnol. 2020 Nov;38(11):1317-1327. doi: 10.1038/s41587-020-0555-7. Epub 2020 Jun 15.

7. Decoding myofibroblast origins in human kidney fibrosis.
Kuppe C et al. Nature. 2020 Nov 11. doi: 10.1038/s41586-020-2941-1. Online ahead of print.

8. A map of cis-regulatory elements and 3D genome structures in zebrafish.
Yang H et al. Nature. 2020 Nov 25. doi: 10.1038/s41586-020-2962-9. Online ahead of print.

9. Single nuclei RNA-seq of mouse placental labyrinth development.
Marsh B et al. Elife. 2020 Nov 3;9:e60266. doi: 10.7554/eLife.60266.

10. Data Sanitization to Reduce Private Information Leakage from Functional Genomics.
Gürsoy G et al. Cell. 2020 Nov 12;183(4):905-917.e16. doi: 10.1016/j.cell.2020.09.036.

11. Defining the Teratoma as a Model for Multi-lineage Human Development.
McDonald D et al. Cell. 2020 Nov 25;183(5):1402-1419.e18. doi: 10.1016/j.cell.2020.10.018. Epub 2020 Nov 4.

12. Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis.
Schupp JC et al. Am J Respir Crit Care Med. 2020 Nov 15;202(10):1419-1429. doi: 10.1164/rccm.202004-0991OC.

13. Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 in lung epithelium.
Schuler BA et al. J Clin Invest. 2020 Nov 12:140766. doi: 10.1172/JCI140766. Online ahead of print.

14. A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer.
Chen H et al. Cancer Cell. 2020 Nov 9;38(5):701-715.e5. doi: 10.1016/j.ccell.2020.08.020. Epub 2020 Oct 1.

15. The landscape of RNA Pol II binding reveals a stepwise transition during ZGA.
Liu B et al. Nature. 2020 Nov;587(7832):139-144. doi: 10.1038/s41586-020-2847-y. Epub 2020 Oct 28.

16. A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells.
Zachariadis V et al. Mol Cell. 2020 Nov 5;80(3):541-553.e5. doi: 10.1016/j.molcel.2020.09.025. Epub 2020 Oct 16.

17. A single-cell atlas and lineage analysis of the adult Drosophila ovary.
Rust K et al. Nat Commun. 2020 Nov 6;11(1):5628. doi: 10.1038/s41467-020-19361-0.

18. snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.
Sun W et al. Nature. 2020 Nov;587(7832):98-102. doi: 10.1038/s41586-020-2856-x. Epub 2020 Oct 28.

19. Astrocytic phagocytosis is a compensatory mechanism for microglial dysfunction.
Konishi H et al. EMBO J. 2020 Nov 16;39(22):e104464. doi: 10.15252/embj.2020104464. Epub 2020 Sep 22.

20. Rapid and Scalable Profiling of Nascent RNA with fastGRO.
Barbieri E et al. Cell Rep. 2020 Nov 10;33(6):108373. doi: 10.1016/j.celrep.2020.108373.

21. Guidelines for reporting single-cell RNA-seq experiments.
Füllgrabe A et al. Nat Biotechnol. 2020 Nov 13. doi: 10.1038/s41587-020-00744-z. Online ahead of print.

22. TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment.
Sun D et al. Nucleic Acids Res. 2020 Nov 12:gkaa1020. doi: 10.1093/nar/gkaa1020. Online ahead of print.

23. RJunBase: a database of RNA splice junctions in human normal and cancerous tissues.
Li Q et al. Nucleic Acids Res. 2020 Nov 12:gkaa1056. doi: 10.1093/nar/gkaa1056. Online ahead of print.

24. RNA Polymerase II-Associated Factor 1 Regulates Stem Cell Features of Pancreatic Cancer Cells, Independently of the PAF1 Complex, via Interactions With PHF5A and DDX3.
Karmakar S et al. Gastroenterology. 2020 Nov;159(5):1898-1915.e6. doi: 10.1053/j.gastro.2020.07.053. Epub 2020 Aug 8.

25. Subnuclear gene positioning through lamina association affects copper tolerance.
Sakamoto Y et al. Nat Commun. 2020 Nov 20;11(1):5914. doi: 10.1038/s41467-020-19621-z.

26. Single-Cell Analysis of Neonatal HSC Ontogeny Reveals Gradual and Uncoordinated Transcriptional Reprogramming that Begins before Birth.
Li Y et al. Cell Stem Cell. 2020 Nov 5;27(5):732-747.e7. doi: 10.1016/j.stem.2020.08.001. Epub 2020 Aug 20.

27. Benchmarking of cell type deconvolution pipelines for transcriptomics data.
Avila Cobos F et al. Nat Commun. 2020 Nov 6;11(1):5650. doi: 10.1038/s41467-020-19015-1.

28. 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. 2020 Nov 21:gkaa1006. doi: 10.1093/nar/gkaa1006. Online ahead of print.

29. Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas.
Tosti L et al. Gastroenterology. 2020 Nov 16:S0016-5085(20)35399-3. doi: 10.1053/j.gastro.2020.11.010. Online ahead of print.

30. Ensemble dimensionality reduction and feature gene extraction for single-cell RNA-seq data.
Sun X et al. Nat Commun. 2020 Nov 17;11(1):5853. doi: 10.1038/s41467-020-19465-7.

31. A Genomic Cluster Containing Novel and Conserved Genes is Associated with Cichlid Fish Dental Developmental Convergence.
Karagic N et al. Mol Biol Evol. 2020 Nov 1;37(11):3165-3174. doi: 10.1093/molbev/msaa153.

32. Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia.
Prudencio M et al. J Clin Invest. 2020 Nov 2;130(11):6080-6092. doi: 10.1172/JCI139741.

33. Triple RNA-Seq Reveals Synergy in a Human Virus-Fungus Co-infection Model.
Seelbinder B et al. Cell Rep. 2020 Nov 17;33(7):108389. doi: 10.1016/j.celrep.2020.108389.

34. PINA 3.0: mining cancer interactome.
Du Y et al. Nucleic Acids Res. 2020 Nov 24:gkaa1075. doi: 10.1093/nar/gkaa1075. Online ahead of print.

35. Opposing functions of Fng1 and the Rpd3 HDAC complex in H4 acetylation in Fusarium graminearum.
Jiang H et al. PLoS Genet. 2020 Nov 2;16(11):e1009185. doi: 10.1371/journal.pgen.1009185. eCollection 2020 Nov.

36. PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments.
Liu P et al. Genome Res. 2020 Nov;30(11):1655-1666. doi: 10.1101/gr.252445.119. Epub 2020 Sep 21.

37. Phenotypic variation of transcriptomic cell types in mouse motor cortex.
Scala F et al. Nature. 2020 Nov 12. doi: 10.1038/s41586-020-2907-3. Online ahead of print.

38. Gbx2 Identifies Two Amacrine Cell Subtypes with Distinct Molecular, Morphological, and Physiological Properties.
Kerstein PC et al. Cell Rep. 2020 Nov 17;33(7):108382. doi: 10.1016/j.celrep.2020.108382.

39. Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids.
Sawada T et al. Mol Psychiatry. 2020 Nov;25(11):2695-2711. doi: 10.1038/s41380-020-0844-z. Epub 2020 Aug 7.

40. Molecular estimation of neurodegeneration pseudotime in older brains.
Mukherjee S et al. Nat Commun. 2020 Nov 13;11(1):5781. doi: 10.1038/s41467-020-19622-y.

41. X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity.
Link JC et al. J Clin Invest. 2020 Nov 2;130(11):5688-5702. doi: 10.1172/JCI140223.

42. Jointly defining cell types from multiple single-cell datasets using LIGER.
Liu J et al. Nat Protoc. 2020 Nov;15(11):3632-3662. doi: 10.1038/s41596-020-0391-8. Epub 2020 Oct 12.

43. HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression.
Srinivasachar Badarinarayan S et al. Nucleic Acids Res. 2020 Nov 4;48(19):10890-10908. doi: 10.1093/nar/gkaa832.

44. RUNX1 and CBFβ-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemia development.
Zhen T et al. Blood. 2020 Nov 19;136(21):2373-2385. doi: 10.1182/blood.2020007747.

45. Single cell RNA-seq reveals developmental plasticity with coexisting oncogenic and immune evasion programs in ETP-ALL.
Anand P et al. Blood. 2020 Nov 23:blood.2019004547. doi: 10.1182/blood.2019004547. Online ahead of print.

46. GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions.
Fang L et al. Nucleic Acids Res. 2020 Nov 5:gkaa995. doi: 10.1093/nar/gkaa995. Online ahead of print.

47. Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles.
Martin-Trujillo A et al. PLoS Genet. 2020 Nov 20;16(11):e1009189. doi: 10.1371/journal.pgen.1009189. eCollection 2020 Nov.

48. Optimized design of antisense oligomers for targeted rRNA depletion.
Phelps WA et al. Nucleic Acids Res. 2020 Nov 22:gkaa1072. doi: 10.1093/nar/gkaa1072. Online ahead of print.

49. Comprehensive mapping of the human cytokine gene regulatory network.
Santoso CS et al. Nucleic Acids Res. 2020 Nov 12:gkaa1055. doi: 10.1093/nar/gkaa1055. Online ahead of print.

50. Neutrophils interact with cholangiocytes to cause cholestatic changes in alcoholic hepatitis.
Takeuchi M et al. Gut. 2020 Nov 19:gutjnl-2020-322540. doi: 10.1136/gutjnl-2020-322540. Online ahead of print.

51. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics.
Kotliar D et al. Cell. 2020 Nov 25;183(5):1383-1401.e19. doi: 10.1016/j.cell.2020.10.002. Epub 2020 Nov 6.

52. Development of specialized sensory neurons engages a nuclear receptor required for functional plasticity.
Rossillo M et al. Genes Dev. 2020 Nov 12. doi: 10.1101/gad.342212.120. Online ahead of print.

53. Functional compensation precedes recovery of tissue mass following acute liver injury.
Walesky CM et al. Nat Commun. 2020 Nov 19;11(1):5785. doi: 10.1038/s41467-020-19558-3.

54. Functional Atlas of Primary miRNA Maturation by the Microprocessor.
Rice GM et al. Mol Cell. 2020 Nov 4:S1097-2765(20)30735-8. doi: 10.1016/j.molcel.2020.10.028. Online ahead of print.

55. Plasmablasts derive from CD23-negative activated B cells after the extinction of IL-4/STAT6 signaling and IRF4 induction.
Pignarre A et al. Blood. 2020 Nov 4:blood.2020005083. doi: 10.1182/blood.2020005083. Online ahead of print.

56. Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes.
Wang A et al. Elife. 2020 Nov 9;9:e62522. doi: 10.7554/eLife.62522.

57. SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution.
Sountoulidis A et al. PLoS Biol. 2020 Nov 20;18(11):e3000675. doi: 10.1371/journal.pbio.3000675. Online ahead of print.

58. Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus.
Raj P et al. Genome Biol. 2020 Nov 19;21(1):281. doi: 10.1186/s13059-020-02184-z.

59. Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4(+) T Cells in COVID-19.
Meckiff BJ et al. Cell. 2020 Nov 25;183(5):1340-1353.e16. doi: 10.1016/j.cell.2020.10.001. Epub 2020 Oct 5.

60. Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus.
Linker SB et al. Genome Res. 2020 Nov;30(11):1643-1654. doi: 10.1101/gr.262196.120.

61. Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis.
Chai P et al. Nucleic Acids Res. 2020 Nov 16:gkaa1051. doi: 10.1093/nar/gkaa1051. Online ahead of print.

62. Decitabine induces gene derepression on monosomic chromosomes: in vitro and in vivo effects in adverse-risk cytogenetics AML.
Greve G et al. Cancer Res. 2020 Nov 17:canres.1430.2020. doi: 10.1158/0008-5472.CAN-20-1430. Online ahead of print.

63. LegumeIP V3: from models to crops-an integrative gene discovery platform for translational genomics in legumes.
Dai X et al. Nucleic Acids Res. 2020 Nov 9:gkaa976. doi: 10.1093/nar/gkaa976. Online ahead of print.

64. Altered intestinal ACE2 levels are associated with inflammation, severe disease and response to anti-cytokine therapy in IBD.
Potdar AA et al. Gastroenterology. 2020 Nov 2:S0016-5085(20)35331-2. doi: 10.1053/j.gastro.2020.10.041. Online ahead of print.

65. UTX maintains functional integrity of murine hematopoietic system by globally regulating aging-associated genes.
Sera Y et al. Blood. 2020 Nov 10:blood.2019001044. doi: 10.1182/blood.2019001044. Online ahead of print.

66. Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development.
Malkani S et al. Cell Rep. 2020 Nov 21:108448. doi: 10.1016/j.celrep.2020.108448. Online ahead of print.

67. GTRD: an integrated view of transcription regulation.
Kolmykov S et al. Nucleic Acids Res. 2020 Nov 24:gkaa1057. doi: 10.1093/nar/gkaa1057. Online ahead of print.

68. Cardiac Pressure Overload Decreases ETV1 Expression in the Left Atrium, Contributing to Atrial Electrical and Structural Remodeling.
Yamaguchi N et al. Circulation. 2020 Nov 23. doi: 10.1161/CIRCULATIONAHA.120.048121. Online ahead of print.

69. Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer.
Wan C et al. Cancer Res. 2020 Nov 6:canres.1674.2020. doi: 10.1158/0008-5472.CAN-20-1674. Online ahead of print.

70. mTORC1 activation in lung mesenchyme drives sex- and age-dependent pulmonary structure and function decline.
Obraztsova K et al. Nat Commun. 2020 Nov 6;11(1):5640. doi: 10.1038/s41467-020-18979-4.

71. Direct RNA sequencing reveals m(6)A modifications on adenovirus RNA are necessary for efficient splicing.
Price AM et al. Nat Commun. 2020 Nov 26;11(1):6016. doi: 10.1038/s41467-020-19787-6.

72. Extracellular traps released by antimicrobial TH17 cells contribute to host defense.
Agak GW et al. J Clin Invest. 2020 Nov 19:141594. doi: 10.1172/JCI141594. Online ahead of print.

73. PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.
Yue Z et al. Nucleic Acids Res. 2020 Nov 27:gkaa1094. doi: 10.1093/nar/gkaa1094. Online ahead of print.

74. Metabolic RNA labeling for probing RNA dynamics in bacteria.
Meng L et al. Nucleic Acids Res. 2020 Nov 27:gkaa1111. doi: 10.1093/nar/gkaa1111. Online ahead of print.

75. Prrx1 Fibroblasts Represent a Pro-fibrotic Lineage in the Mouse Ventral Dermis.
Leavitt T et al. Cell Rep. 2020 Nov 10;33(6):108356. doi: 10.1016/j.celrep.2020.108356.

76. Prolonged Exposure to Microgravity Reduces Cardiac Contractility and Initiates Remodeling in Drosophila.
Walls S et al. Cell Rep. 2020 Nov 23:108445. doi: 10.1016/j.celrep.2020.108445. Online ahead of print.

77. The Ig heavy chain protein but not its message controls early B cell development.
Aslam MA et al. Proc Natl Acad Sci U S A. 2020 Nov 23:202004810. doi: 10.1073/pnas.2004810117. Online ahead of print.

78. Liver Immune Profiling Reveals Pathogenesis and Therapeutics for Biliary Atresia.
Wang J et al. Cell. 2020 Nov 26:S0092-8674(20)31455-0. doi: 10.1016/j.cell.2020.10.048. Online ahead of print.

79. NAIL: an evolutionarily conserved lncRNA essential for licensing coordinated activation of p38 and NFκB in colitis.
Akıncılar SC et al. Gut. 2020 Nov 25:gutjnl-2020-322980. doi: 10.1136/gutjnl-2020-322980. Online ahead of print.

80. Recessive, Deleterious Variants in SMG8 Expand the Role of Nonsense-Mediated Decay in Developmental Disorders in Humans.
Alzahrani F et al. Am J Hum Genet. 2020 Nov 20:S0002-9297(20)30404-3. doi: 10.1016/j.ajhg.2020.11.007. Online ahead of print.

81. STRAP regulates alternative splicing fidelity during lineage commitment of mouse embryonic stem cells.
Jin L et al. Nat Commun. 2020 Nov 23;11(1):5941. doi: 10.1038/s41467-020-19698-6.

82. Author Correction: Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas.
Moncada R et al. Nat Biotechnol. 2020 Nov 23. doi: 10.1038/s41587-020-00776-5. Online ahead of print.