Monthly Letter

1. Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19.
Trump S et al. Nat Biotechnol. 2021 Jun;39(6):705-716. doi: 10.1038/s41587-020-00796-1. Epub 2020 Dec 24.

2. Cross-species RNA-seq for deciphering host-microbe interactions.
Westermann AJ et al. Nat Rev Genet. 2021 Jun;22(6):361-378. doi: 10.1038/s41576-021-00326-y. Epub 2021 Feb 17.

3. High-throughput full-length single-cell RNA-seq automation.
Mamanova L et al. Nat Protoc. 2021 Jun;16(6):2886-2915. doi: 10.1038/s41596-021-00523-3. Epub 2021 May 14.

4. The triumphs and limitations of computational methods for scRNA-seq.
Kharchenko PV et al. Nat Methods. 2021 Jun 21. doi: 10.1038/s41592-021-01171-x. Online ahead of print.

5. Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing.
Datlinger P et al. Nat Methods. 2021 Jun;18(6):635-642. doi: 10.1038/s41592-021-01153-z. Epub 2021 May 31.

6. Global in situ profiling of RNA-RNA spatial interactions with RIC-seq.
Cao C et al. Nat Protoc. 2021 Jun;16(6):2916-2946. doi: 10.1038/s41596-021-00524-2. Epub 2021 May 21.

7. A unified atlas of CD8 T cell dysfunctional states in cancer and infection.
Pritykin Y et al. Mol Cell. 2021 Jun 3;81(11):2477-2493.e10. doi: 10.1016/j.molcel.2021.03.045. Epub 2021 Apr 22.

8. Understanding mast cell heterogeneity at single cell resolution.
Cildir G et al. Trends Immunol. 2021 Jun;42(6):523-535. doi: 10.1016/j.it.2021.04.004. Epub 2021 May 4.

9. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.
Song L et al. Nat Methods. 2021 Jun;18(6):627-630. doi: 10.1038/s41592-021-01142-2. Epub 2021 May 13.

10. MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis.
Slaff B et al. Nat Commun. 2021 Jun 7;12(1):3353. doi: 10.1038/s41467-021-23608-9.

11. Neural G0: a quiescent-like state found in neuroepithelial-derived cells and glioma.
O'Connor SA et al. Mol Syst Biol. 2021 Jun;17(6):e9522. doi: 10.15252/msb.20209522.

12. Vibrio cholerae's mysterious Seventh Pandemic island (VSP-II) encodes novel Zur-regulated zinc starvation genes involved in chemotaxis and cell congregation.
Murphy SG et al. PLoS Genet. 2021 Jun 21;17(6):e1009624. doi: 10.1371/journal.pgen.1009624. Online ahead of print.

13. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics.
Longo SK et al. Nat Rev Genet. 2021 Jun 18. doi: 10.1038/s41576-021-00370-8. Online ahead of print.

14. HOXA13 in etiology and oncogenic potential of Barrett's esophagus.
Janmaat VT et al. Nat Commun. 2021 Jun 7;12(1):3354. doi: 10.1038/s41467-021-23641-8.

15. B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.
Scheid JF et al. Cell. 2021 Jun 10;184(12):3205-3221.e24. doi: 10.1016/j.cell.2021.04.032. Epub 2021 Apr 24.

16. Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process.
Koiwai K et al. Elife. 2021 Jun 16;10:e66954. doi: 10.7554/eLife.66954. Online ahead of print.

17. RNAnue: efficient data analysis for RNA-RNA interactomics.
Schäfer RA et al. Nucleic Acids Res. 2021 Jun 4;49(10):5493-5501. doi: 10.1093/nar/gkab340.

18. Targeting the m(6)A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication.
Burgess HM et al. Genes Dev. 2021 Jun 24. doi: 10.1101/gad.348320.121. Online ahead of print.

19. Extraction of nuclei from archived postmortem tissues for single-nucleus sequencing applications.
Maitra M et al. Nat Protoc. 2021 Jun;16(6):2788-2801. doi: 10.1038/s41596-021-00514-4. Epub 2021 May 10.

20. Early role for a Na(+),K(+)-ATPase (ATP1A3) in brain development.
Smith RS et al. Proc Natl Acad Sci U S A. 2021 Jun 22;118(25):e2023333118. doi: 10.1073/pnas.2023333118.

21. LIQA: long-read isoform quantification and analysis.
Hu Y et al. Genome Biol. 2021 Jun 17;22(1):182. doi: 10.1186/s13059-021-02399-8.

22. NOVA2 regulates neural circRNA biogenesis.
Knupp D et al. Nucleic Acids Res. 2021 Jun 22:gkab523. doi: 10.1093/nar/gkab523. Online ahead of print.

23. Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response.
Zhang Y et al. Proc Natl Acad Sci U S A. 2021 Jun 15;118(24):e2103240118. doi: 10.1073/pnas.2103240118.

24. Microscopic examination of spatial transcriptome using Seq-Scope.
Cho CS et al. Cell. 2021 Jun 24;184(13):3559-3572.e22. doi: 10.1016/j.cell.2021.05.010. Epub 2021 Jun 10.

25. Detection of differentially abundant cell subpopulations in scRNA-seq data.
Zhao J et al. Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2100293118. doi: 10.1073/pnas.2100293118.

26. Replicate sequencing libraries are important for quantification of allelic imbalance.
Mendelevich A et al. Nat Commun. 2021 Jun 7;12(1):3370. doi: 10.1038/s41467-021-23544-8.

27. Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories.
Pokhilko A et al. Genome Res. 2021 Jun;31(6):1069-1081. doi: 10.1101/gr.273961.120. Epub 2021 May 19.

28. A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast.
Pal B et al. EMBO J. 2021 Jun 1;40(11):e107333. doi: 10.15252/embj.2020107333. Epub 2021 May 5.

29. NSrp70 is a lymphocyte-essential splicing factor that controls thymocyte development.
Kim CH et al. Nucleic Acids Res. 2021 Jun 4;49(10):5760-5778. doi: 10.1093/nar/gkab389.

30. A machine learning method for the discovery of minimum marker gene combinations for cell-type identification from single-cell RNA sequencing.
Aevermann BD et al. Genome Res. 2021 Jun 4:gr.275569.121. doi: 10.1101/gr.275569.121. Online ahead of print.

31. Tumor vessel co-option probed by single-cell analysis.
Teuwen LA et al. Cell Rep. 2021 Jun 15;35(11):109253. doi: 10.1016/j.celrep.2021.109253.

32. RNA structure probing reveals the structural basis of Dicer binding and cleavage.
Luo QJ et al. Nat Commun. 2021 Jun 7;12(1):3397. doi: 10.1038/s41467-021-23607-w.

33. Polyploid mitosis and depolyploidization promote chromosomal instability and tumor progression in a Notch-induced tumor model.
Wang XF et al. Dev Cell. 2021 Jun 15:S1534-5807(21)00477-9. doi: 10.1016/j.devcel.2021.05.017. Online ahead of print.

34. Prioritization of cell types responsive to biological perturbations in single-cell data with Augur.
Squair JW et al. Nat Protoc. 2021 Jun 25. doi: 10.1038/s41596-021-00561-x. Online ahead of print.

35. Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish.
Zhu Q et al. Nucleic Acids Res. 2021 Jun 4;49(10):5743-5759. doi: 10.1093/nar/gkab381.

36. Cell type hierarchy reconstruction via reconciliation of multi-resolution cluster tree.
Peng M et al. Nucleic Acids Res. 2021 Jun 14:gkab481. doi: 10.1093/nar/gkab481. Online ahead of print.

37. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish.
Naftaly AS et al. Genome Res. 2021 Jun 15:gr.274282.120. doi: 10.1101/gr.274282.120. Online ahead of print.

38. TET1-mediated DNA hydroxymethylation regulates adult remyelination in mice.
Moyon S et al. Nat Commun. 2021 Jun 7;12(1):3359. doi: 10.1038/s41467-021-23735-3.

39. Model-based prediction of spatial gene expression via generative linear mapping.
Okochi Y et al. Nat Commun. 2021 Jun 17;12(1):3731. doi: 10.1038/s41467-021-24014-x.

40. The architecture of the SARS-CoV-2 RNA genome inside virion.
Cao C et al. Nat Commun. 2021 Jun 24;12(1):3917. doi: 10.1038/s41467-021-22785-x.

41. Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors.
Lei Z et al. Nat Methods. 2021 Jun;18(6):643-651. doi: 10.1038/s41592-021-01172-w. Epub 2021 Jun 7.

42. Human KIT+ myeloid cells facilitate visceral metastasis by melanoma.
Yu CI et al. J Exp Med. 2021 Jun 7;218(6):e20182163. doi: 10.1084/jem.20182163.

43. Minimized combinatorial CRISPR screens identify genetic interactions in autophagy.
Diehl V et al. Nucleic Acids Res. 2021 Jun 4;49(10):5684-5704. doi: 10.1093/nar/gkab309.

44. A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes.
Harman JR et al. Genome Res. 2021 Jun 4. doi: 10.1101/gr.268490.120. Online ahead of print.

45. Single-cell RNA-seq reveals fibroblast heterogeneity and increased mesenchymal fibroblasts in human fibrotic skin diseases.
Deng CC et al. Nat Commun. 2021 Jun 17;12(1):3709. doi: 10.1038/s41467-021-24110-y.

46. Histidine Triad Nucleotide Binding Protein 1 Attenuates Cardiac Hypertrophy via Suppressing Homeobox A5 Expression.
Zhang Y et al. Circulation. 2021 Jun 8. doi: 10.1161/CIRCULATIONAHA.120.051094. Online ahead of print.

47. Optimizing expression quantitative trait locus mapping workflows for single-cell studies.
Cuomo ASE et al. Genome Biol. 2021 Jun 24;22(1):188. doi: 10.1186/s13059-021-02407-x.

48. Global profiling of RNA-binding protein target sites by LACE-seq.
Su R et al. Nat Cell Biol. 2021 Jun;23(6):664-675. doi: 10.1038/s41556-021-00696-9. Epub 2021 Jun 9.

49. Linking the dynamics of chromatin occupancy and transcription with predictive models.
Tran TQ et al. Genome Res. 2021 Jun;31(6):1035-1046. doi: 10.1101/gr.267237.120. Epub 2021 Apr 23.

50. Analysis of off-target effects in CRISPR-based gene drives in the human malaria mosquito.
Garrood WT et al. Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2004838117. doi: 10.1073/pnas.2004838117. Epub 2021 Apr 30.

51. Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells.
Mathew NR et al. Cell Rep. 2021 Jun 22;35(12):109286. doi: 10.1016/j.celrep.2021.109286.

52. Molecular determinants of response to PD-L1 blockade across tumor types.
Banchereau R et al. Nat Commun. 2021 Jun 25;12(1):3969. doi: 10.1038/s41467-021-24112-w.

53. An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium.
Fuchs M et al. Proc Natl Acad Sci U S A. 2021 Jun 22;118(25):e2103579118. doi: 10.1073/pnas.2103579118.

54. CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones.
Bavli D et al. Dev Cell. 2021 Jun 21;56(12):1804-1817.e7. doi: 10.1016/j.devcel.2021.04.026. Epub 2021 May 18.

55. EGFR-HIF1α signaling positively regulates the differentiation of IL-9 producing T helper cells.
Roy S et al. Nat Commun. 2021 Jun 1;12(1):3182. doi: 10.1038/s41467-021-23042-x.

56. Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response.
Yu F et al. Nucleic Acids Res. 2021 Jun 4;49(10):5779-5797. doi: 10.1093/nar/gkab415.

57. HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence.
Sofiadis K et al. Mol Syst Biol. 2021 Jun;17(6):e9760. doi: 10.15252/msb.20209760.

58. Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships.
Fafard-Couture É et al. Genome Biol. 2021 Jun 4;22(1):172. doi: 10.1186/s13059-021-02391-2.

59. Overexpression of human BAG3(P209L) in mice causes restrictive cardiomyopathy.
Kimura K et al. Nat Commun. 2021 Jun 11;12(1):3575. doi: 10.1038/s41467-021-23858-7.

60. Molecular design of the γδT cell receptor ectodomain encodes biologically fit ligand recognition in the absence of mechanosensing.
Mallis RJ et al. Proc Natl Acad Sci U S A. 2021 Jun 29;118(26):e2023050118. doi: 10.1073/pnas.2023050118.

61. Rare variants regulate expression of nearby individual genes in multiple tissues.
Li J et al. PLoS Genet. 2021 Jun 1;17(6):e1009596. doi: 10.1371/journal.pgen.1009596. eCollection 2021 Jun.

62. TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.
Conard AM et al. Nucleic Acids Res. 2021 Jun 14:gkab384. doi: 10.1093/nar/gkab384. Online ahead of print.

63. A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance.
Warshauer JT et al. J Exp Med. 2021 Aug 2;218(8):e20210759. doi: 10.1084/jem.20210759. Epub 2021 Jun 11.

64. Meiosis-specific ZFP541 repressor complex promotes developmental progression of meiotic prophase towards completion during mouse spermatogenesis.
Horisawa-Takada Y et al. Nat Commun. 2021 Jun 1;12(1):3184. doi: 10.1038/s41467-021-23378-4.

65. An AIB1 isoform alters enhancer access and enables progression of early stage triple-negative breast cancer.
Sharif GM et al. Cancer Res. 2021 Jun 16:canres.3625.2020. doi: 10.1158/0008-5472.CAN-20-3625. Online ahead of print.

66. BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.
Gustafsson J et al. Genome Biol. 2021 Jun 8;22(1):174. doi: 10.1186/s13059-021-02386-z.

67. Retinoic acid signaling is critical during the totipotency window in early mammalian development.
Iturbide A et al. Nat Struct Mol Biol. 2021 Jun;28(6):521-532. doi: 10.1038/s41594-021-00590-w. Epub 2021 May 27.

68. The N6-methyladenosine RNA-binding protein YTHDF1 modulates the translation of TRAF6 to mediate the intestinal immune response.
Zong X et al. Nucleic Acids Res. 2021 Jun 4;49(10):5537-5552. doi: 10.1093/nar/gkab343.

69. Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome.
Lago S et al. Nat Commun. 2021 Jun 23;12(1):3885. doi: 10.1038/s41467-021-24198-2.

70. Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation.
Penter L et al. Blood. 2021 Jun 10;137(23):3212-3217. doi: 10.1182/blood.2021010867.

71. Regulation of RNA Polymerase II Activity is Essential for Terminal Erythroid Maturation.
Murphy Z et al. Blood. 2021 Jun 1:blood.2020009903. doi: 10.1182/blood.2020009903. Online ahead of print.

72. Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa.
Li S et al. Nucleic Acids Res. 2021 Jun 17:gkab506. doi: 10.1093/nar/gkab506. Online ahead of print.

73. Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development.
Tian L et al. Immunity. 2021 Jun 8;54(6):1338-1351.e9. doi: 10.1016/j.immuni.2021.03.012. Epub 2021 Apr 15.

74. Reprogramming of microRNA expression via E2F1 downregulation promotes Salmonella infection both in infected and bystander cells.
Aguilar C et al. Nat Commun. 2021 Jun 7;12(1):3392. doi: 10.1038/s41467-021-23593-z.

75. The CD200-CD200R axis promotes squamous cell carcinoma metastasis via regulation of cathepsin K.
Khan IZ et al. Cancer Res. 2021 Jun 28:canres.3251.2020. doi: 10.1158/0008-5472.CAN-20-3251. Online ahead of print.

76. Phospholipids of APOE lipoproteins activate microglia in an isoform-specific manner in preclinical models of Alzheimer's disease.
Fitz NF et al. Nat Commun. 2021 Jun 7;12(1):3416. doi: 10.1038/s41467-021-23762-0.

77. Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding.
Serra F et al. Nucleic Acids Res. 2021 Jun 21;49(11):e66. doi: 10.1093/nar/gkab198.

78. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
Mimitou EP et al. Nat Biotechnol. 2021 Jun 3. doi: 10.1038/s41587-021-00927-2. Online ahead of print.

79. Mouse multipotent progenitor 5 cells are located at the interphase between hematopoietic stem and progenitor cells.
Sommerkamp P et al. Blood. 2021 Jun 10;137(23):3218-3224. doi: 10.1182/blood.2020007876.

80. Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength.
Al-Barghouthi BM et al. Nat Commun. 2021 Jun 7;12(1):3408. doi: 10.1038/s41467-021-23649-0.

81. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells.
Dvir S et al. Cell Rep. 2021 Jun 1;35(9):109198. doi: 10.1016/j.celrep.2021.109198.

82. The Evolutionary History of Wild, Domesticated, and Feral Brassica Oleracea (Brassicaceae).
Mabry ME et al. Mol Biol Evol. 2021 Jun 22:msab183. doi: 10.1093/molbev/msab183. Online ahead of print.

83. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring.
Yeom KH et al. Genome Res. 2021 Jun;31(6):1106-1119. doi: 10.1101/gr.273904.120. Epub 2021 Apr 8.

84. Tumor restriction by type I collagen opposes tumor-promoting effects of cancer-associated fibroblasts.
Bhattacharjee S et al. J Clin Invest. 2021 Jun 1;131(11):e146987. doi: 10.1172/JCI146987.

85. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte M et al. Nat Commun. 2021 Jun 2;12(1):3297. doi: 10.1038/s41467-021-23143-7.

86. Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma.
Hara T et al. Cancer Cell. 2021 Jun 14;39(6):779-792.e11. doi: 10.1016/j.ccell.2021.05.002. Epub 2021 Jun 3.

87. DSCAM/PAK1 pathway suppression reverses neurogenesis deficits in iPSC-derived cerebral organoids from patients with Down syndrome.
Tang XY et al. J Clin Invest. 2021 Jun 15;131(12):e135763. doi: 10.1172/JCI135763.

88. A unique macrophage subpopulation signals directly to progenitor cells to promote regenerative neurogenesis in the zebrafish spinal cord.
Cavone L et al. Dev Cell. 2021 Jun 7;56(11):1617-1630.e6. doi: 10.1016/j.devcel.2021.04.031. Epub 2021 May 24.

89. Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells.
Soares MAF et al. Genes Dev. 2021 Jun 24. doi: 10.1101/gad.348174.120. Online ahead of print.

90. Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts.
Schulz L et al. Genome Biol. 2021 Jun 28;22(1):190. doi: 10.1186/s13059-021-02411-1.

91. Author Correction: PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications.
Shi J et al. Nat Cell Biol. 2021 Jun;23(6):676. doi: 10.1038/s41556-021-00687-w.

92. Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism.
Chopra M et al. Am J Hum Genet. 2021 Jun 3;108(6):1138-1150. doi: 10.1016/j.ajhg.2021.04.007. Epub 2021 Apr 27.