Monthly Letter

1. Single-cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL.
Anand P et al. Blood. 2021 May 6;137(18):2463-2480. doi: 10.1182/blood.2019004547.

2. Discovery of autism/intellectual disability somatic mutations in Alzheimer's brains: mutated ADNP cytoskeletal impairments and repair as a case study.
Ivashko-Pachima Y et al. Mol Psychiatry. 2021 May;26(5):1619-1633. doi: 10.1038/s41380-019-0563-5. Epub 2019 Oct 30.

3. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes.
Gao R et al. Nat Biotechnol. 2021 May;39(5):599-608. doi: 10.1038/s41587-020-00795-2. Epub 2021 Jan 18.

4. Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia.
Okuda K et al. Am J Respir Crit Care Med. 2021 May 15;203(10):1275-1289. doi: 10.1164/rccm.202008-3198OC.

5. High-throughput full-length single-cell RNA-seq automation.
Mamanova L et al. Nat Protoc. 2021 May 14. doi: 10.1038/s41596-021-00523-3. Online ahead of print.

6. The RNA landscape of the human placenta in health and disease.
Gong S et al. Nat Commun. 2021 May 11;12(1):2639. doi: 10.1038/s41467-021-22695-y.

7. Protein structure-based gene expression signatures.
Rahman R et al. Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2014866118. doi: 10.1073/pnas.2014866118.

8. Global in situ profiling of RNA-RNA spatial interactions with RIC-seq.
Cao C et al. Nat Protoc. 2021 May 21. doi: 10.1038/s41596-021-00524-2. Online ahead of print.

9. 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.

10. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.
Song L et al. Nat Methods. 2021 May 13. doi: 10.1038/s41592-021-01142-2. Online ahead of print.

11. Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces.
Ding J et al. Nat Commun. 2021 May 5;12(1):2554. doi: 10.1038/s41467-021-22851-4.

12. RNAnue: efficient data analysis for RNA-RNA interactomics.
Schäfer RA et al. Nucleic Acids Res. 2021 May 21:gkab340. doi: 10.1093/nar/gkab340. Online ahead of print.

13. Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages.
Obradovic A et al. Cell. 2021 May 27;184(11):2988-3005.e16. doi: 10.1016/j.cell.2021.04.038. Epub 2021 May 20.

14. Single-Cell RNA Sequencing Reveals the Cellular Origin and Evolution of Breast Cancer in BRCA1 Mutation Carriers.
Hu L et al. Cancer Res. 2021 May 15;81(10):2600-2611. doi: 10.1158/0008-5472.CAN-20-2123. Epub 2021 Mar 16.

15. Conserved DNA sequence features underlie pervasive RNA polymerase pausing.
Gajos M et al. Nucleic Acids Res. 2021 May 7;49(8):4402-4420. doi: 10.1093/nar/gkab208.

16. Extraction of nuclei from archived postmortem tissues for single-nucleus sequencing applications.
Maitra M et al. Nat Protoc. 2021 May 10. doi: 10.1038/s41596-021-00514-4. Online ahead of print.

17. Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression.
Gao Y et al. Genome Res. 2021 May 25:gr.271346.120. doi: 10.1101/gr.271346.120. Online ahead of print.

18. Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories.
Pokhilko A et al. Genome Res. 2021 May 19. doi: 10.1101/gr.273961.120. Online ahead of print.

19. Novel cell types and developmental lineages revealed by single-cell RNA-seq analysis of the mouse crista ampullaris.
Wilkerson BA et al. Elife. 2021 May 18;10:e60108. doi: 10.7554/eLife.60108. Online ahead of print.

20. A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast.
Pal B et al. EMBO J. 2021 May 5:e107333. doi: 10.15252/embj.2020107333. Online ahead of print.

21. Co-evolution of tumor and immune cells during progression of multiple myeloma.
Liu R et al. Nat Commun. 2021 May 7;12(1):2559. doi: 10.1038/s41467-021-22804-x.

22. A coordinated progression of progenitor cell states initiates urinary tract development.
Sanchez-Ferras O et al. Nat Commun. 2021 May 11;12(1):2627. doi: 10.1038/s41467-021-22931-5.

23. Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts.
Gao J et al. PLoS Biol. 2021 May 18;19(5):e3001229. doi: 10.1371/journal.pbio.3001229. eCollection 2021 May.

24. Mouse totipotent stem cells captured and maintained through spliceosomal repression.
Shen H et al. Cell. 2021 May 27;184(11):2843-2859.e20. doi: 10.1016/j.cell.2021.04.020. Epub 2021 May 14.

25. Intergenic RNA mainly derives from nascent transcripts of known genes.
Agostini F et al. Genome Biol. 2021 May 5;22(1):136. doi: 10.1186/s13059-021-02350-x.

26. Targeting epigenetic and post-transcriptional gene regulation by PSF impairs hormone therapy-refractory cancer growth.
Takayama KI et al. Cancer Res. 2021 May 11:canres.3819.2020. doi: 10.1158/0008-5472.CAN-20-3819. Online ahead of print.

27. Regulation of murine B lymphopoiesis by stromal cells.
Kwang D et al. Immunol Rev. 2021 May 17. doi: 10.1111/imr.12973. Online ahead of print.

28. Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea.
Savary R et al. Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2023298118. doi: 10.1073/pnas.2023298118.

29. Single-cell sequencing reveals suppressive transcriptional programs regulated by MIS/AMH in neonatal ovaries.
Meinsohn MC et al. Proc Natl Acad Sci U S A. 2021 May 18;118(20):e2100920118. doi: 10.1073/pnas.2100920118.

30. PEPPRO: quality control and processing of nascent RNA profiling data.
Smith JP et al. Genome Biol. 2021 May 15;22(1):155. doi: 10.1186/s13059-021-02349-4.

31. Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington's disease.
Paraskevopoulou F et al. Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2020293118. doi: 10.1073/pnas.2020293118.

32. DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing.
Bhattacharya A et al. Nucleic Acids Res. 2021 May 7;49(8):e48. doi: 10.1093/nar/gkab031.

33. Interpretation of T cell states from single-cell transcriptomics data using reference atlases.
Andreatta M et al. Nat Commun. 2021 May 20;12(1):2965. doi: 10.1038/s41467-021-23324-4.

34. Cell-level metadata are indispensable for documenting single-cell sequencing datasets.
Puntambekar S et al. PLoS Biol. 2021 May 4;19(5):e3001077. doi: 10.1371/journal.pbio.3001077. eCollection 2021 May.

35. CAG RNAs induce DNA damage and apoptosis by silencing NUDT16 expression in polyglutamine degeneration.
Peng S et al. Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2022940118. doi: 10.1073/pnas.2022940118.

36. Bile acid-activated macrophages promote biliary epithelial cell proliferation through integrin αvβ6 upregulation following liver injury.
Guillot A et al. J Clin Invest. 2021 May 3;131(9):e132305. doi: 10.1172/JCI132305.

37. PHAROH lncRNA regulates Myc translation in hepatocellular carcinoma via sequestering TIAR.
Yu AT et al. Elife. 2021 May 18;10:e68263. doi: 10.7554/eLife.68263.

38. A joint deep learning model enables simultaneous batch effect correction, denoising and clustering in single-cell transcriptomics.
Lakkis J et al. Genome Res. 2021 May 25:gr.271874.120. doi: 10.1101/gr.271874.120. Online ahead of print.

39. A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity.
Levy S et al. Cell. 2021 May 27;184(11):2973-2987.e18. doi: 10.1016/j.cell.2021.04.005. Epub 2021 May 3.

40. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals.
Li Y et al. Nat Commun. 2021 May 7;12(1):2563. doi: 10.1038/s41467-021-22920-8.

41. SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes.
Elosua-Bayes M et al. Nucleic Acids Res. 2021 May 21;49(9):e50. doi: 10.1093/nar/gkab043.

42. Small molecule Y-320 stimulates ribosome biogenesis, protein synthesis, and aminoglycoside-induced premature termination codon readthrough.
Hosseini-Farahabadi S et al. PLoS Biol. 2021 May 3;19(5):e3001221. doi: 10.1371/journal.pbio.3001221. eCollection 2021 May.

43. scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing.
Wilson GW et al. Genome Biol. 2021 May 7;22(1):144. doi: 10.1186/s13059-021-02364-5.

44. Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways.
Kovalak C et al. Genome Biol. 2021 May 3;22(1):132. doi: 10.1186/s13059-021-02309-y.

45. Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer.
Nath A et al. Nat Commun. 2021 May 24;12(1):3039. doi: 10.1038/s41467-021-23171-3.

46. POINT technology illuminates the processing of polymerase-associated intact nascent transcripts.
Sousa-Luís R et al. Mol Cell. 2021 May 6;81(9):1935-1950.e6. doi: 10.1016/j.molcel.2021.02.034. Epub 2021 Mar 17.

47. DDX3 depletion represses translation of mRNAs with complex 5' UTRs.
Calviello L et al. Nucleic Acids Res. 2021 May 21;49(9):5336-5350. doi: 10.1093/nar/gkab287.

48. AGO2 promotes tumor progression in KRAS-driven mouse models of non-small cell lung cancer.
Tien JC et al. Proc Natl Acad Sci U S A. 2021 May 18;118(20):e2026104118. doi: 10.1073/pnas.2026104118.

49. Single-keratinocyte transcriptomic analyses identify different clonal types and proliferative potential mediated by FOXM1 in human epidermal stem cells.
Enzo E et al. Nat Commun. 2021 May 4;12(1):2505. doi: 10.1038/s41467-021-22779-9.

50. Author Correction: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.
Bonetti A et al. Nat Commun. 2021 May 19;12(1):3128. doi: 10.1038/s41467-021-23542-w.

51. Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing.
Deshmukh AP et al. Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2102050118. doi: 10.1073/pnas.2102050118.

52. Decoupling epithelial-mesenchymal transitions from stromal profiles by integrative expression analysis.
Tyler M et al. Nat Commun. 2021 May 10;12(1):2592. doi: 10.1038/s41467-021-22800-1.

53. CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones.
Bavli D et al. Dev Cell. 2021 May 11:S1534-5807(21)00395-6. doi: 10.1016/j.devcel.2021.04.026. Online ahead of print.

54. Independent component analysis based gene co-expression network inference (ICAnet) to decipher functional modules for better single-cell clustering and batch integration.
Wang W et al. Nucleic Acids Res. 2021 May 21;49(9):e54. doi: 10.1093/nar/gkab089.

55. Neurotensin is an anti-thermogenic peptide produced by lymphatic endothelial cells.
Li J et al. Cell Metab. 2021 May 19:S1550-4131(21)00217-5. doi: 10.1016/j.cmet.2021.04.019. Online ahead of print.

56. Impairment of human terminal erythroid differentiation by histone deacetylase 5 deficiency.
Wang Y et al. Blood. 2021 May 25:blood.2020007401. doi: 10.1182/blood.2020007401. Online ahead of print.

57. Early stem cell aging in the mature brain.
Ibrayeva A et al. Cell Stem Cell. 2021 May 6;28(5):955-966.e7. doi: 10.1016/j.stem.2021.03.018. Epub 2021 Apr 12.

58. Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo.
Little DR et al. Nat Commun. 2021 May 4;12(1):2509. doi: 10.1038/s41467-021-22817-6.

59. 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 May 21:gkab381. doi: 10.1093/nar/gkab381. Online ahead of print.

60. Fibroblast dedifferentiation as a determinant of successful regeneration.
Lin TY et al. Dev Cell. 2021 May 17;56(10):1541-1551.e6. doi: 10.1016/j.devcel.2021.04.016.

61. treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.
Huang R et al. Genome Biol. 2021 May 17;22(1):157. doi: 10.1186/s13059-021-02368-1.

62. Retinoic acid signaling is critical during the totipotency window in early mammalian development.
Iturbide A et al. Nat Struct Mol Biol. 2021 May 27. doi: 10.1038/s41594-021-00590-w. Online ahead of print.

63. 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 May 17:gkab343. doi: 10.1093/nar/gkab343. Online ahead of print.

64. Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures.
García-Pérez R et al. Nat Commun. 2021 May 25;12(1):3116. doi: 10.1038/s41467-021-23397-1.

65. B2 SINE Copies Serve as a Transposable Boundary of DNA Methylation and Histone Modifications in the Mouse.
Ichiyanagi T et al. Mol Biol Evol. 2021 May 19;38(6):2380-2395. doi: 10.1093/molbev/msab033.

66. LSD1 and aberrant DNA methylation mediate persistence of enteroendocrine progenitors that support BRAF mutant colorectal cancer.
Miller SA et al. Cancer Res. 2021 May 25:canres.3562.2020. doi: 10.1158/0008-5472.CAN-20-3562. Online ahead of print.

67. Co-development of central and peripheral neurons with trunk mesendoderm in human elongating multi-lineage organized gastruloids.
Olmsted ZT et al. Nat Commun. 2021 May 21;12(1):3020. doi: 10.1038/s41467-021-23294-7.

68. Tendon and motor phenotypes in the Crtap(-/-) mouse model of recessive Osteogenesis Imperfecta.
Grol MW et al. Elife. 2021 May 26;10:e63488. doi: 10.7554/eLife.63488. Online ahead of print.

69. A transcriptionally distinct subpopulation of healthy acinar cells exhibit features of pancreatic progenitors and pancreatic ductal adenocarcinoma.
Gopalan V et al. Cancer Res. 2021 May 28:canres.0427.2021. doi: 10.1158/0008-5472.CAN-21-0427. Online ahead of print.

70. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics.
Xu L et al. Nat Commun. 2021 May 28;12(1):3209. doi: 10.1038/s41467-021-23553-7.

71. Locus-specific characterization of human endogenous retrovirus expression in prostate, breast, and colon cancers.
Steiner MC et al. Cancer Res. 2021 May 3:canres.3975.2020. doi: 10.1158/0008-5472.CAN-20-3975. Online ahead of print.

72. Generative modeling of single-cell time series with PRESCIENT enables prediction of cell trajectories with interventions.
Yeo GHT et al. Nat Commun. 2021 May 28;12(1):3222. doi: 10.1038/s41467-021-23518-w.

73. Characterizing the tumor microenvironment of metastatic ovarian cancer by single-cell transcriptomics.
Olalekan S et al. Cell Rep. 2021 May 25;35(8):109165. doi: 10.1016/j.celrep.2021.109165.

74. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics.
Popella L et al. Nucleic Acids Res. 2021 May 7;49(8):4705-4724. doi: 10.1093/nar/gkab242.

75. Comparative analyses of gibbon centromeres reveal dynamic genus specific shifts in repeat composition.
Hartley GA et al. Mol Biol Evol. 2021 May 13:msab148. doi: 10.1093/molbev/msab148. Online ahead of print.

76. Promoter G-quadruplex folding precedes transcription and is controlled by chromatin.
Shen J et al. Genome Biol. 2021 May 7;22(1):143. doi: 10.1186/s13059-021-02346-7.

77. Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL.
Alfeghaly C et al. Nucleic Acids Res. 2021 May 21;49(9):4954-4970. doi: 10.1093/nar/gkab245.

78. Loss of function mutations in GEMIN5 cause a neurodevelopmental disorder.
Kour S et al. Nat Commun. 2021 May 7;12(1):2558. doi: 10.1038/s41467-021-22627-w.

79. Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data.
Kiniry SJ et al. Nucleic Acids Res. 2021 May 5:gkab323. doi: 10.1093/nar/gkab323. Online ahead of print.

80. Suppressing the DSCAM/PAK1 pathway reverses neurogenesis deficits in Down Syndrome patient iPSC-derived cerebral organoids.
Tang XY et al. J Clin Invest. 2021 May 4:135763. doi: 10.1172/JCI135763. Online ahead of print.

81. Cross-Species analysis defines the conservation of anatomically-segregated VMH neuron populations.
Affinati AH et al. Elife. 2021 May 21;10:e69065. doi: 10.7554/eLife.69065. Online ahead of print.

82. A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks.
Yuan C et al. Genome Biol. 2021 May 17;22(1):156. doi: 10.1186/s13059-021-02376-1.

83. HDAC3 controls male fertility through enzyme-independent transcriptional regulation at the meiotic exit of spermatogenesis.
Yin H et al. Nucleic Acids Res. 2021 May 21;49(9):5106-5123. doi: 10.1093/nar/gkab313.

84. Phytochrome interacting factor proteins regulate cytokinesis in Arabidopsis.
Zhang Y et al. Cell Rep. 2021 May 11;35(6):109095. doi: 10.1016/j.celrep.2021.109095.

85. Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification.
Meistermann D et al. Cell Stem Cell. 2021 May 10:S1934-5909(21)00185-5. doi: 10.1016/j.stem.2021.04.027. Online ahead of print.

86. Transcriptome-wide association analysis identifies DACH1 as a kidney disease risk gene that contributes to fibrosis.
Doke T et al. J Clin Invest. 2021 May 17;131(10):e141801. doi: 10.1172/JCI141801.

87. The circadian-controlled PIF8-BBX28 module regulates petal senescence in rose flowers by governing mitochondrial ROS homeostasis at night.
Zhang Y et al. Plant Cell. 2021 May 27:koab152. doi: 10.1093/plcell/koab152. Online ahead of print.

88. Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes.
Aylward A et al. PLoS Genet. 2021 May 13;17(5):e1009531. doi: 10.1371/journal.pgen.1009531. Online ahead of print.

89. A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages.
Huffaker TB et al. Nat Commun. 2021 May 11;12(1):2620. doi: 10.1038/s41467-021-22923-5.

90. Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa.
Mathyer ME et al. Nat Commun. 2021 May 7;12(1):2557. doi: 10.1038/s41467-021-22821-w.

91. Decreased GLUT2 and glucose uptake contribute to insulin secretion defects in MODY3/HNF1A hiPSC-derived mutant β cells.
Low BSJ et al. Nat Commun. 2021 May 25;12(1):3133. doi: 10.1038/s41467-021-22843-4.

92. Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology.
Nair RR et al. Elife. 2021 May 4;10:e66050. doi: 10.7554/eLife.66050.

93. MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networks.
Yu H et al. Genome Biol. 2021 May 20;22(1):158. doi: 10.1186/s13059-021-02373-4.

94. 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 May 20:S1534-5807(21)00400-7. doi: 10.1016/j.devcel.2021.04.031. Online ahead of print.

95. Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS.
Sahadevan S et al. Nat Commun. 2021 May 21;12(1):3027. doi: 10.1038/s41467-021-23188-8.