Monthly Letter

1. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis.
Ranzoni AM et al. Cell Stem Cell. 2021 Mar 4;28(3):472-487.e7. doi: 10.1016/j.stem.2020.11.015. Epub 2020 Dec 21.

2. Dissecting transcriptional heterogeneity in primary gastric adenocarcinoma by single cell RNA sequencing.
Zhang M et al. Gut. 2021 Mar;70(3):464-475. doi: 10.1136/gutjnl-2019-320368. Epub 2020 Jun 12.

3. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Stickels RR et al. Nat Biotechnol. 2021 Mar;39(3):313-319. doi: 10.1038/s41587-020-0739-1. Epub 2020 Dec 7.

4. RNA timestamps identify the age of single molecules in RNA sequencing.
Rodriques SG et al. Nat Biotechnol. 2021 Mar;39(3):320-325. doi: 10.1038/s41587-020-0704-z. Epub 2020 Oct 19.

5. Autosomal Clonal Monoallelic Expression: Natural or Artifactual?.
Rv P et al. Trends Genet. 2021 Mar;37(3):206-211. doi: 10.1016/j.tig.2020.10.011. Epub 2020 Nov 21.

6. Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis.
Reimer KA et al. Mol Cell. 2021 Mar 4;81(5):998-1012.e7. doi: 10.1016/j.molcel.2020.12.018. Epub 2021 Jan 12.

7. Mitophagy-mediated adipose inflammation contributes to type 2 diabetes with hepatic insulin resistance.
He F et al. J Exp Med. 2021 Mar 1;218(3):e20201416. doi: 10.1084/jem.20201416.

8. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation.
Jerber J et al. Nat Genet. 2021 Mar;53(3):304-312. doi: 10.1038/s41588-021-00801-6. Epub 2021 Mar 4.

9. Nucleotide resolution profiling of m3C RNA modification by HAC-seq.
Cui J et al. Nucleic Acids Res. 2021 Mar 18;49(5):e27. doi: 10.1093/nar/gkaa1186.

10. Integrating imaging and RNA-seq improves outcome prediction in cervical cancer.
Zhang J et al. J Clin Invest. 2021 Mar 1;131(5):e139232. doi: 10.1172/JCI139232.

11. Genome-wide DNA methylation profiling of esophageal squamous cell carcinoma from global high-incidence regions identifies crucial genes and potential cancer markers.
Talukdar FR et al. Cancer Res. 2021 Mar 19:canres.3445.2020. doi: 10.1158/0008-5472.CAN-20-3445. Online ahead of print.

12. Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching.
Chen M et al. Genome Res. 2021 Mar 19. doi: 10.1101/gr.261115.120. Online ahead of print.

13. scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses.
Wang J et al. Nat Commun. 2021 Mar 25;12(1):1882. doi: 10.1038/s41467-021-22197-x.

14. SPAAC-NAD-seq, a sensitive and accurate method to profile NAD(+)-capped transcripts.
Hu H et al. Proc Natl Acad Sci U S A. 2021 Mar 30;118(13):e2025595118. doi: 10.1073/pnas.2025595118.

15. A high-resolution protein architecture of the budding yeast genome.
Rossi MJ et al. Nature. 2021 Mar 10. doi: 10.1038/s41586-021-03314-8. Online ahead of print.

16. Progenitor cell diversity in the developing mouse neocortex.
Ruan X et al. Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):e2018866118. doi: 10.1073/pnas.2018866118.

17. Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes.
Park E et al. Genome Biol. 2021 Mar 9;22(1):77. doi: 10.1186/s13059-021-02287-1.

18. Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data.
Fan J et al. PLoS Genet. 2021 Mar 4;17(3):e1009080. doi: 10.1371/journal.pgen.1009080. eCollection 2021 Mar.

19. Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells.
Neavin D et al. Genome Biol. 2021 Mar 5;22(1):76. doi: 10.1186/s13059-021-02293-3.

20. Mutant p53 regulates Survivin to foster lung metastasis.
Tang Q et al. Genes Dev. 2021 Mar 18. doi: 10.1101/gad.340505.120. Online ahead of print.

21. RNA-seq of human T cells after hematopoietic stem cell transplantation identifies Linc00402 as a regulator of T cell alloimmunity.
Peltier D et al. Sci Transl Med. 2021 Mar 17;13(585):eaaz0316. doi: 10.1126/scitranslmed.aaz0316.

22. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes.
Ravindra NG et al. PLoS Biol. 2021 Mar 17;19(3):e3001143. doi: 10.1371/journal.pbio.3001143. eCollection 2021 Mar.

23. Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus.
Panwar B et al. Genome Res. 2021 Mar 5. doi: 10.1101/gr.265249.120. Online ahead of print.

24. Alzheimer's disease alters oligodendrocytic glycolytic and ketolytic gene expression.
Saito ER et al. Alzheimers Dement. 2021 Mar 2. doi: 10.1002/alz.12310. Online ahead of print.

25. A noncanonical AR addiction drives enzalutamide resistance in prostate cancer.
He Y et al. Nat Commun. 2021 Mar 9;12(1):1521. doi: 10.1038/s41467-021-21860-7.

26. DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires.
Sidhom JW et al. Nat Commun. 2021 Mar 11;12(1):1605. doi: 10.1038/s41467-021-21879-w.

27. Differences in Postmating Transcriptional Responses between Conspecific and Heterospecific Matings in Drosophila.
Ahmed-Braimah YH et al. Mol Biol Evol. 2021 Mar 9;38(3):986-999. doi: 10.1093/molbev/msaa264.

28. Targeting a Braf/Mapk pathway rescues podocyte lipid peroxidation in CoQ-deficiency kidney disease.
Sidhom EH et al. J Clin Invest. 2021 Mar 1;131(5):e141380. doi: 10.1172/JCI141380.

29. Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor.
Sim CB et al. Circulation. 2021 Mar 8. doi: 10.1161/CIRCULATIONAHA.120.051921. Online ahead of print.

30. Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation.
Robinson DCL et al. Dev Cell. 2021 Mar 10:S1534-5807(21)00165-9. doi: 10.1016/j.devcel.2021.02.025. Online ahead of print.

31. Joint probabilistic modeling of single-cell multi-omic data with totalVI.
Gayoso A et al. Nat Methods. 2021 Mar;18(3):272-282. doi: 10.1038/s41592-020-01050-x. Epub 2021 Feb 15.

32. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.
Butler D et al. Nat Commun. 2021 Mar 12;12(1):1660. doi: 10.1038/s41467-021-21361-7.

33. Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity.
Sorek M et al. Genome Biol. 2021 Mar 4;22(1):73. doi: 10.1186/s13059-021-02301-6.

34. Integration and transfer learning of single-cell transcriptomes via cFIT.
Peng M et al. Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):e2024383118. doi: 10.1073/pnas.2024383118.

35. A single-cell analysis of the Arabidopsis vegetative shoot apex.
Zhang TQ et al. Dev Cell. 2021 Mar 9:S1534-5807(21)00161-1. doi: 10.1016/j.devcel.2021.02.021. Online ahead of print.

36. Blood Transcriptomic Predicts Progression of Pulmonary Fibrosis and Associates Natural Killer Cells.
Huang Y et al. Am J Respir Crit Care Med. 2021 Mar 9. doi: 10.1164/rccm.202008-3093OC. Online ahead of print.

37. Deciphering the state of immune silence in fatal COVID-19 patients.
Bost P et al. Nat Commun. 2021 Mar 5;12(1):1428. doi: 10.1038/s41467-021-21702-6.

38. Proteogenomics of glioblastoma associates molecular patterns with survival.
Yanovich-Arad G et al. Cell Rep. 2021 Mar 2;34(9):108787. doi: 10.1016/j.celrep.2021.108787.

39. Model-based deep embedding for constrained clustering analysis of single cell RNA-seq data.
Tian T et al. Nat Commun. 2021 Mar 25;12(1):1873. doi: 10.1038/s41467-021-22008-3.

40. Robust integration of multiple single-cell RNA sequencing datasets using a single reference space.
Liu Y et al. Nat Biotechnol. 2021 Mar 25. doi: 10.1038/s41587-021-00859-x. Online ahead of print.

41. A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2.
Aynaud MM et al. Nat Commun. 2021 Mar 3;12(1):1405. doi: 10.1038/s41467-021-21653-y.

42. PPARγ marks splenic precursors of multiple nonlymphoid-tissue Treg compartments.
Li C et al. Proc Natl Acad Sci U S A. 2021 Mar 30;118(13):e2025197118. doi: 10.1073/pnas.2025197118.

43. Single Cell RNA-Sequencing Uncovers Paracrine Functions of the Epicardial-Derived Cells in Arrhythmogenic Cardiomyopathy.
Yuan P et al. Circulation. 2021 Mar 17. doi: 10.1161/CIRCULATIONAHA.120.052928. Online ahead of print.

44. Ultrafast functional profiling of RNA-seq data for nonmodel organisms.
Liu P et al. Genome Res. 2021 Mar 17. doi: 10.1101/gr.269894.120. Online ahead of print.

45. Tracing cell-type evolution by cross-species comparison of cell atlases.
Wang J et al. Cell Rep. 2021 Mar 2;34(9):108803. doi: 10.1016/j.celrep.2021.108803.

46. Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq.
Thalalla Gamage S et al. Nat Protoc. 2021 Mar 26. doi: 10.1038/s41596-021-00501-9. Online ahead of print.

47. ELF3 activated by a superenhancer and an autoregulatory feedback loop is required for high-level HLA-C expression on extravillous trophoblasts.
Li Q et al. Proc Natl Acad Sci U S A. 2021 Mar 2;118(9):e2025512118. doi: 10.1073/pnas.2025512118.

48. Cell-type identity of the avian cochlea.
Janesick A et al. Cell Rep. 2021 Mar 23;34(12):108900. doi: 10.1016/j.celrep.2021.108900.

49. Hematopoietic Stem Cell Heterogeneity Is Linked to the Initiation and Therapeutic Response of Myeloproliferative Neoplasms.
Tong J et al. Cell Stem Cell. 2021 Mar 4;28(3):502-513.e6. doi: 10.1016/j.stem.2021.01.018. Epub 2021 Feb 22.

50. Ex utero mouse embryogenesis from pre-gastrulation to late organogenesis.
Aguilera-Castrejon A et al. Nature. 2021 Mar 17. doi: 10.1038/s41586-021-03416-3. Online ahead of print.

51. The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages.
Huang Z et al. Mol Cell. 2021 Mar 4;81(5):953-968.e9. doi: 10.1016/j.molcel.2020.12.040. Epub 2021 Jan 26.

52. POINT technology illuminates the processing of polymerase-associated intact nascent transcripts.
Sousa-Luís R et al. Mol Cell. 2021 Mar 9:S1097-2765(21)00144-1. doi: 10.1016/j.molcel.2021.02.034. Online ahead of print.

53. Evaluation of Ranzoni et al.: Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis.
McKinney-Freeman S et al. Cell Stem Cell. 2021 Mar 4;28(3):357-358. doi: 10.1016/j.stem.2021.02.020.

54. Structure-function analysis of fission yeast cleavage and polyadenylation factor (CPF) subunit Ppn1 and its interactions with Dis2 and Swd22.
Benjamin B et al. PLoS Genet. 2021 Mar 12;17(3):e1009452. doi: 10.1371/journal.pgen.1009452. eCollection 2021 Mar.

55. Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas.
Wu F et al. Nat Commun. 2021 Mar 5;12(1):1465. doi: 10.1038/s41467-021-21704-4.

56. Smoothened-activating lipids drive resistance to CDK4/6 inhibition in Hedgehog-associated medulloblastoma cells and preclinical models.
Daggubati V et al. J Clin Invest. 2021 Mar 15;131(6):e141171. doi: 10.1172/JCI141171.

57. Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage.
Goszczynski DE et al. Genome Res. 2021 Mar 15. doi: 10.1101/gr.267336.120. Online ahead of print.

58. Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons.
Li J et al. PLoS Genet. 2021 Mar 24;17(3):e1009355. doi: 10.1371/journal.pgen.1009355. eCollection 2021 Mar.

59. An early cell shape transition drives evolutionary expansion of the human forebrain.
Benito-Kwiecinski S et al. Cell. 2021 Mar 19:S0092-8674(21)00239-7. doi: 10.1016/j.cell.2021.02.050. Online ahead of print.

60. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis.
Granja JM et al. Nat Genet. 2021 Mar;53(3):403-411. doi: 10.1038/s41588-021-00790-6. Epub 2021 Feb 25.

61. Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria.
Adhikari S et al. PLoS Genet. 2021 Mar 11;17(3):e1009433. doi: 10.1371/journal.pgen.1009433. eCollection 2021 Mar.

62. Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion.
Frangieh CJ et al. Nat Genet. 2021 Mar;53(3):332-341. doi: 10.1038/s41588-021-00779-1. Epub 2021 Mar 1.

63. Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells.
Tauc HM et al. Elife. 2021 Mar 16;10:e62250. doi: 10.7554/eLife.62250.

64. Single cell transcriptomic analysis of murine lung development on hyperoxia-induced damage.
Hurskainen M et al. Nat Commun. 2021 Mar 10;12(1):1565. doi: 10.1038/s41467-021-21865-2.

65. Microglial identity and inflammatory responses are controlled by the combined effects of neurons and astrocytes.
Baxter PS et al. Cell Rep. 2021 Mar 23;34(12):108882. doi: 10.1016/j.celrep.2021.108882.

66. Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes.
Katz N et al. Nat Commun. 2021 Mar 11;12(1):1576. doi: 10.1038/s41467-021-21578-6.

67. Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene.
Muyle A et al. Mol Biol Evol. 2021 Mar 9;38(3):805-818. doi: 10.1093/molbev/msaa229.

68. Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization.
D'Orazio FM et al. Dev Cell. 2021 Mar 8;56(5):641-656.e5. doi: 10.1016/j.devcel.2021.02.007. Epub 2021 Mar 1.

69. The aryl hydrocarbon receptor facilitates the human cytomegalovirus-mediated G1/S block to cell cycle progression.
Naseri-Nosar P et al. Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):e2026336118. doi: 10.1073/pnas.2026336118.

70. Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis.
Mathewson ND et al. Cell. 2021 Mar 4;184(5):1281-1298.e26. doi: 10.1016/j.cell.2021.01.022. Epub 2021 Feb 15.

71. Functional cooperation between co-amplified genes promotes aggressive phenotypes of HER2-positive breast cancer.
Yang Y et al. Cell Rep. 2021 Mar 9;34(10):108822. doi: 10.1016/j.celrep.2021.108822.

72. Maize Decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin.
Long J et al. Plant Cell. 2021 Mar 29:koab098. doi: 10.1093/plcell/koab098. Online ahead of print.

73. Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.
Gao P et al. Genome Biol. 2021 Mar 16;22(1):83. doi: 10.1186/s13059-021-02304-3.

74. Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing.
Cohen YC et al. Nat Med. 2021 Mar;27(3):491-503. doi: 10.1038/s41591-021-01232-w. Epub 2021 Feb 22.

75. Mutant Huntingtin stalls ribosomes and represses protein synthesis in a cellular model of Huntington disease.
Eshraghi M et al. Nat Commun. 2021 Mar 5;12(1):1461. doi: 10.1038/s41467-021-21637-y.

76. Sequential perturbations to mouse corticogenesis following in utero maternal immune activation.
Canales CP et al. Elife. 2021 Mar 5;10:e60100. doi: 10.7554/eLife.60100.

77. Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones.
Kirstein N et al. Elife. 2021 Mar 8;10:e62161. doi: 10.7554/eLife.62161.

78. Venetoclax sensitivity in multiple myeloma is associated with B cell gene expression.
Gupta VA et al. Blood. 2021 Mar 1:blood.2020007899. doi: 10.1182/blood.2020007899. Online ahead of print.

79. Transcriptome and chromatin landscape of iNKT cells are shaped by subset differentiation and antigen exposure.
Murray MP et al. Nat Commun. 2021 Mar 4;12(1):1446. doi: 10.1038/s41467-021-21574-w.

80. Transcriptomic characterization of dying hair cells in the avian cochlea.
Benkafadar N et al. Cell Rep. 2021 Mar 23;34(12):108902. doi: 10.1016/j.celrep.2021.108902.

81. Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.
Lusk R et al. Nat Commun. 2021 Mar 12;12(1):1652. doi: 10.1038/s41467-021-21894-x.

82. Mouse multipotent progenitor 5 cells are located at the interphase between hematopoietic stem and progenitor cells.
Sommerkamp P et al. Blood. 2021 Mar 22:blood.2020007876. doi: 10.1182/blood.2020007876. Online ahead of print.

83. Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia.
Lee JD et al. Nat Methods. 2021 Mar;18(3):293-302. doi: 10.1038/s41592-021-01077-8. Epub 2021 Mar 1.

84. Experimental competition induces immediate and lasting effects on the neurogenome in free-living female birds.
Bentz AB et al. Proc Natl Acad Sci U S A. 2021 Mar 30;118(13):e2016154118. doi: 10.1073/pnas.2016154118.

85. The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic.
Tang Y et al. PLoS Genet. 2021 Mar 19;17(3):e1009461. doi: 10.1371/journal.pgen.1009461. Online ahead of print.

86. Mapping the origin and fate of myeloid cells in distinct compartments of the eye by single-cell profiling.
Wieghofer P et al. EMBO J. 2021 Mar 15;40(6):e105123. doi: 10.15252/embj.2020105123. Epub 2021 Feb 8.

87. Increased longevity due to sexual activity in mole-rats is associated with transcriptional changes in HPA stress axis.
Sahm A et al. Elife. 2021 Mar 16;10:e57843. doi: 10.7554/eLife.57843. Online ahead of print.

88. 2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.
Parker MT et al. Genome Biol. 2021 Mar 1;22(1):72. doi: 10.1186/s13059-021-02296-0.