Monthly Letter

1. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation.
Bonora G et al. Genome Biol. 2021 Sep 27;22(1):279. doi: 10.1186/s13059-021-02432-w.

2. Chemical capping improves template switching and enhances sequencing of small RNAs.
Wulf MG et al. Nucleic Acids Res. 2021 Sep 28:gkab861. doi: 10.1093/nar/gkab861. Online ahead of print.

3. Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer.
Tang K et al. Nucleic Acids Res. 2021 Sep 27;49(17):e99. doi: 10.1093/nar/gkab554.

4. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data.
Lause J et al. Genome Biol. 2021 Sep 6;22(1):258. doi: 10.1186/s13059-021-02451-7.

5. Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data.
Zhao Z et al. Genome Res. 2021 Sep 2:gr.271627.120. doi: 10.1101/gr.271627.120. Online ahead of print.

6. Interplay between the EMT transcription factors ZEB1 and ZEB2 regulates hematopoietic stem and progenitor cell differentiation and hematopoietic lineage fidelity.
Wang J et al. PLoS Biol. 2021 Sep 22;19(9):e3001394. doi: 10.1371/journal.pbio.3001394. Online ahead of print.

7. scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network.
Shao X et al. Nucleic Acids Res. 2021 Sep 9:gkab775. doi: 10.1093/nar/gkab775. Online ahead of print.

8. RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.
Choe D et al. PLoS Genet. 2021 Sep 27;17(9):e1009821. doi: 10.1371/journal.pgen.1009821. Online ahead of print.

9. scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution.
Zhu S et al. Nucleic Acids Res. 2021 Sep 11:gkab795. doi: 10.1093/nar/gkab795. Online ahead of print.

10. DIANA-miTED: a microRNA tissue expression database.
Kavakiotis I et al. Nucleic Acids Res. 2021 Sep 1:gkab733. doi: 10.1093/nar/gkab733. Online ahead of print.

11. Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction.
Ma W et al. Genome Biol. 2021 Sep 9;22(1):264. doi: 10.1186/s13059-021-02480-2.

12. The oncomicropeptide APPLE promotes hematopoietic malignancy by enhancing translation initiation.
Sun L et al. Mol Cell. 2021 Sep 15:S1097-2765(21)00713-9. doi: 10.1016/j.molcel.2021.08.033. Online ahead of print.

13. EpiScanpy: integrated single-cell epigenomic analysis.
Danese A et al. Nat Commun. 2021 Sep 1;12(1):5228. doi: 10.1038/s41467-021-25131-3.

14. High-throughput RNA sequencing of paraformaldehyde-fixed single cells.
Phan HV et al. Nat Commun. 2021 Sep 24;12(1):5636. doi: 10.1038/s41467-021-25871-2.

15. Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans.
Bakken TE et al. Elife. 2021 Sep 2;10:e64875. doi: 10.7554/eLife.64875.

16. NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Moriel N et al. Nat Protoc. 2021 Sep;16(9):4177-4200. doi: 10.1038/s41596-021-00573-7. Epub 2021 Aug 4.

17. Visualization of individual cell division history in complex tissues using iCOUNT.
Denoth-Lippuner A et al. Cell Stem Cell. 2021 Sep 8:S1934-5909(21)00349-0. doi: 10.1016/j.stem.2021.08.012. Online ahead of print.

18. A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery.
Crouchet E et al. Nat Commun. 2021 Sep 17;12(1):5525. doi: 10.1038/s41467-021-25468-9.

19. Tumor-initiating stem cell shapes its microenvironment into an immunosuppressive barrier and pro-tumorigenic niche.
He X et al. Cell Rep. 2021 Sep 7;36(10):109674. doi: 10.1016/j.celrep.2021.109674.

20. Proteogenomic characterization of pancreatic ductal adenocarcinoma.
Cao L et al. Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023.

21. Identifying transcriptional programs underlying cancer drug response with TraCe-seq.
Chang MT et al. Nat Biotechnol. 2021 Sep 16. doi: 10.1038/s41587-021-01005-3. Online ahead of print.

22. Seq Your Destiny: Neural Crest Fate Determination in the Genomic Era.
Gandhi S et al. Annu Rev Genet. 2021 Sep 21. doi: 10.1146/annurev-genet-071719-020954. Online ahead of print.

23. Cell type hierarchy reconstruction via reconciliation of multi-resolution cluster tree.
Peng M et al. Nucleic Acids Res. 2021 Sep 20;49(16):e91. doi: 10.1093/nar/gkab481.

24. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis.
Lohoff T et al. Nat Biotechnol. 2021 Sep 6. doi: 10.1038/s41587-021-01006-2. Online ahead of print.

25. CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication.
Zhang Y et al. Nucleic Acids Res. 2021 Sep 7;49(15):8520-8534. doi: 10.1093/nar/gkab638.

26. Follicular dendritic cells restrict interleukin-4 availability in germinal centers and foster memory B cell generation.
Duan L et al. Immunity. 2021 Sep 18:S1074-7613(21)00362-9. doi: 10.1016/j.immuni.2021.08.028. Online ahead of print.

27. Bcl6 controls meningeal Th17-B cell interaction in murine neuroinflammation.
Hartlehnert M et al. Proc Natl Acad Sci U S A. 2021 Sep 7;118(36):e2023174118. doi: 10.1073/pnas.2023174118.

28. Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma.
DeSisto J et al. Nat Commun. 2021 Sep 20;12(1):5531. doi: 10.1038/s41467-021-25709-x.

29. TCF7L2 lncRNA: a link between bipolar disorder and body mass index through glucocorticoid signaling.
Liu D et al. Mol Psychiatry. 2021 Sep 17. doi: 10.1038/s41380-021-01274-z. Online ahead of print.

30. Single cell DNA sequencing reveals punctuated and gradual clonal evolution in hepatocellular carcinoma.
Guo L et al. Gastroenterology. 2021 Sep 2:S0016-5085(21)03471-5. doi: 10.1053/j.gastro.2021.08.052. Online ahead of print.

31. Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species.
Petrenko N et al. Elife. 2021 Sep 13;10:e67964. doi: 10.7554/eLife.67964.

32. SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators.
Ma X et al. Nucleic Acids Res. 2021 Sep 27;49(17):9633-9647. doi: 10.1093/nar/gkab745.

33. Bio-inspired poly-DL-serine materials resist the foreign-body response.
Zhang D et al. Nat Commun. 2021 Sep 7;12(1):5327. doi: 10.1038/s41467-021-25581-9.

34. Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering.
Madrid E et al. Proc Natl Acad Sci U S A. 2021 Sep 28;118(39):e2109204118. doi: 10.1073/pnas.2109204118.

35. Genomic instability in the naturally and prematurely aged myocardium.
De Majo F et al. Proc Natl Acad Sci U S A. 2021 Sep 7;118(36):e2022974118. doi: 10.1073/pnas.2022974118.

36. STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.
Zimmer JT et al. Mol Cell. 2021 Sep 7:S1097-2765(21)00686-9. doi: 10.1016/j.molcel.2021.08.019. Online ahead of print.

37. Ductal Ngn3-expressing progenitors contribute to adult β cell neogenesis in the pancreas.
Gribben C et al. Cell Stem Cell. 2021 Sep 1:S1934-5909(21)00340-4. doi: 10.1016/j.stem.2021.08.003. Online ahead of print.

38. TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response.
Zeng Z et al. Nucleic Acids Res. 2021 Sep 17:gkab804. doi: 10.1093/nar/gkab804. Online ahead of print.

39. Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences.
Zhan L et al. PLoS Genet. 2021 Sep 13;17(9):e1009772. doi: 10.1371/journal.pgen.1009772. eCollection 2021 Sep.

40. A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons.
Kim GJ et al. Elife. 2021 Sep 22;10:e69795. doi: 10.7554/eLife.69795.

41. Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data.
Zhao Y et al. Nat Commun. 2021 Sep 6;12(1):5261. doi: 10.1038/s41467-021-25534-2.

42. Molecular diversity of diencephalic astrocytes reveals adult astrogenesis regulated by Smad4.
Ohlig S et al. EMBO J. 2021 Sep 22:e107532. doi: 10.15252/embj.2020107532. Online ahead of print.

43. The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems.
Campa AR et al. Nucleic Acids Res. 2021 Sep 20;49(16):9508-9525. doi: 10.1093/nar/gkab704.

44. The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae).
Mabry ME et al. Mol Biol Evol. 2021 Sep 27;38(10):4419-4434. doi: 10.1093/molbev/msab183.

45. β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture.
Mahmood SR et al. Nat Commun. 2021 Sep 2;12(1):5240. doi: 10.1038/s41467-021-25596-2.

46. RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation.
Cui T et al. Nucleic Acids Res. 2021 Sep 22:gkab825. doi: 10.1093/nar/gkab825. Online ahead of print.

47. Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing.
Briggs EM et al. Nat Commun. 2021 Sep 6;12(1):5268. doi: 10.1038/s41467-021-25607-2.

48. Murine AGM single-cell profiling identifies a continuum of hemogenic endothelium differentiation marked by ACE.
Fadlullah MZ et al. Blood. 2021 Sep 13:blood.2020007885. doi: 10.1182/blood.2020007885. Online ahead of print.

49. A longitudinal sampling study of transcriptomic and epigenetic profiles in patients with thrombocytopenia syndrome.
Wang Y et al. Nat Commun. 2021 Sep 24;12(1):5629. doi: 10.1038/s41467-021-25804-z.

50. Isonicotinylation is a histone mark induced by the anti-tuberculosis first-line drug isoniazid.
Jiang Y et al. Nat Commun. 2021 Sep 20;12(1):5548. doi: 10.1038/s41467-021-25867-y.

51. Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells.
Babarinde IA et al. Nucleic Acids Res. 2021 Sep 20;49(16):9132-9153. doi: 10.1093/nar/gkab710.

52. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.
Bucchini F et al. Nucleic Acids Res. 2021 Sep 27;49(17):e101. doi: 10.1093/nar/gkab565.

53. An immune response characterizes early Alzheimer's disease pathology and subjective cognitive impairment in hydrocephalus biopsies.
Huang W et al. Nat Commun. 2021 Sep 27;12(1):5659. doi: 10.1038/s41467-021-25902-y.

54. Conventional type I dendric cells maintain a reservoir of proliferative tumor-antigen specific TCF-1(+) CD8(+) T cells in tumor-draining lymph nodes.
Schenkel JM et al. Immunity. 2021 Sep 8:S1074-7613(21)00360-5. doi: 10.1016/j.immuni.2021.08.026. Online ahead of print.

55. The induction of preterm labor in rhesus macaques is determined by the  strength of immune response to intrauterine infection.
Cappelletti M et al. PLoS Biol. 2021 Sep 8;19(9):e3001385. doi: 10.1371/journal.pbio.3001385. eCollection 2021 Sep.

56. Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer's disease risk in humans.
Ma Y et al. Alzheimers Dement. 2021 Sep 5. doi: 10.1002/alz.12425. Online ahead of print.

57. HDAC1 is required for GATA-1 transcription activity, global chromatin occupancy and hematopoiesis.
Yan B et al. Nucleic Acids Res. 2021 Sep 27;49(17):9783-9798. doi: 10.1093/nar/gkab737.

58. RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data.
Schmidt F et al. Nucleic Acids Res. 2021 Sep 7;49(15):8505-8519. doi: 10.1093/nar/gkab632.

59. Insulin and IGF-1 receptors regulate complex I-dependent mitochondrial bioenergetics and supercomplexes via FoxOs in muscle.
Bhardwaj G et al. J Clin Invest. 2021 Sep 15;131(18):e146415. doi: 10.1172/JCI146415.

60. Resident memory CD8(+) T cells in regional lymph nodes mediate immunity to metastatic melanoma.
Molodtsov AK et al. Immunity. 2021 Sep 14;54(9):2117-2132.e7. doi: 10.1016/j.immuni.2021.08.019.

61. Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.
Glaros V et al. Immunity. 2021 Sep 14;54(9):2005-2023.e10. doi: 10.1016/j.immuni.2021.08.017.

62. Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer.
Tewari AK et al. Cell Rep. 2021 Sep 7;36(10):109665. doi: 10.1016/j.celrep.2021.109665.

63. Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1.
Shangguan S et al. Elife. 2021 Sep 17;10:e69577. doi: 10.7554/eLife.69577. Online ahead of print.

64. Hypoxia regulates overall mRNA homeostasis by inducing Met(1)-linked linear ubiquitination of AGO2 in cancer cells.
Zhang H et al. Nat Commun. 2021 Sep 13;12(1):5416. doi: 10.1038/s41467-021-25739-5.

65. AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana.
Wang Q et al. Nucleic Acids Res. 2021 Sep 27;49(17):9755-9767. doi: 10.1093/nar/gkab706.