Monthly Letter

1. Transcriptional Reprogramming of Distinct Peripheral Sensory Neuron Subtypes after Axonal Injury.
Renthal W et al. Neuron. 2020 Oct 14;108(1):128-144.e9. doi: 10.1016/j.neuron.2020.07.026. Epub 2020 Aug 17.

2. Conserved Interferon-γ Signaling Drives Clinical Response to Immune Checkpoint Blockade Therapy in Melanoma.
Grasso CS et al. Cancer Cell. 2020 Oct 12;38(4):500-515.e3. doi: 10.1016/j.ccell.2020.08.005. Epub 2020 Sep 10.

3. Immobilization after injury alters extracellular matrix and stem cell fate.
Huber AK et al. J Clin Invest. 2020 Oct 1;130(10):5444-5460. doi: 10.1172/JCI136142.

4. Maternal choline supplementation ameliorates Alzheimer's disease pathology by reducing brain homocysteine levels across multiple generations.
Velazquez R et al. Mol Psychiatry. 2020 Oct;25(10):2620-2629. doi: 10.1038/s41380-018-0322-z. Epub 2019 Jan 8.

5. Targeting tumor-associated macrophages and granulocytic myeloid-derived suppressor cells augments PD-1 blockade in cholangiocarcinoma.
Loeuillard E et al. J Clin Invest. 2020 Oct 1;130(10):5380-5396. doi: 10.1172/JCI137110.

6. Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia.
Prudencio M et al. J Clin Invest. 2020 Oct 19:139741. doi: 10.1172/JCI139741. Online ahead of print.

7. Intrinsic Endocardial Defects Contribute to Hypoplastic Left Heart Syndrome.
Miao Y et al. Cell Stem Cell. 2020 Oct 1;27(4):574-589.e8. doi: 10.1016/j.stem.2020.07.015. Epub 2020 Aug 17.

8. Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling.
Furlan M et al. Genome Res. 2020 Oct;30(10):1492-1507. doi: 10.1101/gr.260984.120. Epub 2020 Sep 25.

9. MiR130b from Schlafen4(+) MDSCs stimulates epithelial proliferation and correlates with preneoplastic changes prior to gastric cancer.
Ding L et al. Gut. 2020 Oct;69(10):1750-1761. doi: 10.1136/gutjnl-2019-318817. Epub 2020 Jan 24.

10. Delineation of a molecularly distinct terminally differentiated memory CD8 T cell population.
Milner JJ et al. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25667-25678. doi: 10.1073/pnas.2008571117. Epub 2020 Sep 25.

11. In Situ Maturation and Tissue Adaptation of Type 2 Innate Lymphoid Cell Progenitors.
Zeis P et al. Immunity. 2020 Oct 13;53(4):775-792.e9. doi: 10.1016/j.immuni.2020.09.002. Epub 2020 Sep 30.

12. Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation.
Hu Y et al. Nat Commun. 2020 Oct 13;11(1):5148. doi: 10.1038/s41467-020-18976-7.

13. A gene expression signature of TREM2(hi) macrophages and γδ T cells predicts immunotherapy response.
Xiong D et al. Nat Commun. 2020 Oct 8;11(1):5084. doi: 10.1038/s41467-020-18546-x.

14. Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.
Kim IS et al. Cell Rep. 2020 Oct 6;33(1):108222. doi: 10.1016/j.celrep.2020.108222.

15. LncSEA: a platform for long non-coding RNA related sets and enrichment analysis.
Chen J et al. Nucleic Acids Res. 2020 Oct 12:gkaa806. doi: 10.1093/nar/gkaa806. Online ahead of print.

16. A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes.
Mancuso CA et al. Nucleic Acids Res. 2020 Oct 19:gkaa881. doi: 10.1093/nar/gkaa881. Online ahead of print.

17. RNA timestamps identify the age of single molecules in RNA sequencing.
Rodriques SG et al. Nat Biotechnol. 2020 Oct 19. doi: 10.1038/s41587-020-0704-z. Online ahead of print.

18. A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells.
Zachariadis V et al. Mol Cell. 2020 Oct 3:S1097-2765(20)30655-9. doi: 10.1016/j.molcel.2020.09.025. Online ahead of print.

19. Differences in post-mating transcriptional responses between conspecific and heterospecific matings in Drosophila.
Ahmed-Braimah YH et al. Mol Biol Evol. 2020 Oct 9:msaa264. doi: 10.1093/molbev/msaa264. Online ahead of print.

20. MARS: discovering novel cell types across heterogeneous single-cell experiments.
Brbić M et al. Nat Methods. 2020 Oct 19. doi: 10.1038/s41592-020-00979-3. Online ahead of print.

21. Thymidylate synthase drives the phenotypes of epithelial-to-mesenchymal transition in non-small cell lung cancer.
Siddiqui MA et al. Br J Cancer. 2020 Oct 7. doi: 10.1038/s41416-020-01095-x. Online ahead of print.

22. Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates.
Kawata K et al. Genome Res. 2020 Oct;30(10):1481-1491. doi: 10.1101/gr.264408.120. Epub 2020 Aug 25.

23. MeDAS: a Metazoan Developmental Alternative Splicing database.
Li Z et al. Nucleic Acids Res. 2020 Oct 21:gkaa886. doi: 10.1093/nar/gkaa886. Online ahead of print.

24. tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species.
Zuo Y et al. Nucleic Acids Res. 2020 Oct 17:gkaa888. doi: 10.1093/nar/gkaa888. Online ahead of print.

25. Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers.
Dos Santos M et al. Nat Commun. 2020 Oct 9;11(1):5102. doi: 10.1038/s41467-020-18789-8.

26. PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs.
Jin J et al. Nucleic Acids Res. 2020 Oct 20:gkaa910. doi: 10.1093/nar/gkaa910. Online ahead of print.

27. Stress-induced RNA-chromatin interactions promote endothelial dysfunction.
Calandrelli R et al. Nat Commun. 2020 Oct 15;11(1):5211. doi: 10.1038/s41467-020-18957-w.

28. Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.
Ma S et al. Cell. 2020 Oct 20:S0092-8674(20)31253-8. doi: 10.1016/j.cell.2020.09.056. Online ahead of print.

29. A mouse tissue atlas of small noncoding RNA.
Isakova A et al. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25634-25645. doi: 10.1073/pnas.2002277117. Epub 2020 Sep 25.

30. Transcriptional profile of platelets and iPSC-derived megakaryocytes from whole genome and RNA sequencing.
Kammers K et al. Blood. 2020 Oct 22:blood.2020006115. doi: 10.1182/blood.2020006115. Online ahead of print.

31. Spatial Density and Distribution of Tumor-Associated Macrophages Predict Survival in Non-Small Cell Lung Carcinoma.
Zheng X et al. Cancer Res. 2020 Oct 15;80(20):4414-4425. doi: 10.1158/0008-5472.CAN-20-0069. Epub 2020 Jul 22.

32. The Transcription Co-Repressors MTG8 and MTG16 Regulate Exit of Intestinal Stem Cells From Their Niche and Differentiation Into Enterocyte vs Secretory Lineages.
Baulies A et al. Gastroenterology. 2020 Oct;159(4):1328-1341.e3. doi: 10.1053/j.gastro.2020.06.012. Epub 2020 Jun 15.

33. Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.
Heavner WE et al. Proc Natl Acad Sci U S A. 2020 Oct 6;117(40):25074-25084. doi: 10.1073/pnas.2008013117. Epub 2020 Sep 18.

34. Dynamics and clinical relevance of maternal mRNA clearance during the oocyte-to-embryo transition in humans.
Sha QQ et al. Nat Commun. 2020 Oct 1;11(1):4917. doi: 10.1038/s41467-020-18680-6.

35. Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation.
Xin J et al. Nat Commun. 2020 Oct 1;11(1):4928. doi: 10.1038/s41467-020-18638-8.

36. Clonal tracing reveals diverse patterns of response to immune checkpoint blockade.
Gu SS et al. Genome Biol. 2020 Oct 15;21(1):263. doi: 10.1186/s13059-020-02166-1.

37. TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.
Wang J et al. Nucleic Acids Res. 2020 Oct 9;48(18):e104. doi: 10.1093/nar/gkaa691.

38. The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor.
Turner-Evans DB et al. Neuron. 2020 Oct 14;108(1):145-163.e10. doi: 10.1016/j.neuron.2020.08.006. Epub 2020 Sep 10.

39. Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq.
Qiu Q et al. Nat Methods. 2020 Oct;17(10):991-1001. doi: 10.1038/s41592-020-0935-4. Epub 2020 Aug 31.

40. Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies.
Hughes TK et al. Immunity. 2020 Oct 13;53(4):878-894.e7. doi: 10.1016/j.immuni.2020.09.015.

41. Single-cell transcriptomics identifies divergent developmental lineage trajectories during human pituitary development.
Zhang S et al. Nat Commun. 2020 Oct 19;11(1):5275. doi: 10.1038/s41467-020-19012-4.

42. Obesity-Linked PPARγ S273 Phosphorylation Promotes Insulin Resistance through Growth Differentiation Factor 3.
Hall JA et al. Cell Metab. 2020 Oct 6;32(4):665-675.e6. doi: 10.1016/j.cmet.2020.08.016. Epub 2020 Sep 16.

43. Network analysis of transcriptomic diversity amongst resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system.
Summers KM et al. PLoS Biol. 2020 Oct 8;18(10):e3000859. doi: 10.1371/journal.pbio.3000859. eCollection 2020 Oct.

44. Lung megakaryocytes are immune modulatory cells.
Pariser DN et al. J Clin Invest. 2020 Oct 20:137377. doi: 10.1172/JCI137377. Online ahead of print.

45. Y Chromosome LncRNA Are Involved in Radiation Response of Male Non-Small Cell Lung Cancer Cells.
Brownmiller T et al. Cancer Res. 2020 Oct 1;80(19):4046-4057. doi: 10.1158/0008-5472.CAN-19-4032. Epub 2020 Jul 2.

46. 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.

47. Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen.
Wang HF et al. Cell Rep. 2020 Oct 27;33(4):108309. doi: 10.1016/j.celrep.2020.108309.

48. Elucidation of Proteus mirabilis as a Key Bacterium in Crohn's Disease Inflammation.
Zhang J et al. Gastroenterology. 2020 Oct 1:S0016-5085(20)35217-3. doi: 10.1053/j.gastro.2020.09.036. Online ahead of print.

49. Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing.
Murdock DR et al. J Clin Invest. 2020 Oct 1:141500. doi: 10.1172/JCI141500. Online ahead of print.

50. Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California.
Sailani MR et al. Nat Commun. 2020 Oct 1;11(1):4933. doi: 10.1038/s41467-020-18758-1.

51. Dendritic Cells and Microglia Have Non-redundant Functions in the Inflamed Brain with Protective Effects of Type 1 cDCs.
Gallizioli M et al. Cell Rep. 2020 Oct 20;33(3):108291. doi: 10.1016/j.celrep.2020.108291.

52. Bioinformatic analysis of RHO family of GTPases identifies RAC1 pharmacological inhibition as a new therapeutic strategy for hepatocellular carcinoma.
Bayo J et al. Gut. 2020 Oct 26:gutjnl-2020-321454. doi: 10.1136/gutjnl-2020-321454. Online ahead of print.

53. Single-cell Study of Two Rat Models of Pulmonary Arterial Hypertension Reveals Connections to Human Pathobiology and Drug Repositioning.
Hong J et al. Am J Respir Crit Care Med. 2020 Oct 6. doi: 10.1164/rccm.202006-2169OC. Online ahead of print.

54. Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input.
Handa T et al. Nat Protoc. 2020 Oct;15(10):3334-3360. doi: 10.1038/s41596-020-0375-8. Epub 2020 Aug 17.

55. HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression.
Srinivasachar Badarinarayan S et al. Nucleic Acids Res. 2020 Oct 6:gkaa832. doi: 10.1093/nar/gkaa832. Online ahead of print.

56. Mendelian randomization while jointly modeling cis genetics identifies causal relationships between gene expression and lipids.
van der Graaf A et al. Nat Commun. 2020 Oct 1;11(1):4930. doi: 10.1038/s41467-020-18716-x.

57. High-Fidelity Drug Induced Liver Injury Screen Using Human PSC-derived Organoids.
Shinozawa T et al. Gastroenterology. 2020 Oct 8:S0016-5085(20)35228-8. doi: 10.1053/j.gastro.2020.10.002. Online ahead of print.

58. RASP: an atlas of transcriptome-wide RNA secondary structure probing data.
Li P et al. Nucleic Acids Res. 2020 Oct 17:gkaa880. doi: 10.1093/nar/gkaa880. Online ahead of print.

59. SC2disease: a manually curated database of single-cell transcriptome for human diseases.
Zhao T et al. Nucleic Acids Res. 2020 Oct 3:gkaa838. doi: 10.1093/nar/gkaa838. Online ahead of print.

60. Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage.
Espah Borujeni A et al. Nat Commun. 2020 Oct 5;11(1):5001. doi: 10.1038/s41467-020-18630-2.

61. Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states.
Lin Z et al. Nat Commun. 2020 Oct 28;11(1):5434. doi: 10.1038/s41467-020-19234-6.

62. Fungal oxylipins direct programmed developmental switches in filamentous fungi.
Niu M et al. Nat Commun. 2020 Oct 14;11(1):5158. doi: 10.1038/s41467-020-18999-0.

63. MIR2111-5 locus and shoot-accumulated mature miR2111 systemically enhance nodulation depending on HAR1 in Lotus japonicus.
Okuma N et al. Nat Commun. 2020 Oct 15;11(1):5192. doi: 10.1038/s41467-020-19037-9.

64. The mouse Gene Expression Database (GXD): 2021 update.
Baldarelli RM et al. Nucleic Acids Res. 2020 Oct 26:gkaa914. doi: 10.1093/nar/gkaa914. Online ahead of print.

65. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.
Bastian FB et al. Nucleic Acids Res. 2020 Oct 10:gkaa793. doi: 10.1093/nar/gkaa793. Online ahead of print.

66. Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis.
Pfisterer U et al. Nat Commun. 2020 Oct 7;11(1):5038. doi: 10.1038/s41467-020-18752-7.

67. Interactions between lineage-associated transcription factors govern haematopoietic progenitor states.
Kucinski I et al. EMBO J. 2020 Oct 26:e104983. doi: 10.15252/embj.2020104983. Online ahead of print.

68. snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis.
Sun W et al. Nature. 2020 Oct 28. doi: 10.1038/s41586-020-2856-x. Online ahead of print.

69. Modeling tissue-relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels.
Yilmaz LS et al. Mol Syst Biol. 2020 Oct;16(10):e9649. doi: 10.15252/msb.20209649.

70. The landscape of RNA Pol II binding reveals a stepwise transition during ZGA.
Liu B et al. Nature. 2020 Oct 28. doi: 10.1038/s41586-020-2847-y. Online ahead of print.

71. Cellular taxonomy and spatial organization of the murine ventral posterior hypothalamus.
Mickelsen LE et al. Elife. 2020 Oct 29;9:e58901. doi: 10.7554/eLife.58901.

72. Epigenomic Evaluation of Cholangiocyte TGFβ Signaling Identifies a Selective Role for Histone 3 Lysine 9 Acetylation in Biliary Fibrosis.
Aseem SO et al. Gastroenterology. 2020 Oct 12:S0016-5085(20)35245-8. doi: 10.1053/j.gastro.2020.10.008. Online ahead of print.

73. A Broad Response to Intracellular Long-Chain Polyphosphate in Human Cells.
Bondy-Chorney E et al. Cell Rep. 2020 Oct 27;33(4):108318. doi: 10.1016/j.celrep.2020.108318.

74. Hypoxia induces transcriptional and translational downregulation of the type I interferon (IFN) pathway in multiple cancer cell types.
Miar A et al. Cancer Res. 2020 Oct 28:canres.2306.2019. doi: 10.1158/0008-5472.CAN-19-2306. Online ahead of print.

75. Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4(+) T Cells in COVID-19.
Meckiff BJ et al. Cell. 2020 Oct 5:S0092-8674(20)31307-6. doi: 10.1016/j.cell.2020.10.001. Online ahead of print.

76. Aging Atlas: a multi-omics database for aging biology.
Aging Atlas Consortium et al. Nucleic Acids Res. 2020 Oct 29:gkaa894. doi: 10.1093/nar/gkaa894. Online ahead of print.