Monthly Letter

1. A benchmark study of simulation methods for single-cell RNA sequencing data.
Cao Y et al. Nat Commun. 2021 Nov 25;12(1):6911. doi: 10.1038/s41467-021-27130-w.

2. Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease.
Horgusluoglu E et al. ; Alzheimer's Disease Neuroimaging Initiative (ADNI); Alzheimer Disease Metabolomics Consortium. Alzheimers Dement. 2021 Nov 10. doi: 10.1002/alz.12468. Online ahead of print.

3. Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease.
Lackey L et al. PLoS Genet. 2021 Nov 16;17(11):e1009912. doi: 10.1371/journal.pgen.1009912. Online ahead of print.

4. Comprehensive analyses of RNA-seq and genome-wide data point to enrichment of neuronal cell type subsets in neuropsychiatric disorders.
Olislagers M et al. Mol Psychiatry. 2021 Nov 1. doi: 10.1038/s41380-021-01324-6. Online ahead of print.

5. Single cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome.
Paganos P et al. Elife. 2021 Nov 25;10:e70416. doi: 10.7554/eLife.70416. Online ahead of print.

6. Toward platelet transcriptomics in cancer diagnosis, prognosis and therapy.
Krishnan A et al. Br J Cancer. 2021 Nov 22. doi: 10.1038/s41416-021-01627-z. Online ahead of print.

7. Dissecting mammalian spermatogenesis using spatial transcriptomics.
Chen H et al. Cell Rep. 2021 Nov 2;37(5):109915. doi: 10.1016/j.celrep.2021.109915.

8. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification.
Leader AM et al. Cancer Cell. 2021 Nov 2:S1535-6108(21)00560-2. doi: 10.1016/j.ccell.2021.10.009. Online ahead of print.

9. tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data.
Wang JH et al. Nucleic Acids Res. 2021 Nov 10:gkab1023. doi: 10.1093/nar/gkab1023. Online ahead of print.

10. An integrated taxonomy for monogenic inflammatory bowel disease.
Bolton C et al. Gastroenterology. 2021 Nov 12:S0016-5085(21)03737-9. doi: 10.1053/j.gastro.2021.11.014. Online ahead of print.

11. Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers.
Li QL et al. Nat Commun. 2021 Nov 4;12(1):6407. doi: 10.1038/s41467-021-26600-5.

12. Altered cell and RNA isoform diversity in aging Down syndrome brains.
Palmer CR et al. Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):e2114326118. doi: 10.1073/pnas.2114326118.

13. m6A-express: uncovering complex and condition-specific m6A regulation of gene expression.
Zhang T et al. Nucleic Acids Res. 2021 Nov 18;49(20):e116. doi: 10.1093/nar/gkab714.

14. Glucosylceramide synthase deficiency in the heart compromises β1-adrenergic receptor trafficking.
Andersson L et al. Eur Heart J. 2021 Nov 14;42(43):4481-4492. doi: 10.1093/eurheartj/ehab412.

15. A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit.
Wang R et al. Genome Biol. 2021 Nov 14;22(1):313. doi: 10.1186/s13059-021-02531-8.

16. DISCO: a database of Deeply Integrated human Single-Cell Omics data.
Li M et al. Nucleic Acids Res. 2021 Nov 17:gkab1020. doi: 10.1093/nar/gkab1020. Online ahead of print.

17. Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data.
Sun D et al. Nat Biotechnol. 2021 Nov 11. doi: 10.1038/s41587-021-01091-3. Online ahead of print.

18. Modulating mesendoderm competence during human germ layer differentiation.
Valcourt JR et al. Cell Rep. 2021 Nov 9;37(6):109990. doi: 10.1016/j.celrep.2021.109990.

19. Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits.
Orchard P et al. Genome Res. 2021 Nov 23. doi: 10.1101/gr.268482.120. Online ahead of print.

20. Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface.
Hunter MV et al. Nat Commun. 2021 Nov 1;12(1):6278. doi: 10.1038/s41467-021-26614-z.

21. Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarction.
Janbandhu V et al. Cell Stem Cell. 2021 Nov 5:S1934-5909(21)00421-5. doi: 10.1016/j.stem.2021.10.009. Online ahead of print.

22. Single-cell normalization and association testing unifying CRISPR screen and gene co-expression analyses with Normalisr.
Wang L. Nat Commun. 2021 Nov 4;12(1):6395. doi: 10.1038/s41467-021-26682-1.

23. SPICA: Swiss portal for immune cell analysis.
Andreatta M et al. Nucleic Acids Res. 2021 Nov 8:gkab1055. doi: 10.1093/nar/gkab1055. Online ahead of print.

24. G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum.
Dumetz F et al. Nucleic Acids Res. 2021 Nov 18:gkab1095. doi: 10.1093/nar/gkab1095. Online ahead of print.

25. Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals.
Talon I et al. Genome Biol. 2021 Nov 1;22(1):302. doi: 10.1186/s13059-021-02518-5.

26. TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization.
Ibrahim F et al. Nucleic Acids Res. 2021 Nov 18;49(20):e115. doi: 10.1093/nar/gkab713.

27. Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics.
He Z et al. Am J Hum Genet. 2021 Nov 5:S0002-9297(21)00386-4. doi: 10.1016/j.ajhg.2021.10.009. Online ahead of print.

28. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina.
Lyu P et al. Cell Rep. 2021 Nov 16;37(7):109994. doi: 10.1016/j.celrep.2021.109994.

29. scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies.
Schmid KT et al. Nat Commun. 2021 Nov 16;12(1):6625. doi: 10.1038/s41467-021-26779-7.

30. BAFF attenuates immunosuppressive monocytes in the melanoma tumor microenvironment.
Liu W et al. Cancer Res. 2021 Nov 22:canres.1171.2021. doi: 10.1158/0008-5472.CAN-21-1171. Online ahead of print.

31. Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells.
Franjic D et al. Neuron. 2021 Nov 18:S0896-6273(21)00866-7. doi: 10.1016/j.neuron.2021.10.036. Online ahead of print.

32. Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187-induced plant salt stress tolerance.
Andrés-Barrao C et al. Proc Natl Acad Sci U S A. 2021 Nov 16;118(46):e2107417118. doi: 10.1073/pnas.2107417118.

33. Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes.
Ansari-Pour N et al. Nat Commun. 2021 Nov 26;12(1):6946. doi: 10.1038/s41467-021-27079-w.

34. Patch-seq of mouse DRG neurons reveals candidate genes for specific mechanosensory functions.
Parpaite T et al. Cell Rep. 2021 Nov 2;37(5):109914. doi: 10.1016/j.celrep.2021.109914.

35. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq.
Yan B et al. Genome Res. 2021 Nov 23:gr.275784.121. doi: 10.1101/gr.275784.121. Online ahead of print.

36. Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes.
Michurina A et al. EMBO J. 2021 Nov 22:e106459. doi: 10.15252/embj.2020106459. Online ahead of print.

37. Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments.
Yap K et al. Mol Cell. 2021 Nov 2:S1097-2765(21)00838-8. doi: 10.1016/j.molcel.2021.10.009. Online ahead of print.

38. Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections.
Maehara K et al. Mol Syst Biol. 2021 Nov;17(11):e10323. doi: 10.15252/msb.202110323.

39. Mis-splicing in Huntington's disease: harnessing the power of comparative transcriptomics.
Xing Y et al. Trends Neurosci. 2021 Nov 6:S0166-2236(21)00209-5. doi: 10.1016/j.tins.2021.10.009. Online ahead of print.

40. Locus-specific expression of transposable elements in single cells with CELLO-seq.
Berrens RV et al. Nat Biotechnol. 2021 Nov 15. doi: 10.1038/s41587-021-01093-1. Online ahead of print.

41. Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation.
Georgolopoulos G et al. Nat Commun. 2021 Nov 23;12(1):6790. doi: 10.1038/s41467-021-27159-x.

42. A transposon expression burst accompanies the activation of Y-chromosome fertility genes during Drosophila spermatogenesis.
Lawlor MA et al. Nat Commun. 2021 Nov 25;12(1):6854. doi: 10.1038/s41467-021-27136-4.

43. Skin inflammation activates intestinal stromal fibroblasts and promotes colitis.
Dokoshi T et al. J Clin Invest. 2021 Nov 1;131(21):e147614. doi: 10.1172/JCI147614.

44. Fragmentation of tissue-resident macrophages during isolation confounds analysis of single-cell preparations from mouse hematopoietic tissues.
Millard SM et al. Cell Rep. 2021 Nov 23;37(8):110058. doi: 10.1016/j.celrep.2021.110058.

45. HER3 is an Actionable Target in Advanced Prostate Cancer.
Gil V et al. Cancer Res. 2021 Nov 9:canres.CAN-21-3360-E.2021. doi: 10.1158/0008-5472.CAN-21-3360. Online ahead of print.

46. Correction: Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines.
SoRelle ED et al. Elife. 2021 Nov 11;10:e75422. doi: 10.7554/eLife.75422.

47. A non-classical monocyte-derived macrophage subset provides a splenic replication niche for intracellular Salmonella.
Hoffman D et al. Immunity. 2021 Nov 6:S1074-7613(21)00452-0. doi: 10.1016/j.immuni.2021.10.015. Online ahead of print.

48. Underwater CAM photosynthesis elucidated by Isoetes genome.
Wickell D et al. Nat Commun. 2021 Nov 3;12(1):6348. doi: 10.1038/s41467-021-26644-7.

49. Transcription factor FOXF1 identifies compartmentally distinct mesenchymal cells with a role in lung allograft fibrogenesis.
Braeuer RR et al. J Clin Invest. 2021 Nov 1;131(21):e147343. doi: 10.1172/JCI147343.

50. Impaired glucocorticoid receptor expression in liver disrupts feeding-induced gene expression, glucose uptake, and glycogen storage.
Præstholm SM, Correia CM, Goitea VE, Siersbæk MS, Jørgensen M, Havelund JF, Pedersen TÅ, Færgeman NJ, Grøntved L. Cell Rep. 2021 Nov 2;37(5):109938. doi: 10.1016/j.celrep.2021.109938.

51. G3BP1 binds to guanine quadruplexes in mRNAs to modulate their stabilities.
He X et al. Nucleic Acids Res. 2021 Nov 8;49(19):11323-11336. doi: 10.1093/nar/gkab873.

52. Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1.
Wiegard A et al. Mol Cell. 2021 Nov 5:S1097-2765(21)00907-2. doi: 10.1016/j.molcel.2021.10.015. Online ahead of print.

53. Scaling concepts in 'omics: Nuclear lamin-B scales with tumor growth and often predicts poor prognosis, unlike fibrosis.
Vashisth M et al. Proc Natl Acad Sci U S A. 2021 Nov 30;118(48):e2112940118. doi: 10.1073/pnas.2112940118.

54. Balancing of mitochondrial translation through METTL8-mediated m(3)C modification of mitochondrial tRNAs.
Schöller E et al. Mol Cell. 2021 Nov 8:S1097-2765(21)00910-2. doi: 10.1016/j.molcel.2021.10.018. Online ahead of print.

55. ATR inhibition enables complete tumour regression in ALK-driven NB mouse models.
Szydzik J et al. Nat Commun. 2021 Nov 24;12(1):6813. doi: 10.1038/s41467-021-27057-2.

56. The Lyme Disease agent co-opts adiponectin receptor-mediated signaling in its arthropod vector.
Tang X et al. Elife. 2021 Nov 16;10:e72568. doi: 10.7554/eLife.72568. Online ahead of print.

57. Transcription recycling assays identify PAF1 as a driver for RNA Pol II recycling.
Chen Z et al. Nat Commun. 2021 Nov 3;12(1):6318. doi: 10.1038/s41467-021-26604-1.

58. Monoclonal antibody-mediated neutralization of SARS-CoV-2 in an IRF9-deficient child.
Lévy R et al. Proc Natl Acad Sci U S A. 2021 Nov 9;118(45):e2114390118. doi: 10.1073/pnas.2114390118.

59. Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation.
Finet O et al. Mol Cell. 2021 Nov 15:S1097-2765(21)00953-9. doi: 10.1016/j.molcel.2021.11.003. Online ahead of print.

60. Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs.
Cai L et al. Nucleic Acids Res. 2021 Nov 8:gkab1033. doi: 10.1093/nar/gkab1033. Online ahead of print.

61. Wnt signaling mediates acquisition of blood-brain barrier properties in naïve endothelium derived from human pluripotent stem cells.
Gastfriend BD et al. Elife. 2021 Nov 10;10:e70992. doi: 10.7554/eLife.70992. Online ahead of print.

62. TRIB1 regulates LDL metabolism through CEBPα-mediated effects on the LDL receptor in hepatocytes.
Quiroz-Figueroa K et al. J Clin Invest. 2021 Nov 15;131(22):e146775. doi: 10.1172/JCI146775.

63. Two oppositely-charged sf3b1 mutations cause defective development, impaired immune response, and aberrant selection of intronic branch sites in Drosophila.
Zhang B et al. PLoS Genet. 2021 Nov 1;17(11):e1009861. doi: 10.1371/journal.pgen.1009861. eCollection 2021 Nov.