1. CCPE: cell cycle pseudotime estimation for single cell RNA-seq data Liu J et al. Nucleic Acids Res. 2021 Dec 21:gkab1236. doi: 10.1093/nar/gkab1236. Online ahead of print.
2. DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data Muskovic W et al. Genome Biol. 2021 Dec 2;22(1):329. doi: 10.1186/s13059-021-02547-0.
3. Benchmarking UMI-based single-cell RNA-seq preprocessing workflows You Y et al. Genome Biol. 2021 Dec 14;22(1):339. doi: 10.1186/s13059-021-02552-3.
4. Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons Gao W et al. Genome Res. 2021 Dec 2. doi: 10.1101/gr.275944.121. Online ahead of print.
5. Malignancy and NF-κB signalling strengthen coordination between expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes Perez MF et al. Genome Biol. 2021 Dec 2;22(1):328. doi: 10.1186/s13059-021-02541-6.
6. MNX1-HNF1B axis is indispensable for intraductal papillary mucinous neoplasm lineages Kato H et al. Gastroenterology. 2021 Dec 21:S0016-5085(21)04090-7. doi: 10.1053/j.gastro.2021.12.254. 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 Dec 2;49(21):e122. doi: 10.1093/nar/gkab775.
8. Hepatic MIR20B promotes nonalcoholic fatty liver disease by suppressing PPARA Lee YH et al. Elife. 2021 Dec 29;10:e70472. doi: 10.7554/eLife.70472. Online ahead of print.
9. Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states Isakova A et al. Proc Natl Acad Sci U S A. 2021 Dec 21;118(51):e2113568118. doi: 10.1073/pnas.2113568118.
10. Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq Engel KL et al. Nucleic Acids Res. 2021 Dec 7:gkab1185. doi: 10.1093/nar/gkab1185. Online ahead of print.
11. Identification of Drug Transporter Genomic Variants and Inhibitors that Protect Against Doxorubicin-Induced Cardiotoxicity Magdy T et al. Circulation. 2021 Dec 7. doi: 10.1161/CIRCULATIONAHA.121.055801. Online ahead of print.
12. Foster thy young: enhanced prediction of orphan genes in assembled genomes Li J et al. Nucleic Acids Res. 2021 Dec 20:gkab1238. doi: 10.1093/nar/gkab1238. Online ahead of print.
13. G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum Dumetz F et al. Nucleic Acids Res. 2021 Dec 2;49(21):12486-12501. doi: 10.1093/nar/gkab1095.
14. Single-cell analysis identifies a key role for Hhip in murine coronal suture development Holmes G et al. Nat Commun. 2021 Dec 8;12(1):7132. doi: 10.1038/s41467-021-27402-5.
15. Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development Tatarakis D et al. Cell Rep. 2021 Dec 21;37(12):110140. doi: 10.1016/j.celrep.2021.110140.
16. Grouped-seq for integrated phenotypic and transcriptomic screening of patient-derived tumor organoids Wu Y et al. Nucleic Acids Res. 2021 Dec 10:gkab1201. doi: 10.1093/nar/gkab1201. Online ahead of print.
17. Constructing local cell-specific networks from single-cell data Wang X et al. Proc Natl Acad Sci U S A. 2021 Dec 21;118(51):e2113178118. doi: 10.1073/pnas.2113178118.
18. RpoN/Sfa2-dependent activation of the Pseudomonas aeruginosa H2-T6SS and its cognate arsenal of antibacterial toxins Allsopp LP et al. Nucleic Acids Res. 2021 Dec 20:gkab1254. doi: 10.1093/nar/gkab1254. Online ahead of print.
19. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection Huang Y et al. Plant Cell. 2021 Dec 7:koab291. doi: 10.1093/plcell/koab291. Online ahead of print.
20. Single-cell transcriptomics of LepR-positive skeletal cells reveals heterogeneous stress-dependent stem and progenitor pools Mo C et al. EMBO J. 2021 Dec 27:e108415. doi: 10.15252/embj.2021108415. Online ahead of print.
21. SH2D4A downregulation due to loss of chromosome 8p is associated with poor prognosis and low T cell infiltration in colorectal cancer Matsumoto T et al. Br J Cancer. 2021 Dec 10. doi: 10.1038/s41416-021-01660-y. Online ahead of print.
22. Histone variant H2A.Z regulates zygotic genome activation Ibarra-Morales D et al. Nat Commun. 2021 Dec 1;12(1):7002. doi: 10.1038/s41467-021-27125-7.
23. Inhibition of SARS-CoV-2 coronavirus proliferation by designer antisense-circRNAs Pfafenrot C et al. Nucleic Acids Res. 2021 Dec 2;49(21):12502-12516. doi: 10.1093/nar/gkab1096.
24. Phosphorylation of RAV1/2 by KIN10 is essential for transcriptional activation of CAT6/7, which underlies oxidative stress response in cassava Wang P et al. Cell Rep. 2021 Dec 14;37(11):110119. doi: 10.1016/j.celrep.2021.110119.
25. Cobolt: integrative analysis of multimodal single-cell sequencing data Gong B et al. Genome Biol. 2021 Dec 28;22(1):351. doi: 10.1186/s13059-021-02556-z.
26. Polycomb repressive complex 2 in adult hair follicle stem cells is dispensable for hair regeneration Flora P et al. PLoS Genet. 2021 Dec 14;17(12):e1009948. doi: 10.1371/journal.pgen.1009948. eCollection 2021 Dec.
27. Human embryonic genome activation initiates at the one-cell stage Asami M et al. Cell Stem Cell. 2021 Dec 17:S1934-5909(21)00484-7. doi: 10.1016/j.stem.2021.11.012. Online ahead of print.
28. External signals regulate continuous transcriptional states in hematopoietic stem cells Fast EM et al. Elife. 2021 Dec 23;10:e66512. doi: 10.7554/eLife.66512.
29. Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes White SM et al. Nucleic Acids Res. 2021 Dec 2;49(21):12196-12210. doi: 10.1093/nar/gkab1105.
30. CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation Hu Z et al. Genome Biol. 2021 Dec 13;22(1):337. doi: 10.1186/s13059-021-02561-2.
31. Phospho-RNA sequencing with circAID-p-seq Del Piano A et al. Nucleic Acids Res. 2021 Dec 1:gkab1158. doi: 10.1093/nar/gkab1158. Online ahead of print.
32. Local acetate inhibits brown adipose tissue function Sun W et al. Proc Natl Acad Sci U S A. 2021 Dec 7;118(49):e2116125118. doi: 10.1073/pnas.2116125118.
33. Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition Hoffmann UA et al. Nucleic Acids Res. 2021 Dec 16;49(22):13075-13091. doi: 10.1093/nar/gkab1161.
34. splatPop: simulating population scale single-cell RNA sequencing data Azodi CB et al. Genome Biol. 2021 Dec 15;22(1):341. doi: 10.1186/s13059-021-02546-1.
35. An NK-like CAR T cell transition in CAR T cell dysfunction Good CR et al. Cell. 2021 Dec 9;184(25):6081-6100.e26. doi: 10.1016/j.cell.2021.11.016. Epub 2021 Dec 2.
36. Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology van Rheenen W et al. Nat Genet. 2021 Dec;53(12):1636-1648. doi: 10.1038/s41588-021-00973-1. Epub 2021 Dec 6.
37. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization Wang Y et al. Cell. 2021 Dec 22;184(26):6361-6377.e24. doi: 10.1016/j.cell.2021.11.024. Epub 2021 Dec 6.
38. A transcriptional rheostat couples past activity to future sensory responses Tsukahara T et al. Cell. 2021 Dec 22;184(26):6326-6343.e32. doi: 10.1016/j.cell.2021.11.022. Epub 2021 Dec 7.
39. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps Chen B et al. Cell. 2021 Dec 22;184(26):6262-6280.e26. doi: 10.1016/j.cell.2021.11.031. Epub 2021 Dec 14.
|