Title RNA-Seq 관련 논문 및 바이오뉴스(2023년 1월)
Writer Admin
Date 2023-01-01
Attached File
Newsletter | Jan. 2023 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Cross-species cell-type assignment of single-cell RNA-seq by a heterogeneous graph neural network
Liu X et al. Genome Res. 2022 Dec 16:gr.276868.122. doi: 10.1101/gr.276868.122. Online ahead of print.

2. A Phylogenetic Framework to Simulate Synthetic Inter-species RNA-Seq Data
Bastide P et al. Mol Biol Evol. 2022 Dec 12:msac269. doi: 10.1093/molbev/msac269. Online ahead of print.

3. Meta-analysis of human cancer single cell RNA-seq datasets using the IMMUcan database
Camps J et al. Cancer Res. 2022 Dec 2:CAN-22-0074. doi: 10.1158/0008-5472.CAN-22-0074. Online ahead of print.

4. ONE-seq: epitranscriptome and gene-specific profiling of NAD-capped RNA
Niu K et al. Nucleic Acids Res. 2022 Dec 7:gkac1136. doi: 10.1093/nar/gkac1136. Online ahead of print.

5. Mouse primordial germ-cell-like cells lack piRNAs
Ramakrishna NB et al. Dev Cell. 2022 Dec 5;57(23):2661-2668.e5. doi: 10.1016/j.devcel.2022.11.004.

6. Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research
Zhang Z et al. Mol Biol Evol. 2022 Dec 5;39(12):msac261. doi: 10.1093/molbev/msac261.

7. Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
Talsania K et al. Genome Biol. 2022 Dec 13;23(1):255. doi: 10.1186/s13059-022-02816-6.

8. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
Li Y et al. Cancer Cell. 2022 Dec 20:S1535-6108(22)00565-7. doi: 10.1016/j.ccell.2022.12.001. Online ahead of print.

9. Single-cell transcriptomic and spatial landscapes of the developing human pancreas
Olaniru OE et al. Cell Metab. 2022 Dec 6:S1550-4131(22)00500-9. doi: 10.1016/j.cmet.2022.11.009. Online ahead of print.

10. Pneumolysin promotes host cell necroptosis and bacterial competence during pneumococcal meningitis as shown by whole-animal dual RNA-seq
Jim KK et al. Cell Rep. 2022 Dec 20;41(12):111851. doi: 10.1016/j.celrep.2022.111851.

11. A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation
Neuschulz A et al. Mol Syst Biol. 2022 Dec 27:e11147. doi: 10.15252/msb.202211147. Online ahead of print.

12. Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq
Wessels HH et al. Nat Methods. 2022 Dec 22. doi: 10.1038/s41592-022-01705-x. Online ahead of print.

13. Multiregional single-cell dissection of tumor and immune cells reveals stable lock-and-key features in liver cancer
Ma L et al. Nat Commun. 2022 Dec 7;13(1):7533. doi: 10.1038/s41467-022-35291-5.

14. Deep transfer learning enables lesion tracing of circulating tumor cells
Guo X et al. Nat Commun. 2022 Dec 12;13(1):7687. doi: 10.1038/s41467-022-35296-0.

15. Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm
Bhattacharyya S et al. J Clin Invest. 2022 Dec 1:e153635. doi: 10.1172/JCI153635. Online ahead of print.

16. CoLoC-seq probes the global topology of organelle transcriptomes
Jeandard D et al. Nucleic Acids Res. 2022 Dec 20:gkac1183. doi: 10.1093/nar/gkac1183. Online ahead of print.

17. A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing
Lengyel E et al. Cell Rep. 2022 Dec 20;41(12):111838. doi: 10.1016/j.celrep.2022.111838.

18. Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding
Shen R et al. Nat Commun. 2022 Dec 10;13(1):7640. doi: 10.1038/s41467-022-35288-0.

19. Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing
Begik O et al. Nat Methods. 2022 Dec 19. doi: 10.1038/s41592-022-01714-w. Online ahead of print.

20. Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
Hernandez-Alias X et al. Nucleic Acids Res. 2022 Dec 20:gkac1185. doi: 10.1093/nar/gkac1185. Online ahead of print.

21. Molecular features and evolutionary trajectory of ASCL1(+) and NEUROD1(+) SCLC cells
Zhang X et al. Br J Cancer. 2022 Dec 14. doi: 10.1038/s41416-022-02103-y. Online ahead of print.

22. Regulation of RNA localization during oocyte maturation by dynamic RNA-ER association and remodeling of the ER
Hwang H et al. Cell Rep. 2022 Dec 13;41(11):111802. doi: 10.1016/j.celrep.2022.111802.

23. GeneFriends: gene co-expression databases and tools for humans and model organisms
Raina P et al. Nucleic Acids Res. 2022 Dec 1:gkac1031. doi: 10.1093/nar/gkac1031. Online ahead of print.

24. m(6)A epitranscriptomic modification regulates neural progenitor-to-glial cell transition in the retina
Xin Y et al. Elife. 2022 Dec 2;11:e79994. doi: 10.7554/eLife.79994.

25. Cellular features of localized microenvironments in human meniscal degeneration: a single-cell transcriptomic study
Fu W et al. Elife. 2022 Dec 22;11:e79585. doi: 10.7554/eLife.79585.

26. Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing
Orabi B et al. Nucleic Acids Res. 2022 Dec 8:gkac1112. doi: 10.1093/nar/gkac1112. Online ahead of print.

27. A mineralizing pool of Gli1-expressing progenitors builds the tendon enthesis and demonstrates therapeutic potential
Fang F et al. Cell Stem Cell. 2022 Dec 1;29(12):1669-1684.e6. doi: 10.1016/j.stem.2022.11.007.

28. An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae
Huber M et al. Nat Commun. 2022 Dec 8;13(1):7585. doi: 10.1038/s41467-022-35261-x.

29. Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus
Isaac S et al. Nat Commun. 2022 Dec 13;13(1):7718. doi: 10.1038/s41467-022-35380-5.

30. HIV integration in the human brain is linked to microglial activation and 3D genome remodeling
Plaza-Jennings AL et al. Mol Cell. 2022 Dec 15;82(24):4647-4663.e8. doi: 10.1016/j.molcel.2022.11.016.

31. Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics
Subramanian A et al. Genome Biol. 2022 Dec 27;23(1):267. doi: 10.1186/s13059-022-02820-w.

32. Developmental trajectories of thalamic progenitors revealed by single-cell transcriptome profiling and Shh perturbation
Govek KW et al. Cell Rep. 2022 Dec 6;41(10):111768. doi: 10.1016/j.celrep.2022.111768.

33. Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering
Fang J et al. Genome Biol. 2022 Dec 27;23(1):269. doi: 10.1186/s13059-022-02825-5.

34. Mitochondrial dysfunction induces ALK5-SMAD2-mediated hypovascularization and arteriovenous malformations in mouse retinas
Zhang H et al. Nat Commun. 2022 Dec 10;13(1):7637. doi: 10.1038/s41467-022-35262-w.

35. Activation of ChvG-ChvI regulon by cell wall stress confers resistance to β-lactam antibiotics and initiates surface spreading in Agrobacterium tumefaciens
Williams MA et al. PLoS Genet. 2022 Dec 8;18(12):e1010274. doi: 10.1371/journal.pgen.1010274. eCollection 2022 Dec.

36. Extracellular traps from activated vascular smooth muscle cells drive the progression of atherosclerosis
Zhai M et al. Nat Commun. 2022 Dec 6;13(1):7500. doi: 10.1038/s41467-022-35330-1.

37. KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure
Bi J et al. Nucleic Acids Res. 2022 Dec 7;50(21):12235-50. doi: 10.1093/nar/gkac1118. Online ahead of print.

38. Unscheduled epigenetic modifications cause genome instability and sterility through aberrant R-loops following starvation
Sun B et al. Nucleic Acids Res. 2022 Dec 12:gkac1155. doi: 10.1093/nar/gkac1155. Online ahead of print.

39. Mutation of the polyadenylation complex subunit CstF77 reveals that mRNA 3' end formation and HSP101 levels are critical for a robust heat stress response
Kim M et al. Plant Cell. 2022 Dec 6:koac351. doi: 10.1093/plcell/koac351. Online ahead of print.

40. Predicting response to immune checkpoint blockade in NSCLC with tumour-only RNA-seq
Markham JF et al. Br J Cancer. 2022 Dec 26. doi: 10.1038/s41416-022-02105-w. Online ahead of print.

41. The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory
Craig RJ et al. Plant Cell. 2022 Dec 23:koac347. doi: 10.1093/plcell/koac347. Online ahead of print.

42. Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors
Replogle JM et al. Elife. 2022 Dec 28;11:e81856. doi: 10.7554/eLife.81856. Online ahead of print.

43. Multi-modal characterization and simulation of human epileptic circuitry
Buchin A et al. Cell Rep. 2022 Dec 27;41(13):111873. doi: 10.1016/j.celrep.2022.111873.

44. EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release
Mukherjee K et al. Cell Rep. 2022 Dec 20;41(12):111830. doi: 10.1016/j.celrep.2022.111830.

45. A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules
Castillo KD et al. Cell Rep. 2022 Dec 27;41(13):111879. doi: 10.1016/j.celrep.2022.111879.

46. G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects
Wang F et al. Nucleic Acids Res. 2022 Dec 13:gkac1108. doi: 10.1093/nar/gkac1108. Online ahead of print.

47. Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integrates
Wei Y et al. Mol Cell. 2022 Dec 15;82(24):4585-4587. doi: 10.1016/j.molcel.2022.11.013.

48. Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish
Teefy BB et al. Genome Res. 2022 Dec 28:gr.277301.122. doi: 10.1101/gr.277301.122. Online ahead of print.

49. Engineered cell entry links receptor biology with single-cell genomics
Yu B et al. Cell. 2022 Dec 22;185(26):4904-4920.e22. doi: 10.1016/j.cell.2022.11.016. Epub 2022 Dec 13.

50. RNA degradation eliminates developmental transcripts during murine embryonic stem cell differentiation via CAPRIN1-XRN2
Viegas JO et al. Dev Cell. 2022 Dec 19;57(24):2731-2744.e5. doi: 10.1016/j.devcel.2022.11.014. Epub 2022 Dec 9.

51. Temporal molecular program of human hematopoietic stem and progenitor cells after birth
Zhang Y et al. Dev Cell. 2022 Dec 19;57(24):2745-2760.e6. doi: 10.1016/j.devcel.2022.11.013. Epub 2022 Dec 8.

52. Correlated gene modules uncovered by high-precision single-cell transcriptomics
Chapman AR et al. Proc Natl Acad Sci U S A. 2022 Dec 20;119(51):e2206938119. doi: 10.1073/pnas.2206938119. Epub 2022 Dec 12.

53. B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing
Frede A et al. Immunity. 2022 Dec 13;55(12):2336-2351.e12. doi: 10.1016/j.immuni.2022.11.002. Epub 2022 Dec 2.

54. PALI1 promotes tumor growth through competitive recruitment of PRC2 to G9A-target chromatin for dual epigenetic silencing
Fong KW et al. Mol Cell. 2022 Dec 15;82(24):4611-4626.e7. doi: 10.1016/j.molcel.2022.11.010. Epub 2022 Dec 6.

55. Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing
Vistain L et al. Nat Methods. 2022 Dec;19(12):1578-1589. doi: 10.1038/s41592-022-01684-z. Epub 2022 Dec 1.

56. Identification of a unique subset of tissue-resident memory CD4(+) T cells in Crohn's disease
Yokoi T et al. Proc Natl Acad Sci U S A. 2023 Jan 3;120(1):e2204269120. doi: 10.1073/pnas.2204269120. Epub 2022 Dec 27.

Recent Bio-News
1. 코로나19·독감 등 바이러스 4종 동시 진단 PCR 기기 개발
2. 멀고 험한 치매 정복...알츠하이머 신약 '레카네맙' 임상3상 결과 엇갈린 평가
3. 코로나19 팬데믹으로 청소년 뇌는 3년 더 빨리 늙었다
4. 새로운 비만 치료법 등장…양전하 나노물질로 내장지방 없애
5. WHO "세계인 90%, 코로나 면역…비상사태 종료 가까워"
6. MZ세대 ‘고혈압 환자' 점점 늘어…비만·스트레스 원인
7. 흡연·음주 유도하는 유전자 변이 약 4000개 찾았다
8. 불치 T세포 백혈병 환자에 첫 DNA 편집 치료
9. 알코올은 모든 인체 조직에 영향을 준다
10. 아토피피부염·알레르기 치료에 '유산균' 효과 규명 잇따라
11. "코로나로 후각·미각 잃었다면 체내 항체수준 높을 가능성"
12. [의학사로 보는 세상] 암도 유발하는 '바이러스' 유래는 '독성물질'
13. 코로나 2회 감염자 치명률, 1회 감염자보다 낮아
14. 美 FDA,1형 당뇨병 발병 지연 효과 치료제 최초 승인
15. [의학사로 보는 세상] 코로나 백신 여러번 맞아야 하는 이유
16. 방사선 노출된 부모 유전자, 자녀에게 전해진다
17. 인간만 가진 유전자 155개 추가 발견...인간 고유 질환 비밀 푼다
18. '뇌 먹는 아메바' 국내 첫 사망 사례 발생
19. 체온 마음대로 조절하는 뉴런 발견
20. "햄·베이컨에 쓰이는 발색제 '아질산염' 암 발병률 높여"
- 위 기사는 동아사이언스(https://www.dongascience.com/) 또는 BRIC(https://www.ibric.org/)에서 제공하고 링크클릭시 해당 사이트로 이동하여 기사내용을 보실수 있습니다.
(주)이바이오젠, www.e-biogen.com