Monthly Letter

1. Modular, efficient and constant-memory single-cell RNA-seq preprocessing.
Melsted P, Booeshaghi AS, Liu L, Gao F, Lu L, Min KHJ, da Veiga Beltrame E, Hjörleifsson KE, Gehring J, Pachter L. Nat Biotechnol. 2021 Jul;39(7):813-818. doi: 10.1038/s41587-021-00870-2. Epub 2021 Apr 1.

2. A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data.
Alghamdi N, Chang W, Dang P, Lu X, Wan C, Gampala S, Huang Z, Wang J, Ma Q, Zang Y, Fishel ML, Cao S, Zhang C. Genome Res. 2021 Jul 22:gr.271205.120. doi: 10.1101/gr.271205.120. Online ahead of print.

3. Bcl3 Couples Cancer Stem Cell Enrichment With Pancreatic Cancer Molecular Subtypes.
Ai J, Wörmann SM, Görgülü K, Vallespinos M, Zagorac S, Alcala S, Wu N, Kabacaoglu D, Berninger A, Navarro D, Kaya-Aksoy E, Ruess DA, Ciecielski KJ, Kowalska M, Demir IE, Ceyhan GO, Heid I, Braren R, Riemann M, Schreiner S, Hofmann S, Kutschke M, Jastroch M, Slotta-Huspenina J, Muckenhuber A, Schlitter AM, Schmid RM, Steiger K, Diakopoulos KN, Lesina M, Sainz B Jr, Algül H. Gastroenterology. 2021 Jul;161(1):318-332.e9. doi: 10.1053/j.gastro.2021.03.051. Epub 2021 Apr 2.

4. Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer.
Tang K, Ji X, Zhou M, Deng Z, Huang Y, Zheng G, Cao Z. Nucleic Acids Res. 2021 Jul 2:gkab554. doi: 10.1093/nar/gkab554. Online ahead of print.

5. The triumphs and limitations of computational methods for scRNA-seq.
Kharchenko PV. Nat Methods. 2021 Jul;18(7):723-732. doi: 10.1038/s41592-021-01171-x. Epub 2021 Jun 21.

6. Novel doublesex duplication associated with sexually dimorphic development of dogface butterfly wings.
Rodriguez-Caro F, Fenner J, Bhardwaj S, Cole J, Benson C, Colombara AM, Papa R, Brown MW, Martin A, Range RC, Counterman BA. Mol Biol Evol. 2021 Jul 29:msab228. doi: 10.1093/molbev/msab228. Online ahead of print.

7. Hyperglycaemia Induces Trained Immunity in Macrophages and Their Precursors and Promotes Atherosclerosis.
Edgar L, Akbar N, Braithwaite AT, Krausgruber T, Gallart-Ayala H, Bailey J, Corbin AL, Khoyratty TE, Chai JT, Alkhalil M, Rendeiro AF, Ziberna K, Arya R, Cahill TJ, Bock C, Laurencikiene J, Crabtree MJ, Lemieux ME, Riksen NP, Netea MG, Wheelock CE, Channon KM, Rydén M, Udalova IA, Carnicer R, Choudhury RP. Circulation. 2021 Jul 13. doi: 10.1161/CIRCULATIONAHA.120.046464. Online ahead of print.

8. Bioinformatic analysis of RHO family of GTPases identifies RAC1 pharmacological inhibition as a new therapeutic strategy for hepatocellular carcinoma.
Bayo J, Fiore EJ, Dominguez LM, Cantero MJ, Ciarlantini MS, Malvicini M, Atorrasagasti C, Garcia MG, Rossi M, Cavasotto C, Martinez E, Comin J, Mazzolini GD. Gut. 2021 Jul;70(7):1362-1374. doi: 10.1136/gutjnl-2020-321454. Epub 2020 Oct 26.

9. Single-cell analysis of mosquito hemocytes identifies signatures of immune cell sub-types and cell differentiation.
Kwon H, Mohammed M, Franzén O, Ankarklev J, Smith R. Elife. 2021 Jul 28;10:e66192. doi: 10.7554/eLife.66192. Online ahead of print.

10. Control of tissue development and cell diversity by cell cycle-dependent transcriptional filtering.
Abou Chakra M, Isserlin R, Tran TN, Bader GD. Elife. 2021 Jul 2;10:e64951. doi: 10.7554/eLife.64951.

11. Regulation of murine B lymphopoiesis by stromal cells.
Kwang D, Tjin G, Purton LE. Immunol Rev. 2021 Jul;302(1):47-67. doi: 10.1111/imr.12973. Epub 2021 May 17.

12. Molecular topography of an entire nervous system.
Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM 3rd. Cell. 2021 Jul 2:S0092-8674(21)00758-3. doi: 10.1016/j.cell.2021.06.023. Online ahead of print.

13. TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.
Conard AM, Goodman N, Hu Y, Perrimon N, Singh R, Lawrence C, Larschan E. Nucleic Acids Res. 2021 Jul 2;49(W1):W641-W653. doi: 10.1093/nar/gkab384.

14. Targeting the m(6)A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication.
Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Genes Dev. 2021 Jul 1;35(13-14):1005-1019. doi: 10.1101/gad.348320.121. Epub 2021 Jun 24.

15. NOVA2 regulates neural circRNA biogenesis.
Knupp D, Cooper DA, Saito Y, Darnell RB, Miura P. Nucleic Acids Res. 2021 Jul 9;49(12):6849-6862. doi: 10.1093/nar/gkab523.

16. Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection.
Triana S, Stanifer ML, Metz-Zumaran C, Shahraz M, Mukenhirn M, Kee C, Serger C, Koschny R, Ordoñez-Rueda D, Paulsen M, Benes V, Boulant S, Alexandrov T. Mol Syst Biol. 2021 Jul;17(7):e9833. doi: 10.15252/msb.20209833.

17. RHOX10 drives mouse spermatogonial stem cell establishment through a transcription factor signaling cascade.
Tan K, Song HW, Wilkinson MF. Cell Rep. 2021 Jul 20;36(3):109423. doi: 10.1016/j.celrep.2021.109423.

18. Glucosylceramide synthase deficiency in the heart compromises β1-adrenergic receptor trafficking.
Andersson L, Cinato M, Mardani I, Miljanovic A, Arif M, Koh A, Lindbom M, Laudette M, Bollano E, Omerovic E, Klevstig M, Henricsson M, Fogelstrand P, Swärd K, Ekstrand M, Levin M, Wikström J, Doran S, Hyötyläinen T, Sinisalu L, Orešič M, Tivesten Å, Adiels M, Bergo MO, Proia R, Mardinoglu A, Jeppsson A, Borén J, Levin MC. Eur Heart J. 2021 Jul 23:ehab412. doi: 10.1093/eurheartj/ehab412. Online ahead of print.

19. Single-cell dissection of cellular components and interactions shaping the tumor immune phenotypes in ovarian cancer.
Hornburg M, Desbois M, Lu S, Guan Y, Lo AA, Kaufman S, Elrod A, Lotstein A, DesRochers TM, Munoz-Rodriguez JL, Wang X, Giltnane J, Mayba O, Turley SJ, Bourgon R, Daemen A, Wang Y. Cancer Cell. 2021 Jul 12;39(7):928-944.e6. doi: 10.1016/j.ccell.2021.04.004. Epub 2021 May 6.

20. Neurotensin is an anti-thermogenic peptide produced by lymphatic endothelial cells.
Li J, Li E, Czepielewski RS, Chi J, Guo X, Han YH, Wang D, Wang L, Hu B, Dawes B, Jacobs C, Tenen D, Lin SJ, Lee B, Morris D, Tobias A, Randolph GJ, Cohen P, Tsai L, Rosen ED. Cell Metab. 2021 Jul 6;33(7):1449-1465.e6. doi: 10.1016/j.cmet.2021.04.019. Epub 2021 May 25.

21. Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore.
Pratanwanich PN, Yao F, Chen Y, Koh CWQ, Wan YK, Hendra C, Poon P, Goh YT, Yap PML, Chooi JY, Chng WJ, Ng SB, Thiery A, Goh WSS, Göke J. Nat Biotechnol. 2021 Jul 19. doi: 10.1038/s41587-021-00949-w. Online ahead of print.

22. Polyploid mitosis and depolyploidization promote chromosomal instability and tumor progression in a Notch-induced tumor model.
Wang XF, Yang SA, Gong S, Chang CH, Portilla JM, Chatterjee D, Irianto J, Bao H, Huang YC, Deng WM. Dev Cell. 2021 Jul 12;56(13):1976-1988.e4. doi: 10.1016/j.devcel.2021.05.017. Epub 2021 Jun 18.

23. Molecular characterization of projection neuron subtypes in the mouse olfactory bulb.
Zeppilli S, Ackels T, Attey R, Klimpert N, Kimberly Ritola D, Boeing S, Crombach A, Schaefer AT, Fleischmann A. Elife. 2021 Jul 22;10:e65445. doi: 10.7554/eLife.65445. Online ahead of print.

24. A likelihood-based deconvolution of bulk gene expression data using single-cell references.
Erdmann-Pham DD, Fischer J, Hong J, Song YS. Genome Res. 2021 Jul 22:gr.272344.120. doi: 10.1101/gr.272344.120. Online ahead of print.

25. Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction.
Creamer KM, Kolpa HJ, Lawrence JB. Mol Cell. 2021 Jul 20:S1097-2765(21)00556-6. doi: 10.1016/j.molcel.2021.07.004. Online ahead of print.

26. PseudoGA: cell pseudotime reconstruction based on genetic algorithm.
Mondal PK, Saha US, Mukhopadhyay I. Nucleic Acids Res. 2021 Jul 9:gkab457. doi: 10.1093/nar/gkab457. Online ahead of print.

27. DOT1L complex regulates transcriptional initiation in human erythroleukemic cells.
Wu A, Zhi J, Tian T, Cihan A, Cevher MA, Liu Z, David Y, Muir TW, Roeder RG, Yu M. Proc Natl Acad Sci U S A. 2021 Jul 6;118(27):e2106148118. doi: 10.1073/pnas.2106148118.

28. A safe and effective mucosal RSV vaccine in mice consisting of RSV phosphoprotein and flagellin variant.
Zhao B, Yang J, He B, Li X, Yan H, Liu S, Yang Y, Zhou D, Liu B, Fan X, Zhong M, Zhang E, Zhang F, Zhang Y, Chen YQ, Jiang S, Yan H. Cell Rep. 2021 Jul 20;36(3):109401. doi: 10.1016/j.celrep.2021.109401.

29. Transcriptional profiling of mESC-derived tendon and fibrocartilage cell fate switch.
Kaji DA, Montero AM, Patel R, Huang AH. Nat Commun. 2021 Jul 9;12(1):4208. doi: 10.1038/s41467-021-24535-5.

30. High-resolution, genome-wide mapping of positive supercoiling in chromosomes.
Guo MS, Kawamura R, Littlehale ML, Marko JF, Laub MT. Elife. 2021 Jul 19;10:e67236. doi: 10.7554/eLife.67236. Online ahead of print.

31. Dissecting spatial heterogeneity and the immune-evasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma.
Sun YF, Wu L, Liu SP, Jiang MM, Hu B, Zhou KQ, Guo W, Xu Y, Zhong Y, Zhou XR, Zhang ZF, Liu G, Liu S, Shi YH, Ji Y, Du M, Li NN, Li GB, Zhao ZK, Huang XY, Xu LQ, Yu QC, Peng DH, Qiu SJ, Sun HC, Dean M, Wang XD, Chung WY, Dennison AR, Zhou J, Hou Y, Fan J, Yang XR. Nat Commun. 2021 Jul 2;12(1):4091. doi: 10.1038/s41467-021-24386-0.

32. Engrailed 1 coordinates cytoskeletal reorganization to induce myofibroblast differentiation.
Györfi AH, Matei AE, Fuchs M, Liang C, Rigau AR, Hong X, Zhu H, Luber M, Bergmann C, Dees C, Ludolph I, Horch RE, Distler O, Wang J, Bengsch B, Schett G, Kunz M, Distler JHW. J Exp Med. 2021 Sep 6;218(9):e20201916. doi: 10.1084/jem.20201916. Epub 2021 Jul 14.

33. An unsupervised method for physical cell interaction profiling of complex tissues.
Andrews N, Serviss JT, Geyer N, Andersson AB, Dzwonkowska E, Šutevski I, Heijboer R, Baryawno N, Gerling M, Enge M. Nat Methods. 2021 Jul 12. doi: 10.1038/s41592-021-01196-2. Online ahead of print.

34. Chaperone-like protein DAY plays critical roles in photomorphogenesis.
Lee HS, Choi I, Jeon Y, Ahn HK, Cho H, Kim J, Kim JH, Lee JM, Lee S, Bünting J, Seo DH, Lee T, Lee DH, Lee I, Oh MH, Kim TW, Belkhadir Y, Pai HS. Nat Commun. 2021 Jul 7;12(1):4194. doi: 10.1038/s41467-021-24446-5.

35. Robust integration of multiple single-cell RNA sequencing datasets using a single reference space.
Liu Y, Wang T, Zhou B, Zheng D. Nat Biotechnol. 2021 Jul;39(7):877-884. doi: 10.1038/s41587-021-00859-x. Epub 2021 Mar 25.

36. Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data.
Kiniry SJ, Judge CE, Michel AM, Baranov PV. Nucleic Acids Res. 2021 Jul 2;49(W1):W662-W670. doi: 10.1093/nar/gkab323.

37. Mesothelial cells are not a source of adipocytes in mice.
Westcott GP, Emont MP, Li J, Jacobs C, Tsai L, Rosen ED. Cell Rep. 2021 Jul 13;36(2):109388. doi: 10.1016/j.celrep.2021.109388.

38. Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data.
Nakajima N, Hayashi T, Fujiki K, Shirahige K, Akiyama T, Akutsu T, Nakato R. Nucleic Acids Res. 2021 Jul 22:gkab601. doi: 10.1093/nar/gkab601. Online ahead of print.

39. Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy.
Richter ML, Deligiannis IK, Yin K, Danese A, Lleshi E, Coupland P, Vallejos CA, Matchett KP, Henderson NC, Colome-Tatche M, Martinez-Jimenez CP. Nat Commun. 2021 Jul 12;12(1):4264. doi: 10.1038/s41467-021-24543-5.

40. Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation.
Barile M, Imaz-Rosshandler I, Inzani I, Ghazanfar S, Nichols J, Marioni JC, Guibentif C, Göttgens B. Genome Biol. 2021 Jul 5;22(1):197. doi: 10.1186/s13059-021-02414-y.

41. AP-2alpha-mediated activation of E2F and EZH2 drives melanoma metastasis.
White JR, Thompson DT, Koch KE, Kiriazov BS, Beck AC, van der Heide DM, Grimm BG, Kulak MV, Weigel RJ. Cancer Res. 2021 Jul 1:canres.0772.2021. doi: 10.1158/0008-5472.CAN-21-0772. Online ahead of print.

42. Locus-Specific Characterization of Human Endogenous Retrovirus Expression in Prostate, Breast, and Colon Cancers.
Steiner MC, Marston JL, Iñiguez LP, Bendall ML, Chiappinelli KB, Nixon DF, Crandall KA. Cancer Res. 2021 Jul 1;81(13):3449-3460. doi: 10.1158/0008-5472.CAN-20-3975. Epub 2021 May 3.

43. TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles.
Han M, Liu X, Zhang W, Wang M, Bu W, Chang C, Yu M, Li Y, Tian C, Yang X, Zhu Y, He F. Nucleic Acids Res. 2021 Jul 27:gkab629. doi: 10.1093/nar/gkab629. Online ahead of print.

44. Transcriptome profiles of stem-like cells from primary breast cancers allow identification of ITGA7 as a predictive marker of chemotherapy response.
Gwili N, Jones SJ, Amri WA, Carr IM, Harris S, Hogan BV, Hughes WE, Kim B, Langlands FE, Millican-Slater RA, Pramanik A, Thorne JL, Verghese ET, Wells G, Hamza M, Younis L, El Deeb NMF, Hughes TA. Br J Cancer. 2021 Jul 12. doi: 10.1038/s41416-021-01484-w. Online ahead of print.

45. RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors.
Shigematsu M, Kawamura T, Morichika K, Izumi N, Kiuchi T, Honda S, Pliatsika V, Matsubara R, Rigoutsos I, Katsuma S, Tomari Y, Kirino Y. Nat Commun. 2021 Jul 23;12(1):4498. doi: 10.1038/s41467-021-24681-w.

46. Microglia in Alzheimer's disease at single-cell level. Are there common patterns in humans and mice?.
Chen Y, Colonna M. J Exp Med. 2021 Sep 6;218(9):e20202717. doi: 10.1084/jem.20202717. Epub 2021 Jul 22.

47. Spatiotemporal dynamics of inner ear sensory and non-sensory cells revealed by single-cell transcriptomics.
Jan TA, Eltawil Y, Ling AH, Chen L, Ellwanger DC, Heller S, Cheng AG. Cell Rep. 2021 Jul 13;36(2):109358. doi: 10.1016/j.celrep.2021.109358.

48. Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes.
Zhu C, Wu J, Sun H, Briganti F, Meder B, Wei W, Steinmetz LM. Nat Commun. 2021 Jul 9;12(1):4203. doi: 10.1038/s41467-021-24484-z.

49. Single-cell analyses reveal diverse mechanisms of resistance to EGFR tyrosine kinase inhibitors in lung cancer.
Kashima Y, Shibahara D, Suzuki A, Muto K, Kobayashi IS, Plotnick D, Udagawa H, Izumi H, Shibata Y, Tanaka K, Fujii M, Ohashi A, Seki M, Goto K, Tuchihara K, Suzuki Y, Kobayashi SS. Cancer Res. 2021 Jul 9:canres.2811.2020. doi: 10.1158/0008-5472.CAN-20-2811. Online ahead of print.

50. GapClust is a light-weight approach distinguishing rare cells from voluminous single cell expression profiles.
Fa B, Wei T, Zhou Y, Johnston L, Yuan X, Ma Y, Zhang Y, Yu Z. Nat Commun. 2021 Jul 7;12(1):4197. doi: 10.1038/s41467-021-24489-8.

51. YAP1 nuclear efflux and transcriptional reprograming follow membrane diminution upon VSV-G-induced cell fusion.
Feliciano D, Ott CM, Espinosa-Medina I, Weigel AV, Benedetti L, Milano KM, Tang Z, Lee T, Kliman HJ, Guller SM, Lippincott-Schwartz J. Nat Commun. 2021 Jul 23;12(1):4502. doi: 10.1038/s41467-021-24708-2.

52. Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters.
Shen Y, Pressman A, Janzen E, Chen IA. Nucleic Acids Res. 2021 Jul 9;49(12):e67. doi: 10.1093/nar/gkab199.

53. Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis.
Liu M, Cao S, He L, Gao J, Arab JP, Cui H, Xuan W, Gao Y, Sehrawat TS, Hamdan FH, Ventura-Cots M, Argemi J, Pomerantz WCK, Johnsen SA, Lee JH, Gao F, Ordog T, Mathurin P, Revzin A, Bataller R, Yan H, Shah VH. Nat Commun. 2021 Jul 27;12(1):4560. doi: 10.1038/s41467-021-24843-w.

54. ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses.
Herzner AM, Khan Z, Van Nostrand EL, Chan S, Cuellar T, Chen R, Pechuan-Jorge X, Komuves L, Solon M, Modrusan Z, Haley B, Yeo GW, Behrens TW, Albert ML. J Exp Med. 2021 Sep 6;218(9):e20201833. doi: 10.1084/jem.20201833. Epub 2021 Jul 23.

55. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.
Bucchini F, Del Cortona A, Kreft Ł, Botzki A, Van Bel M, Vandepoele K. Nucleic Acids Res. 2021 Jul 1:gkab565. doi: 10.1093/nar/gkab565. Online ahead of print.

56. Pain and itch processing by subpopulations of molecularly diverse spinal and trigeminal projection neurons.
Wercberger R, Braz JM, Weinrich JA, Basbaum AI. Proc Natl Acad Sci U S A. 2021 Jul 13;118(28):e2105732118. doi: 10.1073/pnas.2105732118.

57. Natural selection shapes maintenance of orthologous sRNAs in divergent host-restricted bacterial genomes.
Thairu MW, Meduri VRS, Degnan PH, Hansen AK. Mol Biol Evol. 2021 Jul 2:msab202. doi: 10.1093/molbev/msab202. Online ahead of print.

58. Rapid spread of a densovirus in a major crop pest following wide-scale adoption of Bt-cotton in China.
Xiao Y, Li W, Yang X, Xu P, Jin M, Yuan H, Zheng W, Soberón M, Bravo A, Wilson K, Wu K. Elife. 2021 Jul 15;10:e66913. doi: 10.7554/eLife.66913. Online ahead of print.

59. The branched-chain amino acid aminotransferase TaBCAT1 modulates amino acid metabolism and positively regulates wheat rust susceptibility.
Corredor-Moreno P, Minter F, Davey PE, Wegel E, Kular B, Brett P, Lewis CM, Morgan YML, Macías Pérez LA, Korolev AV, Hill L, Saunders DGO. Plant Cell. 2021 Jul 2;33(5):1728-1747. doi: 10.1093/plcell/koab049.

60. Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa.
Li S, Weng Y, Li X, Yue Z, Chai Z, Zhang X, Gong X, Pan X, Jin Y, Bai F, Cheng Z, Wu W. Nucleic Acids Res. 2021 Jul 9;49(12):6756-6770. doi: 10.1093/nar/gkab506.

61. RBFOX2 alters splicing outcome in distinct binding modes with multiple protein partners.
Zhou D, Couture S, Scott MS, Abou Elela S. Nucleic Acids Res. 2021 Jul 9:gkab595. doi: 10.1093/nar/gkab595. Online ahead of print.

62. Inconsistent prediction capability of ImmuneCells.Sig across different RNA-seq datasets.
Xiao X, Xu C, Yang W, Yu R. Nat Commun. 2021 Jul 7;12(1):4167. doi: 10.1038/s41467-021-24303-5.

63. M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity.
Bag I, Chen S, Rosin LF, Chen Y, Liu CY, Yu GY, Lei EP. Nat Commun. 2021 Jul 7;12(1):4170. doi: 10.1038/s41467-021-24407-y.

64. Multiplexed functional genomic analysis of 5' untranslated region mutations across the spectrum of prostate cancer.
Lim Y, Arora S, Schuster SL, Corey L, Fitzgibbon M, Wladyka CL, Wu X, Coleman IM, Delrow JJ, Corey E, True LD, Nelson PS, Ha G, Hsieh AC. Nat Commun. 2021 Jul 9;12(1):4217. doi: 10.1038/s41467-021-24445-6.

65. Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells.
Soares MAF, Soares DS, Teixeira V, Heskol A, Bressan RB, Pollard SM, Oliveira RA, Castro DS. Genes Dev. 2021 Jul 1;35(13-14):1020-1034. doi: 10.1101/gad.348174.120. Epub 2021 Jun 24.

66. Chondrocytes in the resting zone of the growth plate are maintained in a Wnt-inhibitory environment.
Hallett SA, Matsushita Y, Ono W, Sakagami N, Mizuhashi K, Tokavanich N, Nagata M, Zhou A, Hirai T, Kronenberg HM, Ono N. Elife. 2021 Jul 26;10:e64513. doi: 10.7554/eLife.64513.

67. The Mediator subunit MED20 organizes the early adipogenic complex to promote development of adipose tissues and diet-induced obesity.
Tang WS, Weng L, Wang X, Liu CQ, Hu GS, Yin ST, Tao Y, Hong NN, Guo H, Liu W, Wang HR, Zhao TJ. Cell Rep. 2021 Jul 6;36(1):109314. doi: 10.1016/j.celrep.2021.109314.

68. Heterogeneity of neurons reprogrammed from spinal cord astrocytes by the proneural factors Ascl1 and Neurogenin2.
Kempf J, Knelles K, Hersbach BA, Petrik D, Riedemann T, Bednarova V, Janjic A, Simon-Ebert T, Enard W, Smialowski P, Götz M, Masserdotti G. Cell Rep. 2021 Jul 20;36(3):109409. doi: 10.1016/j.celrep.2021.109409.

69. Inferring single cell expression profiles from overlapped pooling sequencing data with compressed sensing strategy.
Huang M, Yang Y, Wen X, Xu W, Lu N, Sun X, Tu J, Lu Z. Nucleic Acids Res. 2021 Jul 9:gkab581. doi: 10.1093/nar/gkab581. Online ahead of print.

70. Reply to: "Inconsistent prediction capability of ImmuneCells.Sig across different RNA-seq datasets".
Xiong D, Wang Y, You M. Nat Commun. 2021 Jul 7;12(1):4168. doi: 10.1038/s41467-021-24304-4.

71. Increased APOE ε4 expression is associated with the difference in Alzheimer's disease risk from diverse ancestral backgrounds.
Griswold AJ, Celis K, Bussies PL, Rajabli F, Whitehead PL, Hamilton-Nelson KL, Beecham GW, Dykxhoorn DM, Nuytemans K, Wang L, Gardner OK, Dorfsman DA, Bigio EH, Mesulam MM, Weintraub S, Geula C, Gearing M, McGrath-Martinez E, Dalgard CL, Scott WK, Haines JL, Pericak-Vance MA, Young JI, Vance JM. Alzheimers Dement. 2021 Jul;17(7):1179-1188. doi: 10.1002/alz.12287. Epub 2021 Feb 1.

72. Nasal ciliated cells are primary targets for SARS-CoV-2 replication in the early stage of COVID-19.
Ahn JH, Kim J, Hong SP, Choi SY, Yang MJ, Ju YS, Kim YT, Kim HM, Rahman MDT, Chung MK, Hong SD, Bae H, Lee CS, Koh GY. J Clin Invest. 2021 Jul 1;131(13):e148517. doi: 10.1172/JCI148517.

73. Extracellular matrix protein-1 secretory isoform promotes ovarian cancer through increasing alternative mRNA splicing and stemness.
Yin H, Wang J, Li H, Yu Y, Wang X, Lu L, Lv C, Chang B, Jin W, Guo W, Ren C, Yang G. Nat Commun. 2021 Jul 9;12(1):4230. doi: 10.1038/s41467-021-24315-1.

74. Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons.
Ichihara K, Matsumoto A, Nishida H, Kito Y, Shimizu H, Shichino Y, Iwasaki S, Imami K, Ishihama Y, Nakayama KI. Nucleic Acids Res. 2021 Jul 21;49(13):7298-7317. doi: 10.1093/nar/gkab549.