Monthly Letter

1. Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients.
Bost P, Giladi A, Liu Y, Bendjelal Y, Xu G, David E, Blecher-Gonen R, Cohen M, Medaglia C, Li H, Deczkowska A, Zhang S, Schwikowski B, Zhang Z, Amit I. Cell. 2020 Jun 25;181(7):1475-1488.e12. doi: 10.1016/j.cell.2020.05.006. Epub 2020 May 8.

2. A single-cell atlas of the peripheral immune response in patients with severe COVID-19.
Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T, Simpson LJ, Grant P, Subramanian A, Rogers AJ, Blish CA. Nat Med. 2020 Jun 8. doi: 10.1038/s41591-020-0944-y. Online ahead of print.

3. Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma.
Ooi WF, Nargund AM, Lim KJ, Zhang S, Xing M, Mandoli A, Lim JQ, Ho SWT, Guo Y, Yao X, Lin SJ, Nandi T, Xu C, Ong X, Lee M, Tan AL, Lam YN, Teo JX, Kaneda A, White KP, Lim WK, Rozen SG, Teh BT, Li S, Skanderup AJ, Tan P. Gut. 2020 Jun;69(6):1039-1052. doi: 10.1136/gutjnl-2018-317612. Epub 2019 Sep 21.

4. Tobacco Smoking Increases the Lung Gene Expression of ACE2, the Receptor of SARS-CoV-2.
Cai G, Bossé Y, Xiao F, Kheradmand F, Amos CI. Am J Respir Crit Care Med. 2020 Jun 15;201(12):1557-1559. doi: 10.1164/rccm.202003-0693LE.

5. Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer.
Shu S, Wu HJ, Ge JY, Zeid R, Harris IS, Jovanović B, Murphy K, Wang B, Qiu X, Endress JE, Reyes J, Lim K, Font-Tello A, Syamala S, Xiao T, Reddy Chilamakuri CS, Papachristou EK, D'Santos C, Anand J, Hinohara K, Li W, McDonald TO, Luoma A, Modiste RJ, Nguyen QD, Michel B, Cejas P, Kadoch C, Jaffe JD, Wucherpfennig KW, Qi J, Liu XS, Long H, Brown M, Carroll JS, Brugge JS, Bradner J, Michor F, Polyak K. Mol Cell. 2020 Jun 18;78(6):1096-1113.e8. doi: 10.1016/j.molcel.2020.04.027. Epub 2020 May 15.

6. Opposing Functions of BRD4 Isoforms in Breast Cancer.
Wu SY, Lee CF, Lai HT, Yu CT, Lee JE, Zuo H, Tsai SY, Tsai MJ, Ge K, Wan Y, Chiang CM. Mol Cell. 2020 Jun 18;78(6):1114-1132.e10. doi: 10.1016/j.molcel.2020.04.034. Epub 2020 May 23.

7. Minimal PD-1 expression in mouse and human NK cells under diverse conditions.
Judge SJ, Dunai C, Aguilar EG, Vick SC, Sturgill IR, Khuat LT, Stoffel KM, Van Dyke J, Longo DL, Darrow MA, Anderson SK, Blazar BR, Monjazeb AM, Serody JS, Canter RJ, Murphy WJ. J Clin Invest. 2020 Jun 1;130(6):3051-3068. doi: 10.1172/JCI133353.

8. Single-cell transcriptional analyses of spasmolytic polypeptide-expressing metaplasia arising from acute drug injury and chronic inflammation in the stomach.
Bockerstett KA, Lewis SA, Wolf KJ, Noto CN, Jackson NM, Ford EL, Ahn TH, DiPaolo RJ. Version 2. Gut. 2020 Jun;69(6):1027-1038. doi: 10.1136/gutjnl-2019-318930. Epub 2019 Sep 3.

9. Serine-threonine kinase ROCK2 regulates germinal center B cell positioning and cholesterol biosynthesis.
Ricker E, Chinenov Y, Pannellini T, Flores-Castro D, Ye C, Gupta S, Manni M, Liao JK, Pernis AB. J Clin Invest. 2020 Jun 2:132414. doi: 10.1172/JCI132414. Online ahead of print.

10. SETD2 deficiency accelerates MDS-associated leukemogenesis via S100a9 in NHD13 mice and predicts poor prognosis in MDS.
Chen BY, Song J, Hu CL, Chen SB, Zhang Q, Xu CH, Wu JC, Hou D, Sun M, Zhang YL, Liu N, Yu PC, Liu P, Zong LJ, Zhang JY, Dai RF, Lan F, Huang QH, Zhang SJ, Nimer SD, Chen Z, Chen SJ, Sun XJ, Wang L. Blood. 2020 Jun 18;135(25):2271-2285. doi: 10.1182/blood.2019001963.

11. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Ding J, Adiconis X, Simmons SK, Kowalczyk MS, Hession CC, Marjanovic ND, Hughes TK, Wadsworth MH, Burks T, Nguyen LT, Kwon JYH, Barak B, Ge W, Kedaigle AJ, Carroll S, Li S, Hacohen N, Rozenblatt-Rosen O, Shalek AK, Villani AC, Regev A, Levin JZ. Nat Biotechnol. 2020 Jun;38(6):737-746. doi: 10.1038/s41587-020-0465-8. Epub 2020 Apr 6.

12. Single-Cell RNA-Seq Mapping of Human Thymopoiesis Reveals Lineage Specification Trajectories and a Commitment Spectrum in T Cell Development.
Le J, Park JE, Ha VL, Luong A, Branciamore S, Rodin AS, Gogoshin G, Li F, Loh YE, Camacho V, Patel SB, Welner RS, Parekh C. Immunity. 2020 Jun 16;52(6):1105-1118.e9. doi: 10.1016/j.immuni.2020.05.010.

13. Temporal specificity and heterogeneity of Drosophila immune cells.
Cattenoz PB, Sakr R, Pavlidaki A, Delaporte C, Riba A, Molina N, Hariharan N, Mukherjee T, Giangrande A. EMBO J. 2020 Jun 17;39(12):e104486. doi: 10.15252/embj.2020104486. Epub 2020 Mar 12.

14. Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis.
Shami AN, Zheng X, Munyoki SK, Ma Q, Manske GL, Green CD, Sukhwani M, Orwig KE, Li JZ, Hammoud SS. Dev Cell. 2020 Jun 5:S1534-5807(20)30399-3. doi: 10.1016/j.devcel.2020.05.010. Online ahead of print.

15. Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes.
Heaton H, Talman AM, Knights A, Imaz M, Gaffney DJ, Durbin R, Hemberg M, Lawniczak MKN. Nat Methods. 2020 Jun;17(6):615-620. doi: 10.1038/s41592-020-0820-1. Epub 2020 May 4.

16. Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain.
Huang AY, Li P, Rodin RE, Kim SN, Dou Y, Kenny CJ, Akula SK, Hodge RD, Bakken TE, Miller JA, Lein ES, Park PJ, Lee EA, Walsh CA. Proc Natl Acad Sci U S A. 2020 Jun 23;117(25):13886-13895. doi: 10.1073/pnas.2006163117. Epub 2020 Jun 10.

17. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.
Lavaert M, Liang KL, Vandamme N, Park JE, Roels J, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Vandekerckhove B, Leclercq G, Regev A, Van Vlierberghe P, Guilliams M, Teichmann SA, Saeys Y, Taghon T. Immunity. 2020 Jun 16;52(6):1088-1104.e6. doi: 10.1016/j.immuni.2020.03.019. Epub 2020 Apr 17.

18. A decade of advances in transposon-insertion sequencing.
Cain AK, Barquist L, Goodman AL, Paulsen IT, Parkhill J, van Opijnen T. Nat Rev Genet. 2020 Jun 12:1-15. doi: 10.1038/s41576-020-0244-x. Online ahead of print.

19. CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity.
Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, Tsai SQ. Nat Biotechnol. 2020 Jun 15. doi: 10.1038/s41587-020-0555-7. Online ahead of print.

20. Pan-Genome of Wild and Cultivated Soybeans.
Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z. Cell. 2020 Jun 15:S0092-8674(20)30618-8. doi: 10.1016/j.cell.2020.05.023. Online ahead of print.

21. Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA.
Pan H, Jin M, Ghadiyaram A, Kaur P, Miller HE, Ta HM, Liu M, Fan Y, Mahn C, Gorthi A, You C, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Nucleic Acids Res. 2020 Jun 4;48(10):5639-5655. doi: 10.1093/nar/gkaa284.

22. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
Mereu E, Lafzi A, Moutinho C, Ziegenhain C, McCarthy DJ, Álvarez-Varela A, Batlle E, Sagar, Grün D, Lau JK, Boutet SC, Sanada C, Ooi A, Jones RC, Kaihara K, Brampton C, Talaga Y, Sasagawa Y, Tanaka K, Hayashi T, Braeuning C, Fischer C, Sauer S, Trefzer T, Conrad C, Adiconis X, Nguyen LT, Regev A, Levin JZ, Parekh S, Janjic A, Wange LE, Bagnoli JW, Enard W, Gut M, Sandberg R, Nikaido I, Gut I, Stegle O, Heyn H. Nat Biotechnol. 2020 Jun;38(6):747-755. doi: 10.1038/s41587-020-0469-4. Epub 2020 Apr 6.

23. Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator.
Mizrak D, Bayin NS, Yuan J, Liu Z, Suciu RM, Niphakis MJ, Ngo N, Lum KM, Cravatt BF, Joyner AL, Sims PA. Cell Rep. 2020 Jun 23;31(12):107805. doi: 10.1016/j.celrep.2020.107805.

24. scIGANs: single-cell RNA-seq imputation using generative adversarial networks.
Xu Y, Zhang Z, You L, Liu J, Fan Z, Zhou X. Nucleic Acids Res. 2020 Jun 26:gkaa506. doi: 10.1093/nar/gkaa506. Online ahead of print.

25. A single-cell transcriptomic and anatomic atlas of mouse dorsal raphe Pet1 neurons.
Okaty BW, Sturrock N, Escobedo Lozoya Y, Chang Y, Senft RA, Lyon KA, Alekseyenko OV, Dymecki SM. Elife. 2020 Jun 22;9:e55523. doi: 10.7554/eLife.55523.

26. Expansion of GGC Repeat in GIPC1 Is Associated with Oculopharyngodistal Myopathy.
Deng J, Yu J, Li P, Luan X, Cao L, Zhao J, Yu M, Zhang W, Lv H, Xie Z, Meng L, Zheng Y, Zhao Y, Gang Q, Wang Q, Liu J, Zhu M, Guo X, Su Y, Liang Y, Liang F, Hayashi T, Maeda MH, Sato T, Ura S, Oya Y, Ogasawara M, Iida A, Nishino I, Zhou C, Yan C, Yuan Y, Hong D, Wang Z. Am J Hum Genet. 2020 Jun 4;106(6):793-804. doi: 10.1016/j.ajhg.2020.04.011. Epub 2020 May 14.

27. Targeted Perturb-seq enables genome-scale genetic screens in single cells.
Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, Korbel JO, Merten CA, Velten L, Steinmetz LM. Nat Methods. 2020 Jun;17(6):629-635. doi: 10.1038/s41592-020-0837-5. Epub 2020 Jun 1.

28. Putative cell type discovery from single-cell gene expression data.
Miao Z, Moreno P, Huang N, Papatheodorou I, Brazma A, Teichmann SA. Nat Methods. 2020 Jun;17(6):621-628. doi: 10.1038/s41592-020-0825-9. Epub 2020 May 18.

29. Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract.
Smith JC, Sausville EL, Girish V, Yuan ML, Vasudevan A, John KM, Sheltzer JM. Dev Cell. 2020 Jun 8;53(5):514-529.e3. doi: 10.1016/j.devcel.2020.05.012. Epub 2020 May 16.

30. ATF3 coordinates anti-tumor synergy between epigenetic drugs and protein disulfide isomerase inhibitors.
Duncan RM, Reyes L, Moats K, Robinson RM, Murphy SA, Kaur B, Stessman HAF, Dolloff NG. Cancer Res. 2020 Jun 19:canres.4046.2019. doi: 10.1158/0008-5472.CAN-19-4046. Online ahead of print.

31. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows.
Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, Poppe D, Clément O, Simmons RK, Lister R, Forrest ARR. Genome Biol. 2020 Jun 2;21(1):130. doi: 10.1186/s13059-020-02048-6.

32. A genomic cluster containing novel and conserved genes is associated with cichlid fish dental developmental convergence.
Karagic N, Schneider RF, Meyer A, Hulsey CD. Mol Biol Evol. 2020 Jun 24:msaa153. doi: 10.1093/molbev/msaa153. Online ahead of print.

33. MEIS-mediated suppression of human prostate cancer growth and metastasis through HOXB13-dependent regulation of proteoglycans.
VanOpstall C, Perike S, Brechka H, Gillard M, Lamperis S, Zhu B, Brown R, Bhanvadia R, Vander Griend DJ. Elife. 2020 Jun 18;9:e53600. doi: 10.7554/eLife.53600. Online ahead of print.

34. Dissecting transcriptional heterogeneity in primary gastric adenocarcinoma by single cell RNA sequencing.
Zhang M, Hu S, Min M, Ni Y, Lu Z, Sun X, Wu J, Liu B, Ying X, Liu Y. Gut. 2020 Jun 12:gutjnl-2019-320368. doi: 10.1136/gutjnl-2019-320368. Online ahead of print.

35. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation.
Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer MW. Genes Dev. 2020 Jun 4. doi: 10.1101/gad.335794.119. Online ahead of print.

36. A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation.
Yeo GHT, Lin L, Qi CY, Cha M, Gifford DK, Sherwood RI. Cell Stem Cell. 2020 Jun 4;26(6):938-950.e6. doi: 10.1016/j.stem.2020.04.020. Epub 2020 May 26.

37. Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.
Spakowicz D, Lou S, Barron B, Gomez JL, Li T, Liu Q, Grant N, Yan X, Hoyd R, Weinstock G, Chupp GL, Gerstein M. Genome Biol. 2020 Jun 22;21(1):150. doi: 10.1186/s13059-020-02033-z.

38. Putative regulators for the continuum of erythroid differentiation revealed by single-cell transcriptome of human BM and UCB cells.
Huang P, Zhao Y, Zhong J, Zhang X, Liu Q, Qiu X, Chen S, Yan H, Hillyer C, Mohandas N, Pan X, Xu X. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12868-12876. doi: 10.1073/pnas.1915085117. Epub 2020 May 26.

39. Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Androvic P, Kirdajova D, Tureckova J, Zucha D, Rohlova E, Abaffy P, Kriska J, Valny M, Anderova M, Kubista M, Valihrach L. Cell Rep. 2020 Jun 16;31(11):107777. doi: 10.1016/j.celrep.2020.107777.

40. Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics.
Maddirevula S, Kuwahara H, Ewida N, Shamseldin HE, Patel N, Alzahrani F, AlSheddi T, AlObeid E, Alenazi M, Alsaif HS, Alqahtani M, AlAli M, Al Ali H, Helaby R, Ibrahim N, Abdulwahab F, Hashem M, Hanna N, Monies D, Derar N, Alsagheir A, Alhashem A, Alsaleem B, Alhebbi H, Wali S, Umarov R, Gao X, Alkuraya FS. Genome Biol. 2020 Jun 17;21(1):145. doi: 10.1186/s13059-020-02053-9.

41. Combining single-cell RNA-sequencing with a molecular atlas unveils new markers for Caenorhabditis elegans neuron classes.
Lorenzo R, Onizuka M, Defrance M, Laurent P. Nucleic Acids Res. 2020 Jun 15:gkaa486. doi: 10.1093/nar/gkaa486. Online ahead of print.

42. CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data.
Ni Z, Chen S, Brown J, Kendziorski C. Genome Biol. 2020 Jun 8;21(1):137. doi: 10.1186/s13059-020-02054-8.

43. Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells.
Gao P, Chen C, Howell ED, Li Y, Tober J, Uzun Y, He B, Gao L, Zhu Q, Siekmann AF, Speck NA, Tan K. Genes Dev. 2020 Jun 4. doi: 10.1101/gad.338202.120. Online ahead of print.

44. SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins.
Chen F, Keleş S. Genome Biol. 2020 Jun 12;21(1):139. doi: 10.1186/s13059-020-02039-7.

45. 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize.
Sun Y, Dong L, Zhang Y, Lin D, Xu W, Ke C, Han L, Deng L, Li G, Jackson D, Li X, Yang F. Genome Biol. 2020 Jun 16;21(1):143. doi: 10.1186/s13059-020-02063-7.

46. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.
Ji AL, Rubin AJ, Thrane K, Jiang S, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA. Cell. 2020 Jun 19:S0092-8674(20)30672-3. doi: 10.1016/j.cell.2020.05.039. Online ahead of print.

47. Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing.
Kim D, Lee YS, Jung SJ, Yeo J, Seo JJ, Lee YY, Lim J, Chang H, Song J, Yang J, Kim JS, Jung G, Ahn K, Kim VN. Nat Struct Mol Biol. 2020 Jun;27(6):581-588. doi: 10.1038/s41594-020-0427-3. Epub 2020 May 25.

48. EXOSC10 sculpts the transcriptome during the growth-to-maturation transition in mouse oocytes.
Wu D, Dean J. Nucleic Acids Res. 2020 Jun 4;48(10):5349-5365. doi: 10.1093/nar/gkaa249.

49. Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms.
Levin M, Zalts H, Mostov N, Hashimshony T, Yanai I. Nucleic Acids Res. 2020 Jun 19;48(11):5926-5938. doi: 10.1093/nar/gkaa359.

50. An entropy-based metric for assessing the purity of single cell populations.
Liu B, Li C, Li Z, Wang D, Ren X, Zhang Z. Nat Commun. 2020 Jun 22;11(1):3155. doi: 10.1038/s41467-020-16904-3.

51. scClassify: sample size estimation and multiscale classification of cells using single and multiple reference.
Lin Y, Cao Y, Kim HJ, Salim A, Speed TP, Lin DM, Yang P, Yang JYH. Mol Syst Biol. 2020 Jun;16(6):e9389. doi: 10.15252/msb.20199389.

52. Regional Variation of Splicing QTLs in Human Brain.
Zhang Y, Yang HT, Kadash-Edmondson K, Pan Y, Pan Z, Davidson BL, Xing Y. Am J Hum Genet. 2020 Jun 22:S0002-9297(20)30190-7. doi: 10.1016/j.ajhg.2020.06.002. Online ahead of print.

53. Functional Divergence of the Arabidopsis Florigen-Interacting bZIP Transcription Factors FD and FDP.
Romera-Branchat M, Severing E, Pocard C, Ohr H, Vincent C, Née G, Martinez-Gallegos R, Jang S, Lalaguna FA, Madrigal P, Coupland G. Cell Rep. 2020 Jun 2;31(9):107717. doi: 10.1016/j.celrep.2020.107717.

54. PRMT1-p53 Pathway Controls Epicardial EMT and Invasion.
Jackson-Weaver O, Ungvijanpunya N, Yuan Y, Qian J, Gou Y, Wu J, Shen H, Chen Y, Li M, Richard S, Chai Y, Sucov HM, Xu J. Cell Rep. 2020 Jun 9;31(10):107739. doi: 10.1016/j.celrep.2020.107739.

55. Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications.
Kimura S, Dedon PC, Waldor MK. Nat Chem Biol. 2020 Jun 8. doi: 10.1038/s41589-020-0558-1. Online ahead of print.

56. Spatial organization-dependent EphA2 transcriptional responses revealed by ligand nanocalipers.
Verheyen T, Fang T, Lindenhofer D, Wang Y, Akopyan K, Lindqvist A, Högberg B, Teixeira AI. Nucleic Acids Res. 2020 Jun 4;48(10):5777-5787. doi: 10.1093/nar/gkaa274.

57. RIC-seq for global in situ profiling of RNA-RNA spatial interactions.
Cai Z, Cao C, Ji L, Ye R, Wang D, Xia C, Wang S, Du Z, Hu N, Yu X, Chen J, Wang L, Yang X, He S, Xue Y. Nature. 2020 Jun;582(7812):432-437. doi: 10.1038/s41586-020-2249-1. Epub 2020 May 6.

58. Prediction of condition-specific regulatory genes using machine learning.
Song Q, Lee J, Akter S, Rogers M, Grene R, Li S. Nucleic Acids Res. 2020 Jun 19;48(11):e62. doi: 10.1093/nar/gkaa264.

59. Prp5-Spt8/Spt3 interaction mediates a reciprocal coupling between splicing and transcription.
Shao W, Ding Z, Zheng ZZ, Shen JJ, Shen YX, Pu J, Fan YJ, Query CC, Xu YZ. Nucleic Acids Res. 2020 Jun 19;48(11):5799-5813. doi: 10.1093/nar/gkaa311.

60. Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.
Sas-Chen A, Thomas JM, Matzov D, Taoka M, Nance KD, Nir R, Bryson KM, Shachar R, Liman GLS, Burkhart BW, Gamage ST, Nobe Y, Briney CA, Levy MJ, Fuchs RT, Robb GB, Hartmann J, Sharma S, Lin Q, Florens L, Washburn MP, Isobe T, Santangelo TJ, Shalev-Benami M, Meier JL, Schwartz S. Nature. 2020 Jun 17. doi: 10.1038/s41586-020-2418-2. Online ahead of print.

61. Developmentally Programmed Tankyrase Activity Upregulates β-Catenin and Licenses Progression of Embryonic Genome Activation.
Gambini A, Stein P, Savy V, Grow EJ, Papas BN, Zhang Y, Kenan AC, Padilla-Banks E, Cairns BR, Williams CJ. Dev Cell. 2020 Jun 8;53(5):545-560.e7. doi: 10.1016/j.devcel.2020.04.018. Epub 2020 May 21.

62. GWAS Functional Variant rs2076295 Regulates Desmoplakin (DSP) Expression in Airway Epithelial Cells.
Hao Y, Bates S, Mou H, Yun JH, Pham B, Liu J, Qiu W, Guo F, Morrow JD, Hersh CP, Benway CJ, Gong L, Zhang Y, Rosas IO, Cho MH, Park JA, Castaldi PJ, Du F, Zhou X. Am J Respir Crit Care Med. 2020 Jun 18. doi: 10.1164/rccm.201910-1958OC. Online ahead of print.

63. Dek Modulates Global Intron Retention during Muscle Stem Cells Quiescence Exit.
Yue L, Wan R, Luan S, Zeng W, Cheung TH. Dev Cell. 2020 Jun 22;53(6):661-676.e6. doi: 10.1016/j.devcel.2020.05.006. Epub 2020 Jun 4.

64. Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters.
Ni W, Perez AA, Schreiner S, Nicolet CM, Farnham PJ. Nucleic Acids Res. 2020 Jun 19;48(11):5986-6000. doi: 10.1093/nar/gkaa384.

65. Single-cell transcriptome and antigen-immunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer.
Chen J, Tan Y, Sun F, Hou L, Zhang C, Ge T, Yu H, Wu C, Zhu Y, Duan L, Wu L, Song N, Zhang L, Zhang W, Wang D, Chen C, Wu C, Jiang G, Zhang P. Genome Biol. 2020 Jun 24;21(1):152. doi: 10.1186/s13059-020-02064-6.

66. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes.
Kim S, Piquerez SJM, Ramirez-Prado JS, Mastorakis E, Veluchamy A, Latrasse D, Manza-Mianza D, Brik-Chaouche R, Huang Y, Rodriguez-Granados NY, Concia L, Blein T, Citerne S, Bendahmane A, Bergounioux C, Crespi M, Mahfouz MM, Raynaud C, Hirt H, Ntoukakis V, Benhamed M. Nucleic Acids Res. 2020 Jun 19;48(11):5953-5966. doi: 10.1093/nar/gkaa369.

67. Uncovering the key dimensions of high-throughput biomolecular data using deep learning.
Zhang S, Li X, Lin Q, Lin J, Wong KC. Nucleic Acids Res. 2020 Jun 4;48(10):e56. doi: 10.1093/nar/gkaa191.

68. Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression.
Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremins JE. Nat Neurosci. 2020 Jun;23(6):707-717. doi: 10.1038/s41593-020-0634-6. Epub 2020 May 25.

69. Transcriptome-wide organization of subcellular microenvironments revealed by ATLAS-Seq.
Adekunle DA, Wang ET. Nucleic Acids Res. 2020 Jun 19;48(11):5859-5872. doi: 10.1093/nar/gkaa334.

70. Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing.
Farouni R, Djambazian H, Ferri LE, Ragoussis J, Najafabadi HS. Nat Commun. 2020 Jun 1;11(1):2704. doi: 10.1038/s41467-020-16522-z.

71. 3D model of harlequin ichthyosis reveals inflammatory therapeutic targets.
Enjalbert F, Dewan P, Caley MP, Jones EM, Morse MA, Kelsell DP, Enright AJ, O'Toole EA. J Clin Invest. 2020 Jun 16:132987. doi: 10.1172/JCI132987. Online ahead of print.

72. Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis.
Li Y, Liu Y, Yang H, Zhang T, Naruse K, Tu Q. Genome Res. 2020 Jun 26:gr.258871.119. doi: 10.1101/gr.258871.119. Online ahead of print.

73. The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition.
Bauriedl S, Gerovac M, Heidrich N, Bischler T, Barquist L, Vogel J, Schoen C. Nat Commun. 2020 Jun 4;11(1):2823. doi: 10.1038/s41467-020-16650-6.

74. Early Cardiac Remodeling Promotes Tumor Growth and Metastasis.
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