Monthly Letter

1. 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 Jul;26(7):1070-1076. doi: 10.1038/s41591-020-0944-y. Epub 2020 Jun 8.

2. Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines.
Kagohara LT, Zamuner F, Davis-Marcisak EF, Sharma G, Considine M, Allen J, Yegnasubramanian S, Gaykalova DA, Fertig EJ. Br J Cancer. 2020 Jul;123(1):101-113. doi: 10.1038/s41416-020-0851-5. Epub 2020 May 4.

3. 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 Jul 9;182(1):162-176.e13. doi: 10.1016/j.cell.2020.05.023. Epub 2020 Jun 17.

4. 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 Jul 23;182(2):497-514.e22. doi: 10.1016/j.cell.2020.05.039. Epub 2020 Jun 23.

5. 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 Jul 1;130(7):3654-3670. doi: 10.1172/JCI132414.

6. SIRT1-NOX4 signaling axis regulates cancer cachexia.
Dasgupta A, Shukla SK, Vernucci E, King RJ, Abrego J, Mulder SE, Mullen NJ, Graves G, Buettner K, Thakur R, Murthy D, Attri KS, Wang D, Chaika NV, Pacheco CG, Rai I, Engle DD, Grandgenett PM, Punsoni M, Reames BN, Teoh-Fitzgerald M, Oberley-Deegan R, Yu F, Klute KA, Hollingsworth MA, Zimmerman MC, Mehla K, Sadoshima J, Tuveson DA, Singh PK. J Exp Med. 2020 Jul 6;217(7):e20190745. doi: 10.1084/jem.20190745.

7. Geospatial immune variability illuminates differential evolution of lung adenocarcinoma.
AbdulJabbar K, Raza SEA, Rosenthal R, Jamal-Hanjani M, Veeriah S, Akarca A, Lund T, Moore DA, Salgado R, Al Bakir M, Zapata L, Hiley CT, Officer L, Sereno M, Smith CR, Loi S, Hackshaw A, Marafioti T, Quezada SA, McGranahan N, Le Quesne J; TRACERx Consortium, Swanton C, Yuan Y. Nat Med. 2020 Jul;26(7):1054-1062. doi: 10.1038/s41591-020-0900-x. Epub 2020 May 27.

8. Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-β signaling.
Shrestha N, Liu T, Ji Y, Reinert RB, Torres M, Li X, Zhang M, Tang CA, Hu CA, Liu C, Naji A, Liu M, Lin JD, Kersten S, Arvan P, Qi L. J Clin Invest. 2020 Jul 1;130(7):3499-3510. doi: 10.1172/JCI134874.

9. 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 Jul 1;34(13-14):950-964. doi: 10.1101/gad.338202.120. Epub 2020 Jun 4.

10. Dengue virus targets RBM10 deregulating host cell splicing and innate immune response.
Pozzi B, Bragado L, Mammi P, Torti MF, Gaioli N, Gebhard LG, García Solá ME, Vaz-Drago R, Iglesias NG, García CC, Gamarnik AV, Srebrow A. Nucleic Acids Res. 2020 Jul 9;48(12):6824-6838. doi: 10.1093/nar/gkaa340.

11. Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy.
Couturier CP, Ayyadhury S, Le PU, Nadaf J, Monlong J, Riva G, Allache R, Baig S, Yan X, Bourgey M, Lee C, Wang YCD, Wee Yong V, Guiot MC, Najafabadi H, Misic B, Antel J, Bourque G, Ragoussis J, Petrecca K. Nat Commun. 2020 Jul 8;11(1):3406. doi: 10.1038/s41467-020-17186-5.

12. 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 Jul;583(7817):638-643. doi: 10.1038/s41586-020-2418-2. Epub 2020 Jun 17.

13. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq.
Li B, Gould J, Yang Y, Sarkizova S, Tabaka M, Ashenberg O, Rosen Y, Slyper M, Kowalczyk MS, Villani AC, Tickle T, Hacohen N, Rozenblatt-Rosen O, Regev A. Nat Methods. 2020 Jul 27. doi: 10.1038/s41592-020-0905-x. Online ahead of print.

14. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq.
Policastro RA, Raborn RT, Brendel VP, Zentner GE. Genome Res. 2020 Jul 6;30(6):910-23. doi: 10.1101/gr.261545.120. Online ahead of print.

15. Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes.
Song Q, Ando A, Jiang N, Ikeda Y, Chen ZJ. Genome Biol. 2020 Jul 22;21(1):178. doi: 10.1186/s13059-020-02094-0.

16. Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury.
Kirita Y, Wu H, Uchimura K, Wilson PC, Humphreys BD. Proc Natl Acad Sci U S A. 2020 Jul 7;117(27):15874-15883. doi: 10.1073/pnas.2005477117. Epub 2020 Jun 22.

17. ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses.
David FPA, Litovchenko M, Deplancke B, Gardeux V. Nucleic Acids Res. 2020 Jul 2;48(W1):W403-W414. doi: 10.1093/nar/gkaa412.

18. A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons.
Morton DJ, Jalloh B, Kim L, Kremsky I, Nair RJ, Nguyen KB, Rounds JC, Sterrett MC, Brown B, Le T, Karkare MC, McGaughey KD, Sheng S, Leung SW, Fasken MB, Moberg KH, Corbett AH. PLoS Genet. 2020 Jul 9;16(7):e1008901. doi: 10.1371/journal.pgen.1008901. eCollection 2020 Jul.

19. A long-read RNA-seq approach to identify novel transcripts of very large genes.
Uapinyoying P, Goecks J, Knoblach SM, Panchapakesan K, Bonnemann CG, Partridge TA, Jaiswal JK, Hoffman EP. Genome Res. 2020 Jul 6;30(6):885-97. doi: 10.1101/gr.259903.119. Online ahead of print.

20. Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis.
Strunz M, Simon LM, Ansari M, Kathiriya JJ, Angelidis I, Mayr CH, Tsidiridis G, Lange M, Mattner LF, Yee M, Ogar P, Sengupta A, Kukhtevich I, Schneider R, Zhao Z, Voss C, Stoeger T, Neumann JHL, Hilgendorff A, Behr J, O'Reilly M, Lehmann M, Burgstaller G, Königshoff M, Chapman HA, Theis FJ, Schiller HB. Nat Commun. 2020 Jul 16;11(1):3559. doi: 10.1038/s41467-020-17358-3.

21. Integrated Transcriptome and Network Analysis Reveals Spatiotemporal Dynamics of Calvarial Suturogenesis.
Holmes G, Gonzalez-Reiche AS, Lu N, Zhou X, Rivera J, Kriti D, Sebra R, Williams AA, Donovan MJ, Potter SS, Pinto D, Zhang B, van Bakel H, Jabs EW. Cell Rep. 2020 Jul 7;32(1):107871. doi: 10.1016/j.celrep.2020.107871.

22. Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen.
Mika-Gospodorz B, Giengkam S, Westermann AJ, Wongsantichon J, Kion-Crosby W, Chuenklin S, Wang LC, Sunyakumthorn P, Sobota RM, Subbian S, Vogel J, Barquist L, Salje J. Nat Commun. 2020 Jul 3;11(1):3363. doi: 10.1038/s41467-020-17094-8.

23. A hierarchical Bayesian mixture model for inferring the expression state of genes in transcriptomes.
Thompson A, May MR, Moore BR, Kopp A. Proc Natl Acad Sci U S A. 2020 Jul 24:201919748. doi: 10.1073/pnas.1919748117. Online ahead of print.

24. Pancreatic circulating tumor cell profiling identifies LIN28B as a metastasis driver and drug target.
Franses JW, Philipp J, Missios P, Bhan I, Liu A, Yashaswini C, Tai E, Zhu H, Ligorio M, Nicholson B, Tassoni EM, Desai N, Kulkarni AS, Szabolcs A, Hong TS, Liss AS, Fernandez-Del Castillo C, Ryan DP, Maheswaran S, Haber DA, Daley GQ, Ting DT. Nat Commun. 2020 Jul 3;11(1):3303. doi: 10.1038/s41467-020-17150-3.

25. Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma.
Gojo J, Englinger B, Jiang L, Hübner JM, Shaw ML, Hack OA, Madlener S, Kirchhofer D, Liu I, Pyrdol J, Hovestadt V, Mazzola E, Mathewson ND, Trissal M, Lötsch D, Dorfer C, Haberler C, Halfmann A, Mayr L, Peyrl A, Geyeregger R, Schwalm B, Mauermann M, Pajtler KW, Milde T, Shore ME, Geduldig JE, Pelton K, Czech T, Ashenberg O, Wucherpfennig KW, Rozenblatt-Rosen O, Alexandrescu S, Ligon KL, Pfister SM, Regev A, Slavc I, Berger W, Suvà ML, Kool M, Filbin MG. Cancer Cell. 2020 Jul 13;38(1):44-59.e9. doi: 10.1016/j.ccell.2020.06.004.

26. Long-read cDNA Sequencing Enables a 'Gene-Like' Transcript Annotation of Transposable Elements.
Panda K, Slotkin RK. Plant Cell. 2020 Jul 9:tpc.00115.2020. doi: 10.1105/tpc.20.00115. Online ahead of print.

27. 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 Jul 1;34(13-14):913-930. doi: 10.1101/gad.335794.119. Epub 2020 Jun 4.

28. Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers.
Sun X, Ren Z, Cun Y, Zhao C, Huang X, Zhou J, Hu R, Su X, Ji L, Li P, Mak KLK, Gao F, Yang Y, Xu H, Ding J, Cao N, Li S, Zhang W, Lan P, Sun H, Wang J, Yuan P. Nucleic Acids Res. 2020 Jul 27;48(13):7182-7196. doi: 10.1093/nar/gkaa482.

29. CReSCENT: CanceR Single Cell ExpressioN Toolkit.
Mohanraj S, Díaz-Mejía JJ, Pham MD, Elrick H, Husić M, Rashid S, Luo P, Bal P, Lu K, Patel S, Mahalanabis A, Naidas A, Christensen E, Croucher D, Richards LM, Shooshtari P, Brudno M, Ramani AK, Pugh TJ. Nucleic Acids Res. 2020 Jul 2;48(W1):W372-W379. doi: 10.1093/nar/gkaa437.

30. HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets.
Hounkpe BW, Chenou F, de Lima F, De Paula EV. Nucleic Acids Res. 2020 Jul 14:gkaa609. doi: 10.1093/nar/gkaa609. Online ahead of print.

31. The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice.
Shchuka VM, Abatti LE, Hou H, Khader N, Dorogin A, Wilson MD, Shynlova O, Mitchell JA. PLoS Biol. 2020 Jul 15;18(7):e3000710. doi: 10.1371/journal.pbio.3000710. eCollection 2020 Jul.

32. Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation.
Lee H, Fenster RJ, Pineda SS, Gibbs WS, Mohammadi S, Davila-Velderrain J, Garcia FJ, Therrien M, Novis HS, Gao F, Wilkinson H, Vogt T, Kellis M, LaVoie MJ, Heiman M. Neuron. 2020 Jul 15:S0896-6273(20)30475-X. doi: 10.1016/j.neuron.2020.06.021. Online ahead of print.

33. Immobilization after injury alters extracellular matrix and stem cell fate.
Huber AK, Patel N, Pagani CA, Marini S, Padmanabhan K, Matera DL, Said M, Hwang C, Hsu GC, Poli AA, Strong AL, Visser ND, Greenstein JA, Nelson R, Li S, Longaker MT, Tang Y, Weiss SJ, Baker BM, James AW, Levi B. J Clin Invest. 2020 Jul 16:136142. doi: 10.1172/JCI136142. Online ahead of print.

34. Transposase assisted tagmentation of RNA/DNA hybrid duplexes.
Lu B, Dong L, Yi D, Zhang M, Zhu C, Li X, Yi C. Elife. 2020 Jul 23;9:e54919. doi: 10.7554/eLife.54919. Online ahead of print.

35. Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST.
Cao ZJ, Wei L, Lu S, Yang DC, Gao G. Nat Commun. 2020 Jul 10;11(1):3458. doi: 10.1038/s41467-020-17281-7.

36. A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron.
Ryan D, Jenniches L, Reichardt S, Barquist L, Westermann AJ. Nat Commun. 2020 Jul 16;11(1):3557. doi: 10.1038/s41467-020-17348-5.

37. Single-Cell and Population Transcriptomics Reveal Pan-epithelial Remodeling in Type 2-High Asthma.
Jackson ND, Everman JL, Chioccioli M, Feriani L, Goldfarbmuren KC, Sajuthi SP, Rios CL, Powell R, Armstrong M, Gomez J, Michel C, Eng C, Oh SS, Rodriguez-Santana J, Cicuta P, Reisdorph N, Burchard EG, Seibold MA. Cell Rep. 2020 Jul 7;32(1):107872. doi: 10.1016/j.celrep.2020.107872.

38. 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 Jul 27;48(13):7119-7134. doi: 10.1093/nar/gkaa486.

39. miRSwitch: detecting microRNA arm shift and switch events.
Kern F, Amand J, Senatorov I, Isakova A, Backes C, Meese E, Keller A, Fehlmann T. Nucleic Acids Res. 2020 Jul 2;48(W1):W268-W274. doi: 10.1093/nar/gkaa323.

40. Mapping regulatory variants controlling gene expression in drought response and tolerance in maize.
Liu S, Li C, Wang H, Wang S, Yang S, Liu X, Yan J, Li B, Beatty M, Zastrow-Hayes G, Song S, Qin F. Genome Biol. 2020 Jul 6;21(1):163. doi: 10.1186/s13059-020-02069-1.

41. Lessons from single cell sequencing in CNS cell specification and function.
Li Z, Tyler WA, Haydar TF. Curr Opin Genet Dev. 2020 Jul 14;65:138-143. doi: 10.1016/j.gde.2020.05.043. Online ahead of print.

42. Hemolysis transforms liver macrophages into anti-inflammatory erythrophagocytes.
Pfefferlé M, Ingoglia G, Schaer CA, Yalamanoglu A, Buzzi RM, Dubach IL, Tan G, López-Cano EY, Schulthess N, Hansen K, Humar R, Schaer DJ, Vallelian F. J Clin Invest. 2020 Jul 14:137282. doi: 10.1172/JCI137282. Online ahead of print.

43. IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq.
Ma A, Wang C, Chang Y, Brennan FH, McDermaid A, Liu B, Zhang C, Popovich PG, Ma Q. Nucleic Acids Res. 2020 Jul 2;48(W1):W275-W286. doi: 10.1093/nar/gkaa394.

44. Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data.
Patrick R, Humphreys DT, Janbandhu V, Oshlack A, Ho JWK, Harvey RP, Lo KK. Genome Biol. 2020 Jul 8;21(1):167. doi: 10.1186/s13059-020-02071-7.

45. Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers.
Townes FW, Irizarry RA. Genome Biol. 2020 Jul 3;21(1):160. doi: 10.1186/s13059-020-02078-0.

46. Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera).
Duncan EJ, Leask MP, Dearden PK. Mol Biol Evol. 2020 Jul 1;37(7):1964-1978. doi: 10.1093/molbev/msaa057.

47. The Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis.
Alencar GF, Owsiany KM, K S, Sukhavasi K, Mocci G, Nguyen A, Williams CM, Shamsuzzaman S, Mokry M, Henderson CA, Haskins R, Baylis RA, Finn AV, McNamara CA, Zunder ER, Venkata V, Pasterkamp G, Björkegren J, Bekiranov S, Owens GK. Circulation. 2020 Jul 17. doi: 10.1161/CIRCULATIONAHA.120.046672. Online ahead of print.

48. Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring.
Frost HR. Nucleic Acids Res. 2020 Jul 7:gkaa582. doi: 10.1093/nar/gkaa582. Online ahead of print.

49. Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy.
Lee YR, Khan K, Armfield-Uhas K, Srikanth S, Thompson NA, Pardo M, Yu L, Norris JW, Peng Y, Gripp KW, Aleck KA, Li C, Spence E, Choi TI, Kwon SJ, Park HM, Yu D, Do Heo W, Mooney MR, Baig SM, Wentzensen IM, Telegrafi A, McWalter K, Moreland T, Roadhouse C, Ramsey K, Lyons MJ, Skinner C, Alexov E, Katsanis N, Stevenson RE, Choudhary JS, Adams DJ, Kim CH, Davis EE, Schwartz CE. Nat Commun. 2020 Jul 23;11(1):3698. doi: 10.1038/s41467-020-17452-6.

50. Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance.
Eyler CE, Matsunaga H, Hovestadt V, Vantine SJ, van Galen P, Bernstein BE. Genome Biol. 2020 Jul 15;21(1):174. doi: 10.1186/s13059-020-02085-1.

51. RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares.
Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB. N Engl J Med. 2020 Jul 16;383(3):218-228. doi: 10.1056/NEJMoa2004114.

52. Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?.
Pique-Regi R, Romero R, Tarca AL, Luca F, Xu Y, Alazizi A, Leng Y, Hsu CD, Gomez-Lopez N. Elife. 2020 Jul 14;9:e58716. doi: 10.7554/eLife.58716.

53. Genomic Binding Patterns of Forkhead Box Protein O1 Reveal its Unique Role in Cardiac Hypertrophy.
Pfleger J, Coleman RC, Ibetti J, Roy R, Kyriazis ID, Gao E, Drosatos K, Koch WJ. Circulation. 2020 Jul 9. doi: 10.1161/CIRCULATIONAHA.120.046356. Online ahead of print.

54. Vav3 Mediates Pseudomonas aeruginosa Adhesion to the Cystic Fibrosis Airway Epithelium.
Badaoui M, Zoso A, Idris T, Bacchetta M, Simonin J, Lemeille S, Wehrle-Haller B, Chanson M. Cell Rep. 2020 Jul 7;32(1):107842. doi: 10.1016/j.celrep.2020.107842.

55. RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.
Liu Q, Shvarts T, Sliz P, Gregory RI. Nucleic Acids Res. 2020 Jul 2;48(W1):W218-W229. doi: 10.1093/nar/gkaa395.

56. Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions.
Twittenhoff C, Brandenburg VB, Righetti F, Nuss AM, Mosig A, Dersch P, Narberhaus F. Nucleic Acids Res. 2020 Jul 9;48(12):e71. doi: 10.1093/nar/gkaa404.

57. Baseline Frequency of Inflammatory Cxcl9-Expressing Tumor-Associated Macrophages Predicts Response to Avelumab Treatment.
Qu Y, Wen J, Thomas G, Yang W, Prior W, He W, Sundar P, Wang X, Potluri S, Salek-Ardakani S. Cell Rep. 2020 Jul 7;32(1):107873. doi: 10.1016/j.celrep.2020.107873.

58. X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity.
Link JC, Wiese CB, Chen X, Avetisyan R, Ronquillo E, Ma F, Guo X, Yao J, Allison M, Chen YI, Rotter JI, El-Sayed Moustafa JS, Small KS, Iwase S, Pellegrini M, Vergnes L, Arnold AP, Reue K. J Clin Invest. 2020 Jul 23:140223. doi: 10.1172/JCI140223. Online ahead of print.

59. SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis.
Bajczyk M, Lange H, Bielewicz D, Szewc L, Bhat SS, Dolata J, Kuhn L, Szweykowska-Kulinska Z, Gagliardi D, Jarmolowski A. Nucleic Acids Res. 2020 Jul 9;48(12):6839-6854. doi: 10.1093/nar/gkaa373.

60. Targeting tumor-associated macrophages and granulocytic-myeloid-derived suppressor cells augments pd-1 blockade in cholangiocarcinoma.
Loeuillard E, Yang J, Buckarma E, Wang J, Liu Y, Conboy CB, Pavelko KD, Li Y, O'Brien D, Wang C, Graham RP, Smoot RL, Dong H, Rizvi S. J Clin Invest. 2020 Jul 14:137110. doi: 10.1172/JCI137110. Online ahead of print.

61. Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics.
Choi K, Chen Y, Skelly DA, Churchill GA. Genome Biol. 2020 Jul 27;21(1):183. doi: 10.1186/s13059-020-02103-2.

62. Anti-inflammatory functions of the glucocorticoid receptor require DNA binding.
Escoter-Torres L, Greulich F, Quagliarini F, Wierer M, Uhlenhaut NH. Nucleic Acids Res. 2020 Jul 3:gkaa565. doi: 10.1093/nar/gkaa565. Online ahead of print.

63. Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.
Wan YW, Al-Ouran R, Mangleburg CG, Perumal TM, Lee TV, Allison K, Swarup V, Funk CC, Gaiteri C, Allen M, Wang M, Neuner SM, Kaczorowski CC, Philip VM, Howell GR, Martini-Stoica H, Zheng H, Mei H, Zhong X, Kim JW, Dawson VL, Dawson TM, Pao PC, Tsai LH, Haure-Mirande JV, Ehrlich ME, Chakrabarty P, Levites Y, Wang X, Dammer EB, Srivastava G, Mukherjee S, Sieberts SK, Omberg L, Dang KD, Eddy JA, Snyder P, Chae Y, Amberkar S, Wei W, Hide W, Preuss C, Ergun A, Ebert PJ, Airey DC, Mostafavi S, Yu L, Klein HU; Accelerating Medicines Partnership-Alzheimer’s Disease Consortium, Carter GW, Collier DA, Golde TE, Levey AI, Bennett DA, Estrada K, Townsend TM, Zhang B, Schadt E, De Jager PL, Price ND, Ertekin-Taner N, Liu Z, Shulman JM, Mangravite LM, Logsdon BA. Cell Rep. 2020 Jul 14;32(2):107908. doi: 10.1016/j.celrep.2020.107908.

64. Flexible experimental designs for valid single-cell RNA-sequencing experiments allowing batch effects correction.
Song F, Chan GMA, Wei Y. Nat Commun. 2020 Jul 1;11(1):3274. doi: 10.1038/s41467-020-16905-2.

65. Regulation of Female Germline Specification via Small RNA Mobility in Arabidopsis.
Su Z, Wang N, Hou Z, Li B, Li D, Liu Y, Cai H, Qin Y, Chen X. Plant Cell. 2020 Jul 23:tpc.00126.2020. doi: 10.1105/tpc.20.00126. Online ahead of print.

66. Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells.
Moudgil A, Wilkinson MN, Chen X, He J, Cammack AJ, Vasek MJ, Lagunas T Jr, Qi Z, Lalli MA, Guo C, Morris SA, Dougherty JD, Mitra RD. Cell. 2020 Jul 18:S0092-8674(20)30814-X. doi: 10.1016/j.cell.2020.06.037. Online ahead of print.

67. Author Correction: Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model.
Townes FW, Hicks SC, Aryee MJ, Irizarry RA. Genome Biol. 2020 Jul 22;21(1):179. doi: 10.1186/s13059-020-02109-w.

68. Maturational Changes in Mouse Cutaneous Touch and Piezo2-Mediated Mechanotransduction.
Michel N, Narayanan P, Shomroni O, Schmidt M. Cell Rep. 2020 Jul 21;32(3):107912. doi: 10.1016/j.celrep.2020.107912.

69. Argonaute binding within 3'-untranslated regions poorly predicts gene repression.
Chu Y, Kilikevicius A, Liu J, Johnson KC, Yokota S, Corey DR. Nucleic Acids Res. 2020 Jul 27;48(13):7439-7453. doi: 10.1093/nar/gkaa478.

70. Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis.
Szulzewsky F, Arora S, Hoellerbauer P, King C, Nathan E, Chan M, Cimino PJ, Ozawa T, Kawauchi D, Pajtler KW, Gilbertson RJ, Paddison PJ, Vasioukhin V, Gujral TS, Holland EC. Genes Dev. 2020 Jul 16. doi: 10.1101/gad.338681.120. Online ahead of print.

71. Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo.
Yang M, Woolfenden HC, Zhang Y, Fang X, Liu Q, Vigh ML, Cheema J, Yang X, Norris M, Yu S, Carbonell A, Brodersen P, Wang J, Ding Y. Nucleic Acids Res. 2020 Jul 11:gkaa577. doi: 10.1093/nar/gkaa577. Online ahead of print.