Monthly Letter

1. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.
Replogle JM, Norman TM, Xu A, Hussmann JA, Chen J, Cogan JZ, Meer EJ, Terry JM, Riordan DP, Srinivas N, Fiddes IT, Arthur JG, Alvarado LJ, Pfeiffer KA, Mikkelsen TS, Weissman JS, Adamson B. Nat Biotechnol. 2020 Aug;38(8):954-961. doi: 10.1038/s41587-020-0470-y. Epub 2020 Mar 30.

2. Integrative analyses of single-cell transcriptome and regulome using MAESTRO.
Wang C, Sun D, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X, Xie Y, Meyer CA, Brown M, Tang M, Long H, Liu T, Liu XS. Genome Biol. 2020 Aug 7;21(1):198. doi: 10.1186/s13059-020-02116-x.

3. Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk HD, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE; Deutsche COVID-19 OMICS Initiative (DeCOI). Cell. 2020 Aug 5:S0092-8674(20)30992-2. doi: 10.1016/j.cell.2020.08.001. Online ahead of print.

4. CD81 Controls Beige Fat Progenitor Cell Growth and Energy Balance via FAK Signaling.
Oguri Y, Shinoda K, Kim H, Alba DL, Bolus WR, Wang Q, Brown Z, Pradhan RN, Tajima K, Yoneshiro T, Ikeda K, Chen Y, Cheang RT, Tsujino K, Kim CR, Greiner VJ, Datta R, Yang CD, Atabai K, McManus MT, Koliwad SK, Spiegelman BM, Kajimura S. Cell. 2020 Aug 6;182(3):563-577.e20. doi: 10.1016/j.cell.2020.06.021. Epub 2020 Jul 1.

5. 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 Aug 24;54(4):529-547.e12. doi: 10.1016/j.devcel.2020.05.010. Epub 2020 Jun 5.

6. Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing.
Maynard A, McCoach CE, Rotow JK, Harris L, Haderk F, Kerr DL, Yu EA, Schenk EL, Tan W, Zee A, Tan M, Gui P, Lea T, Wu W, Urisman A, Jones K, Sit R, Kolli PK, Seeley E, Gesthalter Y, Le DD, Yamauchi KA, Naeger DM, Bandyopadhyay S, Shah K, Cech L, Thomas NJ, Gupta A, Gonzalez M, Do H, Tan L, Bacaltos B, Gomez-Sjoberg R, Gubens M, Jahan T, Kratz JR, Jablons D, Neff N, Doebele RC, Weissman J, Blakely CM, Darmanis S, Bivona TG. Cell. 2020 Aug 7:S0092-8674(20)30882-5. doi: 10.1016/j.cell.2020.07.017. Online ahead of print.

7. Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer.
Katzenelenbogen Y, Sheban F, Yalin A, Yofe I, Svetlichnyy D, Jaitin DA, Bornstein C, Moshe A, Keren-Shaul H, Cohen M, Wang SY, Li B, David E, Salame TM, Weiner A, Amit I. Cell. 2020 Aug 20;182(4):872-885.e19. doi: 10.1016/j.cell.2020.06.032. Epub 2020 Aug 11.

8. Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn's Disease.
Mitsialis V, Wall S, Liu P, Ordovas-Montanes J, Parmet T, Vukovic M, Spencer D, Field M, McCourt C, Toothaker J, Bousvaros A; Boston Children’s Hospital Inflammatory Bowel Disease Center; Brigham and Women’s Hospital Crohn’s and Colitis Center, Shalek AK, Kean L, Horwitz B, Goldsmith J, Tseng G, Snapper SB, Konnikova L. Gastroenterology. 2020 Aug;159(2):591-608.e10. doi: 10.1053/j.gastro.2020.04.074. Epub 2020 May 16.

9. Single-cell RNA-seq analysis revealed long-lasting adverse effects of tamoxifen on neurogenesis in prenatal and adult brains.
Lee CM, Zhou L, Liu J, Shi J, Geng Y, Liu M, Wang J, Su X, Barad N, Wang J, Sun YE, Lin Q. Proc Natl Acad Sci U S A. 2020 Aug 11;117(32):19578-19589. doi: 10.1073/pnas.1918883117. Epub 2020 Jul 29.

10. Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data.
Calgaro M, Romualdi C, Waldron L, Risso D, Vitulo N. Genome Biol. 2020 Aug 3;21(1):191. doi: 10.1186/s13059-020-02104-1.

11. 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 Aug 11;117(32):19339-19346. doi: 10.1073/pnas.1919748117. Epub 2020 Jul 24.

12. BRD4 prevents the accumulation of R-loops and protects against transcription-replication collision events and DNA damage.
Lam FC, Kong YW, Huang Q, Vu Han TL, Maffa AD, Kasper EM, Yaffe MB. Nat Commun. 2020 Aug 14;11(1):4083. doi: 10.1038/s41467-020-17503-y.

13. PAF1 Regulates Stem Cell Features of Pancreatic Cancer Cells, Independently of the PAF1 Complex, via Interactions with PHF5A and DDX3.
Karmakar S, Rauth S, Nallasamy P, Perumal N, Nimmakalaya RK, Leon F, Gupta R, Barkeer S, Venkata RC, Raman V, Rachagani S, Ponnusamy MP, Batra SK. Gastroenterology. 2020 Aug 8:S0016-5085(20)35025-3. doi: 10.1053/j.gastro.2020.07.053. Online ahead of print.

14. 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 Aug 20;182(4):992-1008.e21. doi: 10.1016/j.cell.2020.06.037. Epub 2020 Jul 24.

15. Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia.
Prudencio M, Humphrey J, Pickles S, Brown AL, Hill SE, Kachergus J, Shi J, Heckman M, Spiegel M, Cook C, Song Y, Yue M, Daughrity L, Carlomagno Y, Jansen-West K, Fernandez De Castro C, DeTure M, Koga S, Wang YC, Sivakumar P, Bodo C, Candalija A, Talbot K, Selvaraj BT, Burr K, Chandran S, Newcombe J, Lashley T, Hubbard I, Catalano D, Kim D, Propp N, Fennessey S, Fagegaltier D, Phatnani H, Secrier M, Fisher EM, Oskarsson B, van Blitterswijk M, Rademakers R, Graff-Radford NR, Boeve B, Knopman DS, Petersen R, Josephs K, Thompson EA, Raj T, Ward ME, Dickson D, Gendron TF, Fratta P, Petrucelli L. J Clin Invest. 2020 Aug 13:139741. doi: 10.1172/JCI139741. Online ahead of print.

16. An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes.
Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA, Kucukural A, Zhu L. Elife. 2020 Aug 24;9:e55792. doi: 10.7554/eLife.55792. Online ahead of print.

17. Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage.
Park SR, Namkoong S, Friesen L, Cho CS, Zhang ZZ, Chen YC, Yoon E, Kim CH, Kwak H, Kang HM, Lee JH. Cell Rep. 2020 Aug 25;32(8):108077. doi: 10.1016/j.celrep.2020.108077.

18. 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 Aug;17(8):793-798. doi: 10.1038/s41592-020-0905-x. Epub 2020 Jul 27.

19. A DNA hypomethylating drug alters the tumor microenvironment and improves the effectiveness of immune checkpoint inhibitors in a mouse model of pancreatic cancer.
Gonda TA, Fang J, Salas M, Do C, Hsu E, Zhukovskaya A, Siegel A, Takahashi R, Lopez-Bujanda ZA, Drake CG, Manji GA, Wang TC, Olive KP, Tycko B. Cancer Res. 2020 Aug 14:canres.0285.2020. doi: 10.1158/0008-5472.CAN-20-0285. Online ahead of print.

20. A systematic evaluation of single-cell RNA-sequencing imputation methods.
Hou W, Ji Z, Ji H, Hicks SC. Genome Biol. 2020 Aug 27;21(1):218. doi: 10.1186/s13059-020-02132-x.

21. Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates.
Kawata K, Wakida H, Yamada T, Taniue K, Han H, Seki M, Suzuki Y, Akimitsu N. Genome Res. 2020 Aug 25:gr.264408.120. doi: 10.1101/gr.264408.120. Online ahead of print.

22. Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data.
Demirdjian L, Xu Y, Bahrami-Samani E, Pan Y, Stein S, Xie Z, Park E, Wu YN, Xing Y. Am J Hum Genet. 2020 Aug 6:S0002-9297(20)30235-4. doi: 10.1016/j.ajhg.2020.07.005. Online ahead of print.

23. Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis.
Raimundo F, Vallot C, Vert JP. Genome Biol. 2020 Aug 24;21(1):212. doi: 10.1186/s13059-020-02128-7.

24. A metabolic labeling method detects m(6)A transcriptome-wide at single base resolution.
Shu X, Cao J, Cheng M, Xiang S, Gao M, Li T, Ying X, Wang F, Yue Y, Lu Z, Dai Q, Cui X, Ma L, Wang Y, He C, Feng X, Liu J. Nat Chem Biol. 2020 Aug;16(8):887-895. doi: 10.1038/s41589-020-0526-9. Epub 2020 Apr 27.

25. A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis.
Ramesh A, Schubert RD, Greenfield AL, Dandekar R, Loudermilk R, Sabatino JJ Jr, Koelzer MT, Tran EB, Koshal K, Kim K, Pröbstel AK, Banerji D; University of California, San Francisco MS-EPIC Team, Guo CY, Green AJ, Bove RM, DeRisi JL, Gelfand JM, Cree BAC, Zamvil SS, Baranzini SE, Hauser SL, Wilson MR. Proc Natl Acad Sci U S A. 2020 Aug 28:202008523. doi: 10.1073/pnas.2008523117. Online ahead of print.

26. A comprehensive rat transcriptome built from large scale RNA-seq-based annotation.
Ji X, Li P, Fuscoe JC, Chen G, Xiao W, Shi L, Ning B, Liu Z, Hong H, Wu J, Liu J, Guo L, Kreil DP, Łabaj PP, Zhong L, Bao W, Huang Y, He J, Zhao Y, Tong W, Shi T. Nucleic Acids Res. 2020 Aug 4:gkaa638. doi: 10.1093/nar/gkaa638. Online ahead of print.

27. Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli.
Hör J, Di Giorgio S, Gerovac M, Venturini E, Förstner KU, Vogel J. Nucleic Acids Res. 2020 Aug 19:gkaa676. doi: 10.1093/nar/gkaa676. Online ahead of print.

28. A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples.
Dao Thi VL, Herbst K, Boerner K, Meurer M, Kremer LP, Kirrmaier D, Freistaedter A, Papagiannidis D, Galmozzi C, Stanifer ML, Boulant S, Klein S, Chlanda P, Khalid D, Barreto Miranda I, Schnitzler P, Kräusslich HG, Knop M, Anders S. Sci Transl Med. 2020 Aug 12;12(556):eabc7075. doi: 10.1126/scitranslmed.abc7075. Epub 2020 Jul 27.

29. 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 Aug 6;107(2):196-210. doi: 10.1016/j.ajhg.2020.06.002. Epub 2020 Jun 25.

30. Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics.
Doing G, Koeppen K, Occipinti P, Harty CE, Hogan DA. PLoS Genet. 2020 Aug 19;16(8):e1008783. doi: 10.1371/journal.pgen.1008783. Online ahead of print.

31. Quantification of translation uncovers the functions of the alternative transcriptome.
Calviello L, Hirsekorn A, Ohler U. Nat Struct Mol Biol. 2020 Aug;27(8):717-725. doi: 10.1038/s41594-020-0450-4. Epub 2020 Jun 29.

32. The m(6)A RNA demethylase FTO is a HIF-independent synthetic lethal partner with the VHL tumor suppressor.
Xiao Y, Thakkar KN, Zhao H, Broughton J, Li Y, Seoane JA, Diep AN, Metzner TJ, von Eyben R, Dill DL, Brooks JD, Curtis C, Leppert JT, Ye J, Peehl DM, Giaccia AJ, Sinha S, Rankin EB. Proc Natl Acad Sci U S A. 2020 Aug 19:202000516. doi: 10.1073/pnas.2000516117. Online ahead of print.

33. High throughput error corrected Nanopore single cell transcriptome sequencing.
Lebrigand K, Magnone V, Barbry P, Waldmann R. Nat Commun. 2020 Aug 12;11(1):4025. doi: 10.1038/s41467-020-17800-6.

34. Robust partitioning of microRNA targets from downstream regulatory changes.
Patel RK, West JD, Jiang Y, Fogarty EA, Grimson A. Nucleic Acids Res. 2020 Aug 21:gkaa687. doi: 10.1093/nar/gkaa687. Online ahead of print.

35. Predicting antigen specificity of single T cells based on TCR CDR3 regions.
Fischer DS, Wu Y, Schubert B, Theis FJ. Mol Syst Biol. 2020 Aug;16(8):e9416. doi: 10.15252/msb.20199416.

36. Intrinsic Endocardial Defects Contribute to Hypoplastic Left Heart Syndrome.
Miao Y, Tian L, Martin M, Paige SL, Galdos FX, Li J, Klein A, Zhang H, Ma N, Wei Y, Stewart M, Lee S, Moonen JR, Zhang B, Grossfeld P, Mital S, Chitayat D, Wu JC, Rabinovitch M, Nelson TJ, Nie S, Wu SM, Gu M. Cell Stem Cell. 2020 Aug 10:S1934-5909(20)30353-2. doi: 10.1016/j.stem.2020.07.015. Online ahead of print.

37. NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome.
Yakhnin AV, FitzGerald PC, McIntosh C, Yakhnin H, Kireeva M, Turek-Herman J, Mandell ZF, Kashlev M, Babitzke P. Proc Natl Acad Sci U S A. 2020 Aug 17:202006873. doi: 10.1073/pnas.2006873117. Online ahead of print.

38. TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.
Wang J, Li B, Marques S, Steinmetz LM, Wei W, Pelechano V. Nucleic Acids Res. 2020 Aug 20:gkaa691. doi: 10.1093/nar/gkaa691. Online ahead of print.

39. Ageing compromises mouse thymus function and remodels epithelial cell differentiation.
Baran-Gale J, Morgan MD, Maio S, Dhalla F, Calvo-Asensio I, Deadman ME, Handel AE, Maynard A, Chen S, Green F, Sit RV, Neff NF, Darmanis S, Tan W, May AP, Marioni JC, Ponting CP, Holländer GA. Elife. 2020 Aug 25;9:e56221. doi: 10.7554/eLife.56221. Online ahead of print.

40. Single-Cell RNA Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology.
Gillen AE, Riemondy KA, Amani V, Griesinger AM, Gilani A, Venkataraman S, Madhavan K, Prince E, Sanford B, Hankinson TC, Handler MH, Vibhakar R, Jones KL, Mitra S, Hesselberth JR, Foreman NK, Donson AM. Cell Rep. 2020 Aug 11;32(6):108023. doi: 10.1016/j.celrep.2020.108023.

41. Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells.
Holloway EM, Wu JH, Czerwinski M, Sweet CW, Wu A, Tsai YH, Huang S, Stoddard AE, Capeling MM, Glass I, Spence JR. Dev Cell. 2020 Aug 24;54(4):516-528.e7. doi: 10.1016/j.devcel.2020.07.023.

42. Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action.
McFarland JM, Paolella BR, Warren A, Geiger-Schuller K, Shibue T, Rothberg M, Kuksenko O, Colgan WN, Jones A, Chambers E, Dionne D, Bender S, Wolpin BM, Ghandi M, Tirosh I, Rozenblatt-Rosen O, Roth JA, Golub TR, Regev A, Aguirre AJ, Vazquez F, Tsherniak A. Nat Commun. 2020 Aug 27;11(1):4296. doi: 10.1038/s41467-020-17440-w.

43. LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy.
Nichterwitz S, Nijssen J, Storvall H, Schweingruber C, Comley LH, Allodi I, Lee MV, Deng Q, Sandberg R, Hedlund E. Genome Res. 2020 Aug;30(8):1083-1096. doi: 10.1101/gr.265017.120. Epub 2020 Aug 20.

44. Single Cell Transcriptional Analyses Identify Lineage-Specific Epithelial Responses to Inflammation and Metaplastic Development in the Gastric Corpus.
Bockerstett KA, Lewis SA, Noto CN, Ford EL, Saenz JB, Jackson NM, Ahn TH, Mills JC, DiPaolo RJ. Gastroenterology. 2020 Aug 21:S0016-5085(20)35066-6. doi: 10.1053/j.gastro.2020.08.027. Online ahead of print.

45. Transcriptional Reprogramming of Distinct Peripheral Sensory Neuron Subtypes after Axonal Injury.
Renthal W, Tochitsky I, Yang L, Cheng YC, Li E, Kawaguchi R, Geschwind DH, Woolf CJ. Neuron. 2020 Aug 14:S0896-6273(20)30570-5. doi: 10.1016/j.neuron.2020.07.026. Online ahead of print.

46. Diploid genome architecture revealed by multi-omic data of hybrid mice.
Han Z, Cui K, Placek K, Hong N, Lin C, Chen W, Zhao K, Jin W. Genome Res. 2020 Aug;30(8):1097-1106. doi: 10.1101/gr.257568.119. Epub 2020 Aug 5.

47. RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes.
Nip KM, Chiu R, Yang C, Chu J, Mohamadi H, Warren RL, Birol I. Genome Res. 2020 Aug;30(8):1191-1200. doi: 10.1101/gr.260174.119. Epub 2020 Aug 17.

48. Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.
Tavares CDJ, Aigner S, Sharabi K, Sathe S, Mutlu B, Yeo GW, Puigserver P. Proc Natl Acad Sci U S A. 2020 Aug 26:202000643. doi: 10.1073/pnas.2000643117. Online ahead of print.

49. Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data.
Fortelny N, Bock C. Genome Biol. 2020 Aug 3;21(1):190. doi: 10.1186/s13059-020-02100-5.

50. Single-Cell Analysis of Neonatal HSC Ontogeny Reveals Gradual and Uncoordinated Transcriptional Reprogramming that Begins before Birth.
Li Y, Kong W, Yang W, Patel RM, Casey EB, Okeyo-Owuor T, White JM, Porter SN, Morris SA, Magee JA. Cell Stem Cell. 2020 Aug 14:S1934-5909(20)30397-0. doi: 10.1016/j.stem.2020.08.001. Online ahead of print.

51. Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma.
Wouters J, Kalender-Atak Z, Minnoye L, Spanier KI, De Waegeneer M, Bravo González-Blas C, Mauduit D, Davie K, Hulselmans G, Najem A, Dewaele M, Pedri D, Rambow F, Makhzami S, Christiaens V, Ceyssens F, Ghanem G, Marine JC, Poovathingal S, Aerts S. Nat Cell Biol. 2020 Aug;22(8):986-998. doi: 10.1038/s41556-020-0547-3. Epub 2020 Aug 3.

52. The role of the NMD factor UPF3B in olfactory sensory neurons.
Tan K, Jones SH, Lake BB, Dumdie JN, Shum EY, Zhang L, Chen S, Sohni A, Pandya S, Gallo RL, Zhang K, Cook-Andersen H, Wilkinson MF. Elife. 2020 Aug 10;9:e57525. doi: 10.7554/eLife.57525.

53. Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. Nat Med. 2020 Aug;26(8):1307. doi: 10.1038/s41591-020-0976-3.

54. TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.
Yu T, Mu Z, Fang Z, Liu X, Gao X, Liu J. Genome Res. 2020 Aug;30(8):1181-1190. doi: 10.1101/gr.257766.119. Epub 2020 Aug 17.

55. Regulation of dynamic pigment cell states at single-cell resolution.
Perillo M, Oulhen N, Foster S, Spurrell M, Calestani C, Wessel G. Elife. 2020 Aug 19;9:e60388. doi: 10.7554/eLife.60388.

56. Clusters of polymorphic transmembrane genes control resistance to schistosomes in snail vectors.
Tennessen JA, Bollmann SR, Peremyslova E, Kronmiller BA, Sergi C, Hamali B, Blouin MS. Elife. 2020 Aug 26;9:e59395. doi: 10.7554/eLife.59395. Online ahead of print.

57. ATF4 Regulates MYB to Increase γ-Globin in Response to Loss of β-Globin.
Boontanrart MY, Schröder MS, Stehli GM, Banović M, Wyman SK, Lew RJ, Bordi M, Gowen BG, DeWitt MA, Corn JE. Cell Rep. 2020 Aug 4;32(5):107993. doi: 10.1016/j.celrep.2020.107993.

58. A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals.
Örd T, Puurand T, Örd D, Annilo T, Möls M, Remm M, Örd T. PLoS Genet. 2020 Aug 3;16(8):e1008981. doi: 10.1371/journal.pgen.1008981. eCollection 2020 Aug.

59. Runx2+ Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling.
Chen S, Jing J, Yuan Y, Feng J, Han X, Wen Q, Ho TV, Lee C, Chai Y. Cell Rep. 2020 Aug 11;32(6):108007. doi: 10.1016/j.celrep.2020.108007.

60. State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia.
Rockne RC, Branciamore S, Qi J, Frankhouser DE, O'Meally D, Hua WK, Cook G, Carnahan E, Zhang L, Marom A, Wu H, Maestrini D, Wu X, Yuan YC, Liu Z, Wang LD, Forman S, Carlesso N, Kuo YH, Marcucci G. Cancer Res. 2020 Aug 1;80(15):3157-3169. doi: 10.1158/0008-5472.CAN-20-0354. Epub 2020 May 15.

61. CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation.
Tellier M, Zaborowska J, Caizzi L, Mohammad E, Velychko T, Schwalb B, Ferrer-Vicens I, Blears D, Nojima T, Cramer P, Murphy S. Nucleic Acids Res. 2020 Aug 20;48(14):7712-7727. doi: 10.1093/nar/gkaa514.

62. Comprehensive multi-omics analysis uncovers a group of TGF-β-regulated genes among lncRNA EPR direct transcriptional targets.
Zapparoli E, Briata P, Rossi M, Brondolo L, Bucci G, Gherzi R. Nucleic Acids Res. 2020 Aug 5:gkaa628. doi: 10.1093/nar/gkaa628. Online ahead of print.

63. Antibody-free enzyme-assisted chemical approach for detection of N(6)-methyladenosine.
Wang Y, Xiao Y, Dong S, Yu Q, Jia G. Nat Chem Biol. 2020 Aug;16(8):896-903. doi: 10.1038/s41589-020-0525-x. Epub 2020 Apr 27.

64. On the cross-population generalizability of gene expression prediction models.
Keys KL, Mak ACY, White MJ, Eckalbar WL, Dahl AW, Mefford J, Mikhaylova AV, Contreras MG, Elhawary JR, Eng C, Hu D, Huntsman S, Oh SS, Salazar S, Lenoir MA, Ye JC, Thornton TA, Zaitlen N, Burchard EG, Gignoux CR. PLoS Genet. 2020 Aug 14;16(8):e1008927. doi: 10.1371/journal.pgen.1008927. eCollection 2020 Aug.

65. Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi.
Li SJ, Zhang X, Lukeš J, Li BQ, Wang JF, Qu LH, Hide G, Lai DH, Lun ZR. Nucleic Acids Res. 2020 Aug 27:gkaa700. doi: 10.1093/nar/gkaa700. Online ahead of print.

66. Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation.
Pinkard O, McFarland S, Sweet T, Coller J. Nat Commun. 2020 Aug 14;11(1):4104. doi: 10.1038/s41467-020-17879-x.

67. Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input.
Handa T, Harada A, Maehara K, Sato S, Nakao M, Goto N, Kurumizaka H, Ohkawa Y, Kimura H. Nat Protoc. 2020 Aug 17. doi: 10.1038/s41596-020-0375-8. Online ahead of print.

68. Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems.
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