Monthly Letter

1. Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium.
Schmidt ST, Yu FB, Blainey PC, May AP, Quake SR. Proc Natl Acad Sci U S A. 2019 Oct 28. pii: 201904273. doi: 10.1073/pnas.1904273116.

2. A DNAH17 missense variant causes flagella destabilization and asthenozoospermia.
Zhang B, Ma H, Khan T, Ma A, Li T, Zhang H, Gao J, Zhou J, Li Y, Yu C, Bao J, Ali A, Murtaza G, Yin H, Gao Q, Jiang X, Zhang F, Liu C, Khan I, Zubair M, Hussain HMJ, Khan R, Yousaf A, Yuan L, Lu Y, Xu X, Wang Y, Tao Q, Hao Q, Fang H, Cheng H, Zhang Y, Shi Q. J Exp Med. 2019 Oct 28. pii: jem.20182365. doi: 10.1084/jem.20182365.

3. A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion.
Cai XC, Zhang T, Kim EJ, Jiang M, Wang K, Wang J, Chen S, Zhang N, Wu H, Li F, Dela Seña CC, Zeng H, Vivcharuk V, Niu X, Zheng W, Lee JP, Chen Y, Barsyte D, Szewczyk M, Hajian T, Ibáñez G, Dong A, Dombrovski L, Zhang Z, Deng H, Min J, Arrowsmith CH, Mazutis L, Shi L, Vedadi M, Brown PJ, Xiang J, Qin LX, Xu W, Luo M. Elife. 2019 Oct 28;8. pii: e47110. doi: 10.7554/eLife.47110.

4. Combinatorial prediction of marker panels from single-cell transcriptomic data.
Delaney C, Schnell A, Cammarata LV, Yao-Smith A, Regev A, Kuchroo VK, Singer M. Mol Syst Biol. 2019 Oct;15(10):e9005. doi: 10.15252/msb.20199005.

5. Biological process activity transformation of single cell gene expression for cross-species alignment.
Ding H, Blair A, Yang Y, Stuart JM. Nat Commun. 2019 Oct 25;10(1):4899. doi: 10.1038/s41467-019-12924-w.

6. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration.
Menon M, Mohammadi S, Davila-Velderrain J, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP. Nat Commun. 2019 Oct 25;10(1):4902. doi: 10.1038/s41467-019-12780-8.

7. Identification and dynamic quantification of regulatory elements using total RNA.
Duttke SH, Chang MW, Heinz S, Benner C. Genome Res. 2019 Oct 24. doi: 10.1101/gr.253492.119.

8. FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.
Vahrenkamp JM, Szczotka K, Dodson MK, Jarboe EA, Soisson AP, Gertz J. Genome Res. 2019 Oct 24. doi: 10.1101/gr.249656.119.

9. The Tudor SND1 protein is an m6A RNA reader essential for replication of Kaposi's sarcoma-associated herpesvirus.
Baquero-Perez B, Antanaviciute A, Yonchev ID, Carr IM, Wilson SA, Whitehouse A. Elife. 2019 Oct 24;8. pii: e47261. doi: 10.7554/eLife.47261.

10. Rat Model of Cockayne Syndrome Neurological Disease.
Xu Y, Wu Z, Liu L, Liu J, Wang Y. Cell Rep. 2019 Oct 22;29(4):800-809.e5. doi: 10.1016/j.celrep.2019.09.028.

11. Single cell analysis reveals immune cell-adipocyte crosstalk regulating the transcription of thermogenic adipocytes.
Rajbhandari P, Arneson D, Hart SK, Ahn IS, Diamante G, Santos LC, Zaghari N, Feng AC, Thomas BJ, Vergnes L, Lee SD, Rajbhandari AK, Reue K, Smale ST, Yang X, Tontonoz P. Elife. 2019 Oct 23;8. pii: e49501. doi: 10.7554/eLife.49501.

12. Discovery proteomics in aging human skeletal muscle finds change in spliceosome, immunity, proteostasis and mitochondria.
Ubaida-Mohien C, Lyashkov A, Gonzalez-Freire M, Tharakan R, Shardell M, Moaddel R, Semba RD, Chia CW, Gorospe M, Sen R, Ferrucci L. Elife. 2019 Oct 23;8. pii: e49874. doi: 10.7554/eLife.49874.

13. Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans.
Zhao G, Li K, Li B, Wang Z, Fang Z, Wang X, Zhang Y, Luo T, Zhou Q, Wang L, Xie Y, Wang Y, Chen Q, Xia L, Tang Y, Tang B, Xia K, Li J. Nucleic Acids Res. 2019 Oct 23. pii: gkz923. doi: 10.1093/nar/gkz923.

14. AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana.
Togninalli M, Seren Ü, Freudenthal JA, Monroe JG, Meng D, Nordborg M, Weigel D, Borgwardt K, Korte A, Grimm DG. Nucleic Acids Res. 2019 Oct 23. pii: gkz925. doi: 10.1093/nar/gkz925.

15. A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures.
Kondratova M, Czerwinska U, Sompairac N, Amigorena SD, Soumelis V, Barillot E, Zinovyev A, Kuperstein I. Nat Commun. 2019 Oct 22;10(1):4808. doi: 10.1038/s41467-019-12270-x.

16. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.
Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Genome Biol. 2019 Oct 21;20(1):213. doi: 10.1186/s13059-019-1842-9.

17. Correction: Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation.
Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, ..., Farrer LA. Mol Psychiatry. 2019 Oct 21. doi: 10.1038/s41380-019-0529-7.

18. Mutational inactivation of mTORC1 repressor gene DEPDC5 in human gastrointestinal stromal tumors.
Pang Y, Xie F, Cao H, Wang C, Zhu M, Liu X, Lu X, Huang T, Shen Y, Li K, Jia X, Li Z, Zheng X, Wang S, He Y, Wang L, Fletcher JA, Wang Y. Proc Natl Acad Sci U S A. 2019 Oct 21. pii: 201914542. doi: 10.1073/pnas.1914542116.

19. Hearing loss mutations alter the functional properties of human P2X2 receptor channels through distinct mechanisms.
George B, Swartz KJ, Li M. Proc Natl Acad Sci U S A. 2019 Oct 21. pii: 201912156. doi: 10.1073/pnas.1912156116.

20. Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.
Inoue F, Kreimer A, Ashuach T, Ahituv N, Yosef N. Cell Stem Cell. 2019 Oct 14. pii: S1934-5909(19)30421-7. doi: 10.1016/j.stem.2019.09.010.

21. De Novo Mutations in FOXJ1 Result in a Motile Ciliopathy with Hydrocephalus and Randomization of Left/Right Body Asymmetry.
Wallmeier J, Frank D, Shoemark A, Nöthe-Menchen T, Cindric S, Olbrich H, Loges NT, Aprea I, Dougherty GW, Pennekamp P, Kaiser T, Mitchison HM, Hogg C, Carr SB, Zariwala MA, Ferkol T, Leigh MW, Davis SD, Atkinson J, Dutcher SK, Knowles MR, Thiele H, Altmüller J, Krenz H, Wöste M, Brentrup A, Ahrens F, Vogelberg C, Morris-Rosendahl DJ, Omran H. Am J Hum Genet. 2019 Oct 17. pii: S0002-9297(19)30362-3. doi: 10.1016/j.ajhg.2019.09.022.

22. De novo compartment deconvolution and weight estimation of tumor samples using DECODER.
Peng XL, Moffitt RA, Torphy RJ, Volmar KE, Yeh JJ. Nat Commun. 2019 Oct 18;10(1):4729. doi: 10.1038/s41467-019-12517-7.

23. DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data.
Arisdakessian C, Poirion O, Yunits B, Zhu X, Garmire LX. Genome Biol. 2019 Oct 18;20(1):211. doi: 10.1186/s13059-019-1837-6.

24. Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior.
Kim DW, Yao Z, Graybuck LT, Kim TK, Nguyen TN, Smith KA, Fong O, Yi L, Koulena N, Pierson N, Shah S, Lo L, Pool AH, Oka Y, Pachter L, Cai L, Tasic B, Zeng H, Anderson DJ. Cell. 2019 Oct 17;179(3):713-728.e17. doi: 10.1016/j.cell.2019.09.020.

25. Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease.
Szabo PA, Levitin HM, Miron M, Snyder ME, Senda T, Yuan J, Cheng YL, Bush EC, Dogra P, Thapa P, Farber DL, Sims PA. Nat Commun. 2019 Oct 17;10(1):4706. doi: 10.1038/s41467-019-12464-3.

26. Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton.
Wang K, Wang D, Zheng X, Qin A, Zhou J, Guo B, Chen Y, Wen X, Ye W, Zhou Y, Zhu Y. Nat Commun. 2019 Oct 17;10(1):4714. doi: 10.1038/s41467-019-12575-x.

27. Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy.
Zammataro L, Lopez S, Bellone S, Pettinella F, Bonazzoli E, Perrone E, Zhao S, Menderes G, Altwerger G, Han C, Zeybek B, Bianchi A, Manzano A, Manara P, Cocco E, Buza N, Hui P, Wong S, Ravaggi A, Bignotti E, Romani C, Todeschini P, Zanotti L, Odicino F, Pecorelli S, Donzelli C, Ardighieri L, Angioli R, Raspagliesi F, Scambia G, Choi J, Dong W, Bilguvar K, Alexandrov LB, Silasi DA, Huang GS, Ratner E, Azodi M, Schwartz PE, Pirazzoli V, Stiegler AL, Boggon TJ, Lifton RP, Schlessinger J, Santin AD. Proc Natl Acad Sci U S A. 2019 Oct 17. pii: 201911385. doi: 10.1073/pnas.1911385116.

28. Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses.
O'Flanagan CH, Campbell KR, Zhang AW, Kabeer F, Lim JLP, Biele J, Eirew P, Lai D, McPherson A, Kong E, Bates C, Borkowski K, Wiens M, Hewitson B, Hopkins J, Pham J, Ceglia N, Moore R, Mungall AJ, McAlpine JN; CRUK IMAXT Grand Challenge Team, Shah SP, Aparicio S. Genome Biol. 2019 Oct 17;20(1):210. doi: 10.1186/s13059-019-1830-0.

29. Identification of a γc Receptor Antagonist that Prevents Reprogramming of Human Tissue-resident Cytotoxic T Cells by IL15 and IL21.
Ciszewski C, Discepolo V, Pacis A, Doerr N, Tastet O, Mayassi T, Maglio M, Basheer A, Al-Mawsawi LQ, Green P, Auricchio R, Troncone R, Waldmann TA, Azimi N, Tagaya Y, Barreiro LB, Jabri B. Gastroenterology. 2019 Oct 14. pii: S0016-5085(19)41440-6. doi: 10.1053/j.gastro.2019.10.006.

30. Nucleotide resolution profiling of m7G tRNA modification by TRAC-Seq.
Lin S, Liu Q, Jiang YZ, Gregory RI. Nat Protoc. 2019 Oct 16. doi: 10.1038/s41596-019-0226-7.

31. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses.
Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ. Immunity. 2019 Oct 15;51(4):696-708.e9. doi: 10.1016/j.immuni.2019.09.004.

32. Radiation drives the evolution of orthotopic xenografts initiated from glioblastoma stem-like cells.
McAbee JH, Rath BH, Valdez K, Young DL, Wu X, Shankavaram UT, Camphausen K, Tofilon PJ. Cancer Res. 2019 Oct 15. pii: canres.2452.2019. doi: 10.1158/0008-5472.CAN-19-2452.

33. Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids.
Chhabra S, Liu L, Goh R, Kong X, Warmflash A. PLoS Biol. 2019 Oct 15;17(10):e3000498. doi: 10.1371/journal.pbio.3000498. eCollection 2019 Oct.

34. High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell.
Chen S, Lake BB, Zhang K. Nat Biotechnol. 2019 Oct 14. doi: 10.1038/s41587-019-0290-0.

35. Wnt activator FOXB2 drives the neuroendocrine differentiation of prostate cancer.
Moparthi L, Pizzolato G, Koch S. Proc Natl Acad Sci U S A. 2019 Oct 14. pii: 201906484. doi: 10.1073/pnas.1906484116.

36. Recognition of human gastrointestinal cancer neoantigens by circulating PD-1+ lymphocytes.
Gros A, Tran E, Parkhurst MR, Ilyas S, Pasetto A, Groh EM, Robbins PF, Yossef R, Garcia-Garijo A, Fajardo CA, Prickett TD, Jia L, Gartner JJ, Ray S, Ngo L, Wunderllich JR, Yang JC, Rosenberg SA. J Clin Invest. 2019 Oct 14. pii: 127967. doi: 10.1172/JCI127967.

37. Transcriptome dynamics of the Myxococcus xanthus multicellular developmental program.
Muñoz-Dorado J, Moraleda-Muñoz A, Marcos-Torres FJ, Contreras-Moreno FJ, Martin-Cuadrado AB, Schrader JM, Higgs PI, Pérez J. Elife. 2019 Oct 14;8. pii: e50374. doi: 10.7554/eLife.50374.

38. TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision.
Chen Z, Ji Z, Ngiow SF, Manne S, Cai Z, Huang AC, Johnson J, Staupe RP, Bengsch B, Xu C, Yu S, Kurachi M, Herati RS, Vella LA, Baxter AE, Wu JE, Khan O, Beltra JC, Giles JR, Stelekati E, McLane LM, Lau CW, Yang X, Berger SL, Vahedi G, Ji H, Wherry EJ. Immunity. 2019 Oct 7. pii: S1074-7613(19)30409-1. doi: 10.1016/j.immuni.2019.09.013.

39. Rare-variant collapsing analyses for complex traits: guidelines and applications.
Povysil G, Petrovski S, Hostyk J, Aggarwal V, Allen AS, Goldstein DB. Nat Rev Genet. 2019 Oct 11. doi: 10.1038/s41576-019-0177-4.

40. TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes.
Miklas JW, Clark E, Levy S, Detraux D, Leonard A, Beussman K, Showalter MR, Smith AT, Hofsteen P, Yang X, Macadangdang J, Manninen T, Raftery D, Madan A, Suomalainen A, Kim DH, Murry CE, Fiehn O, Sniadecki NJ, Wang Y, Ruohola-Baker H. Nat Commun. 2019 Oct 11;10(1):4671. doi: 10.1038/s41467-019-12482-1.

41. A systematic evaluation of single cell RNA-seq analysis pipelines.
Vieth B, Parekh S, Ziegenhain C, Enard W, Hellmann I. Nat Commun. 2019 Oct 11;10(1):4667. doi: 10.1038/s41467-019-12266-7.

42. MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions.
Baran Y, Bercovich A, Sebe-Pedros A, Lubling Y, Giladi A, Chomsky E, Meir Z, Hoichman M, Lifshitz A, Tanay A. Genome Biol. 2019 Oct 11;20(1):206. doi: 10.1186/s13059-019-1812-2.

43. DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data.
Zeng W, Chen X, Duren Z, Wang Y, Jiang R, Wong WH. Nat Commun. 2019 Oct 10;10(1):4613. doi: 10.1038/s41467-019-12547-1.

44. KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors.
Feng C, Song C, Liu Y, Qian F, Gao Y, Ning Z, Wang Q, Jiang Y, Li Y, Li M, Chen J, Zhang J, Li C. Nucleic Acids Res. 2019 Oct 10. pii: gkz881. doi: 10.1093/nar/gkz881.

45. Cell-type-specific transcriptome and histone modification dynamics during cellular reprogramming in the Arabidopsis stomatal lineage.
Lee LR, Wengier DL, Bergmann DC. Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21914-21924. doi: 10.1073/pnas.1911400116. Epub 2019 Oct 8.

46. A clonal expression biomarker associates with lung cancer mortality.
Biswas D, Birkbak NJ, Rosenthal R, Hiley CT, Lim EL, Papp K, Boeing S, Krzystanek M, Djureinovic D, La Fleur L, Greco M, Döme B, Fillinger J, Brunnström H, Wu Y, Moore DA, Skrzypski M, Abbosh C, Litchfield K, Al Bakir M, Watkins TBK, Veeriah S, Wilson GA, Jamal-Hanjani M, Moldvay J, Botling J, Chinnaiyan AM, Micke P, Hackshaw A, Bartek J, Csabai I, Szallasi Z, Herrero J, McGranahan N, Swanton C; TRACERx Consortium. Nat Med. 2019 Oct 7. doi: 10.1038/s41591-019-0595-z.

47. Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling.
Wang P, Tang W, Li Z, Zou Z, Zhou Y, Li R, Xiong T, Wang J, Zou P. Nat Chem Biol. 2019 Oct 7. doi: 10.1038/s41589-019-0368-5.

48. An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations.
Dube U, Del-Aguila JL, Li Z, Budde JP, Jiang S, Hsu S, Ibanez L, Fernandez MV, Farias F, Norton J, Gentsch J, Wang F; Dominantly Inherited Alzheimer Network (DIAN), Salloway S, Masters CL, Lee JH, Graff-Radford NR, Chhatwal JP, Bateman RJ, Morris JC, Karch CM, Harari O, Cruchaga C. Nat Neurosci. 2019 Oct 7. doi: 10.1038/s41593-019-0501-5.

49. Histone deacetylase 3 controls a transcriptional network required for B cell maturation.
Stengel KR, Bhaskara S, Wang J, Liu Q, Ellis JD, Sampathi S, Hiebert SW. Nucleic Acids Res. 2019 Oct 5. pii: gkz816. doi: 10.1093/nar/gkz816.

50. APAatlas: decoding alternative polyadenylation across human tissues.
Hong W, Ruan H, Zhang Z, Ye Y, Liu Y, Li S, Jing Y, Zhang H, Diao L, Liang H, Han L. Nucleic Acids Res. 2019 Oct 5. pii: gkz876. doi: 10.1093/nar/gkz876.

51. METTL3-mediated m6A modification of HDGF mRNA promotes gastric cancer progression and has prognostic significance.
Wang Q, Chen C, Ding Q, Zhao Y, Wang Z, Chen J, Jiang Z, Zhang Y, Xu G, Zhang J, Zhou J, Sun B, Zou X, Wang S. Gut. 2019 Oct 3. pii: gutjnl-2019-319639. doi: 10.1136/gutjnl-2019-319639.

52. Zebrafish MITF-low melanoma subtype models reveal transcriptional subclusters and MITF-independent residual disease.
Travnickova J, Wojciechowska S, Khamseh A, Gautier P, Brown DV, Lefevre T, Brombin A, Ewing A, Capper A, Spitzer M, Dilshat R, Semple CA, Mathers ME, Lister JA, Steingrímsson E, Voet T, Ponting CP, Patton EE. Cancer Res. 2019 Oct 3. pii: canres.0037.2019. doi: 10.1158/0008-5472.CAN-19-0037.

53. The RIPK4-IRF6 signalling axis safeguards epidermal differentiation and barrier function.
Oberbeck N, Pham VC, Webster JD, Reja R, Huang CS, Zhang Y, Roose-Girma M, Warming S, Li Q, Birnberg A, Wong W, Sandoval W, Kőműves LG, Yu K, Dugger DL, Maltzman A, Newton K, Dixit VM. Nature. 2019 Oct 2. doi: 10.1038/s41586-019-1615-3.

54. Structural Elucidation of Bisulfite Adducts to Pseudouridine That Result in Deletion Signatures during Reverse Transcription of RNA.
Fleming AM, Alenko A, Kitt JP, Orendt AM, Flynn PF, Harris JM, Burrows CJ. J Am Chem Soc. 2019 Oct 16;141(41):16450-16460. doi: 10.1021/jacs.9b08630. Epub 2019 Oct 2.

55. LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data.
Wan C, Chang W, Zhang Y, Shah F, Lu X, Zang Y, Zhang A, Cao S, Fishel ML, Ma Q, Zhang C. Nucleic Acids Res. 2019 Oct 10;47(18):e111. doi: 10.1093/nar/gkz655.

56. Nonparametric expression analysis using inferential replicate counts.
Zhu A, Srivastava A, Ibrahim JG, Patro R, Love MI. Nucleic Acids Res. 2019 Oct 10;47(18):e105. doi: 10.1093/nar/gkz622.

57. RRAD mutation causes electrical and cytoskeletal defects in cardiomyocytes derived from a familial case of Brugada syndrome.
Belbachir N, Portero V, Al Sayed ZR, Gourraud JB, Dilasser F, Jesel L, Guo H, Wu H, Gaborit N, Guilluy C, Girardeau A, Bonnaud S, Simonet F, Karakachoff M, Pattier S, Scott C, Burel S, Marionneau C, Chariau C, Gaignerie A, David L, Genin E, Deleuze JF, Dina C, Sauzeau V, Loirand G, Baró I, Schott JJ, Probst V, Wu JC, Redon R, Charpentier F, Le Scouarnec S. Eur Heart J. 2019 Oct 1;40(37):3081-3094. doi: 10.1093/eurheartj/ehz308.