Monthly Letter

1. Transcriptional dynamics of pluripotent stem cell-derived endothelial cell differentiation revealed by single-cell RNA sequencing.
McCracken IR, Taylor RS, Kok FO, de la Cuesta F, Dobie R, Henderson BEP, Mountford JC, Caudrillier A, Henderson NC, Ponting CP, Baker AH. Eur Heart J. 2019 Jun 26. pii: ehz351. doi: 10.1093/eurheartj/ehz351.

2. A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing.
Tettey TT, Gao X, Shao W, Li H, Story BA, Chitsazan AD, Glaser RL, Goode ZH, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. Cell Rep. 2019 Jun 25;27(13):3770-3779.e7. doi: 10.1016/j.celrep.2019.05.099.

3. Single-Cell RNA-Seq Reveals Developmental Origins and Ontogenetic Stability of Neurexin Alternative Splicing Profiles.
Lukacsovich D, Winterer J, Que L, Luo W, Lukacsovich T, Földy C. Cell Rep. 2019 Jun 25;27(13):3752-3759.e4. doi: 10.1016/j.celrep.2019.05.090.

4. Fetal and trophoblast PI3K p110α have distinct roles in regulating resource supply to the growing fetus in mice.
López-Tello J, Pérez-García V, Khaira J, Kusinski LC, Cooper WN, Andreani A, Grant I, Fernández de Liger E, Lam BY, Hemberger M, Sandovici I, Constancia M, Sferruzzi-Perri AN. Elife. 2019 Jun 26;8. pii: e45282. doi: 10.7554/eLife.45282.

5. Neural crest-specific deletion of Rbfox2 in mice leads to craniofacial abnormalities including cleft palate.
Cibi DM, Mia MM, Guna Shekeran S, Yun LS, Sandireddy R, Gupta P, Hota M, Sun L, Ghosh S, Singh MK. Elife. 2019 Jun 26;8. pii: e45418. doi: 10.7554/eLife.45418.

6. Claudin-18 expression in oesophagogastric adenocarcinomas: a tissue microarray study of 523 molecularly profiled cases.
Coati I, Lotz G, Fanelli GN, Brignola S, Lanza C, Cappellesso R, Pellino A, Pucciarelli S, Spolverato G, Guzzardo V, Munari G, Zaninotto G, Scarpa M, Mastracci L, Farinati F, Realdon S, Pilati P, Lonardi S, Valeri N, Rugge M, Kiss A, Loupakis F, Fassan M. Br J Cancer. 2019 Jun 25. doi: 10.1038/s41416-019-0508-4.

7. Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells.
Tibbitt CA, Stark JM, Martens L, Ma J, Mold JE, Deswarte K, Oliynyk G, Feng X, Lambrecht BN, De Bleser P, Nylén S, Hammad H, Arsenian Henriksson M, Saeys Y, Coquet JM. Immunity. 2019 Jun 14. pii: S1074-7613(19)30234-1. doi: 10.1016/j.immuni.2019.05.014.

8. Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming.
Zhou Y, Liu Z, Welch JD, Gao X, Wang L, Garbutt T, Keepers B, Ma H, Prins JF, Shen W, Liu J, Qian L. Cell Stem Cell. 2019 Jun 12. pii: S1934-5909(19)30224-3. doi: 10.1016/j.stem.2019.05.020.

9. Atlas of Subcellular RNA Localization Revealed by APEX-Seq.
Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY. Cell. 2019 Jun 14. pii: S0092-8674(19)30555-0. doi: 10.1016/j.cell.2019.05.027.

10. Integrated multiomic analysis reveals comprehensive tumour heterogeneity and novel immunophenotypic classification in hepatocellular carcinomas.
Zhang Q, Lou Y, Yang J, Wang J, Feng J, Zhao Y, Wang L, Huang X, Fu Q, Ye M, Zhang X, Chen Y, Ma C, Ge H, Wang J, Wu J, Wei T, Chen Q, Wu J, Yu C, Xiao Y, Feng X, Guo G, Liang T, Bai X. Gut. 2019 Jun 21. pii: gutjnl-2019-318912. doi: 10.1136/gutjnl-2019-318912.

11. An Atlas of Human Glycosylation Pathways Enables Display of the Human Glycome by Gene Engineered Cells.
Narimatsu Y, Joshi HJ, Nason R, Van Coillie J, Karlsson R, Sun L, Ye Z, Chen YH, Schjoldager KT, Steentoft C, Furukawa S, Bensing BA, Sullam PM, Thompson AJ, Paulson JC, Büll C, Adema GJ, Mandel U, Hansen L, Bennett EP, Varki A, Vakhrushev SY, Yang Z, Clausen H. Mol Cell. 2019 Jun 10. pii: S1097-2765(19)30389-2. doi: 10.1016/j.molcel.2019.05.017.

12. CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing.
de Kanter JK, Lijnzaad P, Candelli T, Margaritis T, Holstege FCP. Nucleic Acids Res. 2019 Jun 21. pii: gkz543. doi: 10.1093/nar/gkz543.

13. Species-specific mechanisms of cytotoxicity toward immune cells determine the successful outcome of Vibrio infections.
Rubio T, Oyanedel D, Labreuche Y, Toulza E, Luo X, Bruto M, Chaparro C, Torres M, de Lorgeril J, Haffner P, Vidal-Dupiol J, Lagorce A, Petton B, Mitta G, Jacq A, Le Roux F, Charrière GM, Destoumieux-Garzón D. Proc Natl Acad Sci U S A. 2019 Jun 20. pii: 201905747. doi: 10.1073/pnas.1905747116.

14. Current best practices in single-cell RNA-seq analysis: a tutorial.
Luecken MD, Theis FJ. Mol Syst Biol. 2019 Jun 19;15(6):e8746. doi: 10.15252/msb.20188746. Review.

15. Germline mutations in the transcription factor IKZF5 cause thrombocytopenia.
Lentaigne C, Greene D, Sivapalaratnam S, Favier R, Seyres D, Thys C, Grassi L, Mangles S, Sibson K, Stubbs MJ, Burden F, Bordet JC, Armari-Alla C, Erber W, Farrow S, Gleadall N, Gomez K, Megy K, Papadia S, Penkett CJ, Sims MC, Stefanucci L, Stephens JC, Read RJ, Stirrups KE, Ouwehand WH, Laffan MA, Frontini M, Freson K, Turro E. Blood. 2019 Jun 19. pii: blood.2019000782. doi: 10.1182/blood.2019000782.

16. Single-Cell Transcriptomics Identifies the Adaptation of Scart1+ Vγ6+ T Cells to Skin Residency as Activated Effector Cells.
Tan L, Sandrock I, Odak I, Aizenbud Y, Wilharm A, Barros-Martins J, Tabib Y, Borchers A, Amado T, Gangoda L, Herold MJ, Schmidt-Supprian M, Kisielow J, Silva-Santos B, Koenecke C, Hovav AH, Krebs C, Prinz I, Ravens S. Cell Rep. 2019 Jun 18;27(12):3657-3671.e4. doi: 10.1016/j.celrep.2019.05.064.

17. Rational Reprogramming of Cellular States by Combinatorial Perturbation.
Duan J, Li B, Bhakta M, Xie S, Zhou P, Munshi NV, Hon GC. Cell Rep. 2019 Jun 18;27(12):3486-3499.e6. doi: 10.1016/j.celrep.2019.05.079.

18. Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2-Jhdm1b-Mkk6-Glis1-Nanog-Essrb-Sall4.
Wang B, Wu L, Li D, Liu Y, Guo J, Li C, Yao Y, Wang Y, Zhao G, Wang X, Fu M, Liu H, Cao S, Wu C, Yu S, Zhou C, Qin Y, Kuang J, Ming J, Chu S, Yang X, Zhu P, Pan G, Chen J, Liu J, Pei D. Cell Rep. 2019 Jun 18;27(12):3473-3485.e5. doi: 10.1016/j.celrep.2019.05.068.

19. Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals.
Perez S, Kaspi A, Domovitz T, Davidovich A, Lavi-Itzkovitz A, Meirson T, Alison Holmes J, Dai CY, Huang CF, Chung RT, Nimer A, El-Osta A, Yaari G, Stemmer SM, Yu ML, Haviv I, Gal-Tanamy M. PLoS Genet. 2019 Jun 19;15(6):e1008181. doi: 10.1371/journal.pgen.1008181.

20. SMARTer single cell total RNA sequencing.
Verboom K, Everaert C, Bolduc N, Livak KJ, Yigit N, Rombaut D, Anckaert J, Lee S, Venø MT, Kjems J, Speleman F, Mestdagh P, Vandesompele J. Nucleic Acids Res. 2019 Jun 19. pii: gkz535. doi: 10.1093/nar/gkz535.

21. Complete Tracheal Ring Deformity: A Translational Genomics Approach to Pathogenesis.
Sinner DI, Carey B, Zgherea D, Kaufman KM, Leesman L, Wood RE, Rutter MJ, de Alarcon A, Elluru RG, Harley JB, Whitsett JA, Trapnell BC. Am J Respir Crit Care Med. 2019 Jun 19. doi: 10.1164/rccm.201809-1626OC.

22. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.
McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. Nat Methods. 2019 Jun 17. doi: 10.1038/s41592-019-0433-8.

23. Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells.
Rooijers K, Markodimitraki CM, Rang FJ, de Vries SS, Chialastri A, de Luca KL, Mooijman D, Dey SS, Kind J. Nat Biotechnol. 2019 Jun 17. doi: 10.1038/s41587-019-0150-y.

24. Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells.
Fu X, Wu X, Djekidel MN, Zhang Y. Nat Cell Biol. 2019 Jun 17. doi: 10.1038/s41556-019-0343-0.

25. The Open Chromatin Landscape of Non-small Cell Lung Carcinoma.
Wang Z, Tu K, Xia L, Luo K, Luo W, Tang J, Lu K, Hu X, He Y, Qiao W, Zhou Y, Zhang J, Cao F, Dai S, Tian P, Wang Y, Liu L, Che G, Zhou Q, Xie D, Li W. Cancer Res. 2019 Jun 17. pii: canres.3663.2018. doi: 10.1158/0008-5472.CAN-18-3663.

26. Role of Patient and Disease Factors in Adjuvant Systemic Therapy Decision Making for Early-Stage, Operable Breast Cancer: Update of the ASCO Endorsement of the Cancer Care Ontario Guideline.
Henry NL, Somerfield MR, Abramson VG, Ismaila N, Allison KH, Anders CK, Chingos DT, Eisen A, Ferrari BL, Openshaw TH, Spears PA, Vikas P, Stearns V. J Clin Oncol. 2019 Jun 17:JCO1900948. doi: 10.1200/JCO.19.00948.

27. Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver.
Çalışkan M, Manduchi E, Rao HS, Segert JA, Beltrame MH, Trizzino M, Park Y, Baker SW, Chesi A, Johnson ME, Hodge KM, Leonard ME, Loza B, Xin D, Berrido AM, Hand NJ, Bauer RC, Wells AD, Olthoff KM, Shaked A, Rader DJ, Grant SFA, Brown CD. Am J Hum Genet. 2019 Jun 5. pii: S0002-9297(19)30197-1. doi: 10.1016/j.ajhg.2019.05.010.

28. Systematic Functional Interrogation of Genes in GWAS Loci Identified ATF1 as a Key Driver in Colorectal Cancer Modulated by a Promoter-Enhancer Interaction.
Tian J, Chang J, Gong J, Lou J, Fu M, Li J, Ke J, Zhu Y, Gong Y, Yang Y, Zou D, Peng X, Yang N, Mei S, Wang X, Zhong R, Cai K, Miao X. Am J Hum Genet. 2019 Jun 11. pii: S0002-9297(19)30190-9. doi: 10.1016/j.ajhg.2019.05.004.

29. Morphological classification of pancreatic ductal adenocarcinoma that predicts molecular subtypes and correlates with clinical outcome.
N Kalimuthu S, Wilson GW, Grant RC, Seto M, O'Kane G, Vajpeyi R, Notta F, Gallinger S, Chetty R. Gut. 2019 Jun 14. pii: gutjnl-2019-318217. doi: 10.1136/gutjnl-2019-318217.

30. Single-molecule long-read sequencing reveals the chromatin basis of gene expression.
Wang Y, Wang A, Liu Z, Thurman AL, Powers LS, Zou M, Zhao Y, Hefel A, Li Y, Zabner J, Au KF. Genome Res. 2019 Jun 14. pii: gr.251116.119. doi: 10.1101/gr.251116.119.

31. Integration of Single-Cell Genomics Datasets.
Adey AC. Cell. 2019 Jun 13;177(7):1677-1679. doi: 10.1016/j.cell.2019.05.034.

32. Simulating multiple faceted variability in single cell RNA sequencing.
Zhang X, Xu C, Yosef N. Nat Commun. 2019 Jun 13;10(1):2611. doi: 10.1038/s41467-019-10500-w.

33. Endothelial ERK1/2 signaling maintains integrity of the quiescent endothelium.
Ricard N, Scott RP, Booth CJ, Velazquez H, Cilfone NA, Baylon JL, Gulcher JR, Quaggin SE, Chittenden TW, Simons M. J Exp Med. 2019 Jun 13. pii: jem.20182151. doi: 10.1084/jem.20182151.

34. Hepatocellular Carcinomas With Mutational Activation of Beta Catenin Require Choline and can be Detected by Positron Emission Tomography.
Gougelet A, Sartor C, Senni N, Calderaro J, Fartoux L, Lequoy M, Wendum D, Talbot JN, Prignon A, Chalaye J, Imbeaud S, Zucman-Rossi J, Tordjmann T, Godard C, Bossard P, Rosmorduc O, Amaddeo G, Colnot S. Gastroenterology. 2019 Jun 10. pii: S0016-5085(19)40988-8. doi: 10.1053/j.gastro.2019.05.069.

35. Tumor Heterogeneity Underlies Differential Cisplatin Sensitivity in Mouse Models of Small-Cell Lung Cancer.
Böttger F, Semenova EA, Song JY, Ferone G, van der Vliet J, Cozijnsen M, Bhaskaran R, Bombardelli L, Piersma SR, Pham TV, Jimenez CR, Berns A. Cell Rep. 2019 Jun 11;27(11):3345-3358.e4. doi: 10.1016/j.celrep.2019.05.057.

36. N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses.
Broszeit F, Tzarum N, Zhu X, Nemanichvili N, Eggink D, Leenders T, Li Z, Liu L, Wolfert MA, Papanikolaou A, Martínez-Romero C, Gagarinov IA, Yu W, García-Sastre A, Wennekes T, Okamatsu M, Verheije MH, Wilson IA, Boons GJ, de Vries RP. Cell Rep. 2019 Jun 11;27(11):3284-3294.e6. doi: 10.1016/j.celrep.2019.05.048.

37. Clinical, Histopathological, and Molecular Diagnostics in Lethal Lung Developmental Disorders.
Vincent M, Karolak JA, Deutsch G, Gambin T, Popek E, Isidor B, Szafranski P, Le Caignec C, Stankiewicz P. Am J Respir Crit Care Med. 2019 Jun 12. doi: 10.1164/rccm.201903-0495TR.

38. LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis.
Zhang C, Gao M, Seitz NC, Angel W, Hallworth A, Wiratan L, Darwish O, Alkharouf N, Dawit T, Lin D, Egoshi R, Wang X, McClung CR, Lu H. Nat Commun. 2019 Jun 11;10(1):2543. doi: 10.1038/s41467-019-10485-6.

39. Tumor-associated reactive astrocytes aid the evolution of immunosuppressive environment in glioblastoma.
Henrik Heiland D, Ravi VM, Behringer SP, Frenking JH, Wurm J, Joseph K, Garrelfs NWC, Strähle J, Heynckes S, Grauvogel J, Franco P, Mader I, Schneider M, Potthoff AL, Delev D, Hofmann UG, Fung C, Beck J, Sankowski R, Prinz M, Schnell O. Nat Commun. 2019 Jun 11;10(1):2541. doi: 10.1038/s41467-019-10493-6.

40. Loss of the HIF pathway in a widely distributed intertidal crustacean, the copepod Tigriopus californicus.
Graham AM, Barreto FS. Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12913-12918. doi: 10.1073/pnas.1819874116. Epub 2019 Jun 10.

41. Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.
Welch JD, Kozareva V, Ferreira A, Vanderburg C, Martin C, Macosko EZ. Cell. 2019 Jun 13;177(7):1873-1887.e17. doi: 10.1016/j.cell.2019.05.006. Epub 2019 Jun 6.

42. Comprehensive Integration of Single-Cell Data.
Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R. Cell. 2019 Jun 13;177(7):1888-1902.e21. doi: 10.1016/j.cell.2019.05.031. Epub 2019 Jun 6.

43. Intraductal Papillary Mucinous Neoplasms Arise from Multiple Independent Clones, Each With Distinct Mutations.
Fischer CG, Guthrie VB, Braxton AM, Zheng L, Wang P, Song Q, Griffin JF, Chianchiano PE, Hosoda W, Niknafs N, Springer S, Molin MD, Masica D, Scharpf RB, Thompson ED, He J, Wolfgang CL, Hruban RH, Roberts NJ, Lennon AM, Jiao Y, Karchin R, Wood LD. Gastroenterology. 2019 Jun 5. pii: S0016-5085(19)40987-6. doi: 10.1053/j.gastro.2019.06.001.

44. Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization.
Zhang L, Zhang S. Nucleic Acids Res. 2019 Jun 8. pii: gkz488. doi: 10.1093/nar/gkz488.

45. GRID-seq for comprehensive analysis of global RNA-chromatin interactions.
Zhou B, Li X, Luo D, Lim DH, Zhou Y, Fu XD. Nat Protoc. 2019 Jun 7. doi: 10.1038/s41596-019-0172-4.

46. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.
Shao W, Guo T, Toussaint NC, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser CD, Poyet C, Ljubicic J, Rupp N, Rüschoff JH, Zhong Q, Beyer A, Ji J, Collins BC, Liu Y, Rätsch G, Wild PJ, Aebersold R. Nat Commun. 2019 Jun 7;10(1):2524. doi: 10.1038/s41467-019-10513-5.

47. Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy.
Takata A, Nakashima M, Saitsu H, Mizuguchi T, Mitsuhashi S, Takahashi Y, Okamoto N, Osaka H, Nakamura K, Tohyama J, Haginoya K, Takeshita S, Kuki I, Okanishi T, Goto T, Sasaki M, Sakai Y, Miyake N, Miyatake S, Tsuchida N, Iwama K, Minase G, Sekiguchi F, Fujita A, Imagawa E, Koshimizu E, Uchiyama Y, Hamanaka K, Ohba C, Itai T, Aoi H, Saida K, Sakaguchi T, Den K, Takahashi R, Ikeda H, Yamaguchi T, Tsukamoto K, Yoshitomi S, Oboshi T, Imai K, Kimizu T, Kobayashi Y, Kubota M, Kashii H, Baba S, Iai M, Kira R, Hara M, Ohta M, Miyata Y, Miyata R, Takanashi JI, Matsui J, Yokochi K, Shimono M, Amamoto M, Takayama R, Hirabayashi S, Aiba K, Matsumoto H, Nabatame S, Shiihara T, Kato M, Matsumoto N. Nat Commun. 2019 Jun 7;10(1):2506. doi: 10.1038/s41467-019-10482-9.

48. In vivo nuclear capture and molecular profiling identifies Gmeb1 as a transcriptional regulator essential for dopamine neuron function.
Tuesta LM, Djekidel MN, Chen R, Lu F, Wang W, Sabatini BL, Zhang Y. Nat Commun. 2019 Jun 7;10(1):2508. doi: 10.1038/s41467-019-10267-0.

49. Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features.
Barros de Andrade E Sousa L, Jonkers I, Syx L, Dunkel I, Chaumeil J, Picard C, Foret B, Chen CJ, Lis JT, Heard E, Schulz EG, Marsico A. Genome Res. 2019 Jun 7. pii: gr.245027.118. doi: 10.1101/gr.245027.118.

50. Multiplex profiling of peritoneal metastases from gastric adenocarcinoma identified novel targets and molecular subtypes that predict treatment response.
Wang R, Song S, Harada K, Ghazanfari Amlashi F, Badgwell B, Pizzi MP, Xu Y, Zhao W, Dong X, Jin J, Wang Y, Scott A, Ma L, Huo L, Vicente D, Blum Murphy M, Shanbhag N, Tatlonghari G, Thomas I, Rogers J, Kobayashi M, Vykoukal J, Estrella JS, Roy-Chowdhuri S, Han G, Zhang S, Mao X, Song X, Zhang J, Gu J, Johnson RL, Calin GA, Peng G, Lee JS, Hanash SM, Futreal A, Wang Z, Wang L, Ajani JA. Gut. 2019 Jun 6. pii: gutjnl-2018-318070. doi: 10.1136/gutjnl-2018-318070.

51. Aryl Hydrocarbon Receptor Signaling Prevents Activation of Hepatic Stellate Cells and Liver Fibrogenesis in Mice.
Yan J, Tung HC, Li S, Niu Y, Garbacz WG, Lu P, Bi Y, Li Y, He J, Xu M, Ren S, Monga SP, Schwabe RF, Yang D, Xie W. Gastroenterology. 2019 Jun 3. pii: S0016-5085(19)40984-0. doi: 10.1053/j.gastro.2019.05.066.

52. Exome sequencing in multiple sclerosis families identifies 12 candidate genes and nominates biological pathways for the genesis of disease.
Vilariño-Güell C, Zimprich A, Martinelli-Boneschi F, Herculano B, Wang Z, Matesanz F, Urcelay E, Vandenbroeck K, Leyva L, Gris D, Massaad C, Quandt JA, Traboulsee AL, Encarnacion M, Bernales CQ, Follett J, Yee IM, Criscuoli MG, Deutschländer A, Reinthaler EM, Zrzavy T, Mascia E, Zauli A, Esposito F, Alcina A, Izquierdo G, Espino-Paisán L, Mena J, Antigüedad A, Urbaneja-Romero P, Ortega-Pinazo J, Song W, Sadovnick AD. PLoS Genet. 2019 Jun 6;15(6):e1008180. doi: 10.1371/journal.pgen.1008180. eCollection 2019 Jun.

53. PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription.
Steinbach N, Hasson D, Mathur D, Stratikopoulos EE, Sachidanandam R, Bernstein E, Parsons RE. Nucleic Acids Res. 2019 Jun 20;47(11):5573-5586. doi: 10.1093/nar/gkz272.

54. Naturally acquired immunity against immature Plasmodium falciparum gametocytes.
Dantzler KW, Ma S, Ngotho P, Stone WJR, Tao D, Rijpma S, De Niz M, Nilsson Bark SK, Jore MM, Raaijmakers TK, Early AM, Ubaida-Mohien C, Lemgruber L, Campo JJ, Teng AA, Le TQ, Walker CL, Hermand P, Deterre P, Davies DH, Felgner P, Morlais I, Wirth DF, Neafsey DE, Dinglasan RR, Laufer M, Huttenhower C, Seydel K, Taylor T, Bousema T, Marti M. Sci Transl Med. 2019 Jun 5;11(495). pii: eaav3963. doi: 10.1126/scitranslmed.aav3963.

55. CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries.
Hardigan AA, Roberts BS, Moore DE, Ramaker RC, Jones AL, Myers RM. Nucleic Acids Res. 2019 Jun 5. pii: gkz425. doi: 10.1093/nar/gkz425.

56. A practical guide to methods controlling false discoveries in computational biology.
Korthauer K, Kimes PK, Duvallet C, Reyes A, Subramanian A, Teng M, Shukla C, Alm EJ, Hicks SC. Genome Biol. 2019 Jun 4;20(1):118. doi: 10.1186/s13059-019-1716-1.

57. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.
Frésard L, Smail C, Ferraro NM, Teran NA, Li X, Smith KS, Bonner D, Kernohan KD, Marwaha S, Zappala Z, Balliu B, Davis JR, Liu B, Prybol CJ, Kohler JN, Zastrow DB, Reuter CM, Fisk DG, Grove ME, Davidson JM, Hartley T, Joshi R, Strober BJ, Utiramerur S; Undiagnosed Diseases Network; Care4Rare Canada Consortium, Lind L, Ingelsson E, Battle A, Bejerano G, Bernstein JA, Ashley EA, Boycott KM, Merker JD, Wheeler MT, Montgomery SB. Nat Med. 2019 Jun;25(6):911-919. doi: 10.1038/s41591-019-0457-8. Epub 2019 Jun 3.

58. A comprehensive single cell transcriptional landscape of human hematopoietic progenitors.
Pellin D, Loperfido M, Baricordi C, Wolock SL, Montepeloso A, Weinberg OK, Biffi A, Klein AM, Biasco L. Nat Commun. 2019 Jun 3;10(1):2395. doi: 10.1038/s41467-019-10291-0.

59. Single-cell transcriptomics unveils gene regulatory network plasticity.
Iacono G, Massoni-Badosa R, Heyn H. Genome Biol. 2019 Jun 4;20(1):110. doi: 10.1186/s13059-019-1713-4.

60. APOBEC3B interaction with PRC2 modulates microenvironment to promote HCC progression.
Wang D, Li X, Li J, Lu Y, Zhao S, Tang X, Chen X, Li J, Zheng Y, Li S, Sun R, Yan M, Yu D, Cao G, Yang Y. Gut. 2019 Jun 1. pii: gutjnl-2018-317601. doi: 10.1136/gutjnl-2018-317601.

61. HOT or not: examining the basis of high-occupancy target regions.
Wreczycka K, Franke V, Uyar B, Wurmus R, Bulut S, Tursun B, Akalin A. Nucleic Acids Res. 2019 Jun 20;47(11):5735-5745. doi: 10.1093/nar/gkz460.

62. Cycloheximide can distort measurements of mRNA levels and translation efficiency.
Santos DA, Shi L, Tu BP, Weissman JS. Nucleic Acids Res. 2019 Jun 4;47(10):4974-4985. doi: 10.1093/nar/gkz205.

63. Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay.
Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R. Nucleic Acids Res. 2019 Jun 4;47(10):5293-5306. doi: 10.1093/nar/gkz193.

64. Author Correction: Recapitulating endocrine cell clustering in culture promotes maturation of human stem-cell-derived β cells.
Nair GG, Liu JS, Russ HA, Tran S, Saxton MS, Chen R, Juang C, Li ML, Nguyen VQ, Giacometti S, Puri S, Xing Y, Wang Y, Szot GL, Oberholzer J, Bhushan A, Hebrok M. Nat Cell Biol. 2019 Jun;21(6):792. doi: 10.1038/s41556-019-0316-3.

65. Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders.
Hjelm BE, Rollins B, Morgan L, Sequeira A, Mamdani F, Pereira F, Damas J, Webb MG, Weber MD, Schatzberg AF, Barchas JD, Lee FS, Akil H, Watson SJ, Myers RM, Chao EC, Kimonis V, Thompson PM, Bunney WE, Vawter MP. Nucleic Acids Res. 2019 Jun 4;47(10):e59. doi: 10.1093/nar/gkz164.

66. Cell-specific network constructed by single-cell RNA sequencing data.
Dai H, Li L, Zeng T, Chen L. Nucleic Acids Res. 2019 Jun 20;47(11):e62. doi: 10.1093/nar/gkz172.

67. Cell lineage inference from SNP and scRNA-Seq data.
Ding J, Lin C, Bar-Joseph Z. Nucleic Acids Res. 2019 Jun 4;47(10):e56. doi: 10.1093/nar/gkz146.

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