|
1.
Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response.
Montoya DJ, Andrade P, Silva BJA, Teles RMB, Ma F, Bryson B, Sadanand S, Noel T, Lu J, Sarno E, Arnvig KB, Young D, Lahiri R, Williams DL, Fortune S, Bloom BR, Pellegrini M, Modlin RL.
Cell Rep. 2019 Mar 26;26(13):3574-3585.e3. doi: 10.1016/j.celrep.2019.02.109.
2.
Cycloheximide can distort measurements of mRNA levels and translation efficiency.
Santos DA, Shi L, Tu BP, Weissman JS.
Nucleic Acids Res. 2019 Mar 27. pii: gkz205. doi: 10.1093/nar/gkz205.
3.
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 Mar 27. pii: gkz193. doi: 10.1093/nar/gkz193.
4.
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 Mar 26. doi: 10.1038/s41556-019-0316-3.
5.
TCP4 and PIF3 antagonistically regulate organ-specific light induction of SAUR16/50 to modulate cotyledon opening during de-etiolation in Arabidopsis.
Dong J, Sun N, Yang J, Deng Z, Lan J, Qin G, He H, Deng XW, Irish VF, Chen H, Wei N.
Plant Cell. 2019 Mar 25. pii: tpc.00803.2018. doi: 10.1105/tpc.18.00803.
6.
The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes.
Schield DR, Card DC, Hales NR, Perry BW, Pasquesi GM, Blackmon H, Adams RH, Corbin AB, Smith CF, Ramesh B, Demuth JP, Betrán E, Tollis M, Meik JM, Mackessy SP, Castoe TA.
Genome Res. 2019 Mar 21. doi: 10.1101/gr.240952.118.
7.
Gene expression does not support the developmental hourglass model in three animals with spiralian development.
Wu L, Ferger KE, Lambert JD.
Mol Biol Evol. 2019 Mar 20. pii: msz065. doi: 10.1093/molbev/msz065.
8.
A non-enzymatic method for dissection of mouse bladder urothelial tissue.
Lu M, Zhu K, Schulam PG, Chai TC.
Nat Protoc. 2019 Mar 20. doi: 10.1038/s41596-019-0142-x.
9.
Dissecting Cell Lineage Specification and Sex Fate Determination in Gonadal Somatic Cells Using Single-Cell Transcriptomics.
Stévant I, Kühne F, Greenfield A, Chaboissier MC, Dermitzakis ET, Nef S.
Cell Rep. 2019 Mar 19;26(12):3272-3283.e3. doi: 10.1016/j.celrep.2019.02.069.
10.
Vitamin D-Binding Protein Deficiency and Homozygous Deletion of the GC Gene.
Henderson CM, Fink SL, Bassyouni H, Argiropoulos B, Brown L, Laha TJ, Jackson KJ, Lewkonia R, Ferreira P, Hoofnagle AN, Marcadier JL.
N Engl J Med. 2019 Mar 21;380(12):1150-1157. doi: 10.1056/NEJMoa1807841.
11.
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
Wolf FA, Hamey FK, Plass M, Solana J, Dahlin JS, Göttgens B, Rajewsky N, Simon L, Theis FJ.
Genome Biol. 2019 Mar 19;20(1):59. doi: 10.1186/s13059-019-1663-x.
12.
Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning.
Deng Y, Bao F, Dai Q, Wu LF, Altschuler SJ.
Nat Methods. 2019 Mar 18. doi: 10.1038/s41592-019-0353-7.
13.
Mechanical Stretch Increases Expression of CXCL1 in Liver Sinusoidal Endothelial Cells to Recruit Neutrophils, Generate Sinusoidal Microthombi, and Promote Portal Hypertension.
Hilscher MB, Sehrawat T, Arab Verdugo JP, Zeng Z, Gao J, Liu M, Kostallari E, Gao Y, Simonetto DA, Yaqoob U, Cao S, Revzin A, Beyder A, Wang R, Kamath PS, Kubes P, Shah VH.
Gastroenterology. 2019 Mar 11. pii: S0016-5085(19)33554-1. doi: 10.1053/j.gastro.2019.03.013.
14.
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 Mar 14. pii: gkz164. doi: 10.1093/nar/gkz164.
15.
Human Induced Pluripotent Stem Cell Model of Trastuzumab-Induced Cardiac Dysfunction in Breast Cancer Patients.
Kitani T, Ong SG, Lam CK, Rhee JW, Zhang JZ, Oikonomopoulos A, Ma N, Tian L, Lee J, Telli ML, Witteles RM, Sharma A, Sayed N, Wu JC.
Circulation. 2019 Mar 14. doi: 10.1161/CIRCULATIONAHA.118.037357.
16.
Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing.
Ranum PT, Goodwin AT, Yoshimura H, Kolbe DL, Walls WD, Koh JY, He DZZ, Smith RJH.
Cell Rep. 2019 Mar 12;26(11):3160-3171.e3. doi: 10.1016/j.celrep.2019.02.053.
17.
p53 Promotes Cancer Cell Adaptation to Glutamine Deprivation by Upregulating Slc7a3 to Increase Arginine Uptake.
Lowman XH, Hanse EA, Yang Y, Ishak Gabra MB, Tran TQ, Li H, Kong M.
Cell Rep. 2019 Mar 12;26(11):3051-3060.e4. doi: 10.1016/j.celrep.2019.02.037.
18.
Cell-specific network constructed by single-cell RNA sequencing data.
Dai H, Li L, Zeng T, Chen L.
Nucleic Acids Res. 2019 Mar 13. pii: gkz172. doi: 10.1093/nar/gkz172.
19.
Enhanced fatty acid scavenging and glycerophospholipid metabolism accompanies melanocyte neoplasia progression in zebrafish.
Henderson F, Johnston HR, Badrock AP, Jones EA, Forster D, Nagaraju RT, Evangelou C, Kamarashev J, Green M, Fairclough M, Barinaga-Rementeria Ramirez I, He S, Snaar-Jagalska BE, Hollywood K, Dunn WB, Spaink HP, Smith MP, Lorigan P, Claude E, Williams KJ, McMahon AW, Hurlstone A.
Cancer Res. 2019 Mar 12. pii: canres.2409.2018. doi: 10.1158/0008-5472.CAN-18-2409.
20.
Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming.
Francesconi M, Di Stefano B, Berenguer C, de Andrés-Aguayo L, Plana-Carmona M, Mendez-Lago M, Guillaumet-Adkins A, Rodriguez-Esteban G, Gut M, Gut IG, Heyn H, Lehner B, Graf T.
Elife. 2019 Mar 12;8. pii: e41627. doi: 10.7554/eLife.41627.
21.
Endothelial miR-30c suppresses tumor growth via inhibition of TGF-β-induced Serpine1.
McCann JV, Xiao L, Kim DJ, Khan OF, Kowalski PS, Anderson DG, Pecot CV, Azam SH, Parker JS, Tsai YS, Wolberg AS, Turner SD, Tatsumi K, Mackman N, Dudley AC.
J Clin Invest. 2019 Mar 11;130. pii: 123106. doi: 10.1172/JCI123106. eCollection 2019 Mar 11.
22.
Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic.
Tomkovich S, Dejea CM, Winglee K, Drewes JL, Chung L, Housseau F, Pope JL, Gauthier J, Sun X, Mühlbauer M, Liu X, Fathi P, Anders RA, Besharati S, Perez-Chanona E, Yang Y, Ding H, Wu X, Wu S, White JR, Gharaibeh RZ, Fodor AA, Wang H, Pardoll DM, Jobin C, Sears CL.
J Clin Invest. 2019 Mar 11;130. pii: 124196. doi: 10.1172/JCI124196. eCollection 2019 Mar 11.
23.
Diverse tumour susceptibility in Collaborative Cross mice: identification of a new mouse model for human gastric tumourigenesis.
Wang P, Wang Y, Langley SA, Zhou YX, Jen KY, Sun Q, Brislawn C, Rojas CM, Wahl KL, Wang T, Fan X, Jansson JK, Celniker SE, Zou X, Threadgill DW, Snijders AM, Mao JH.
Gut. 2019 Mar 6. pii: gutjnl-2018-316691. doi: 10.1136/gutjnl-2018-316691.
24.
Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.
Cheng S, Pei Y, He L, Peng G, Reinius B, Tam PPL, Jing N, Deng Q.
Cell Rep. 2019 Mar 5;26(10):2593-2607.e3. doi: 10.1016/j.celrep.2019.02.031.
25.
GNAI1 and GNAI3 Reduce Colitis-Associated Tumorigenesis in Mice by Blocking IL6 Signaling and Downregulating Expression of GNAI2.
Li ZW, Sun B, Gong T, Guo S, Zhang J, Wang J, Sugawara A, Jiang M, Yan J, Gurary A, Zhen X, Gao B, Xiao SY, Chen W, Ma C, Zhu C, Farrar C, Chan OTM, Xin C, Winnicki A, Winnicki J, Tang M, Park R, Winnicki M, Diener K, Wang Z, Liu Q, Chu CH, Yue P, Alpert L, Hui GS, Fei P, Turkson J, Yang W, Wu G, Tao A, Ramos JW, Moisyadi S, Holcombe RF, Jia W, Birnbaumer L, Zhou X, Chu WM.
Gastroenterology. 2019 Mar 2. pii: S0016-5085(19)32508-9. doi: 10.1053/j.gastro.2019.02.040.
26.
HCV-induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response.
Hamdane N, Jühling F, Crouchet E, El Saghire H, Thumann C, Oudot MA, Bandiera S, Saviano A, Ponsolles C, Roca Suarez AA, Li S, Fujiwara N, Ono A, Davidson I, Bardeesy N, Schmidl C, Bock C, Schuster C, Lupberger J, Habersetzer F, Doffoël M, Piardi T, Sommacale D, Imamura M, Uchida T, Ohdan H, Aikata H, Chayama K, Boldanova T, Pessaux P, Fuchs BC, Hoshida Y, Zeisel MB, Duong FHT, Baumert TF.
Gastroenterology. 2019 Mar 2. pii: S0016-5085(19)32506-5. doi: 10.1053/j.gastro.2019.02.038.
27.
Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas.
Newman S, Fan L, Pribnow A, Silkov A, Rice SV, Lee S, Shao Y, Shaner B, Mulder H, Nakitandwe J, Shurtleff S, Azzato EM, Wu G, Zhou X, Barnhill R, Easton J, Nichols KE, Ellison DW, Downing JR, Pappo A, Potter PM, Zhang J, Bahrami A.
Nat Med. 2019 Mar 4. doi: 10.1038/s41591-019-0373-y.
28.
Genomic and molecular characterization of preterm birth.
Knijnenburg TA, Vockley JG, Chambwe N, Gibbs DL, Humphries C, Huddleston KC, Klein E, Kothiyal P, Tasseff R, Dhankani V, Bodian DL, Wong WSW, Glusman G, Mauldin DE, Miller M, Slagel J, Elasady S, Roach JC, Kramer R, Leinonen K, Linthorst J, Baveja R, Baker R, Solomon BD, Eley G, Iyer RK, Maxwell GL, Bernard B, Shmulevich I, Hood L, Niederhuber JE.
Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5819-5827. doi: 10.1073/pnas.1716314116. Epub 2019 Mar 4.
29.
The Long Non-Coding RNA CPR Regulates Cardiomyocyte Proliferation and Cardiac Repair.
Ponnusamy M, Liu F, Zhang YH, Li RB, Zhai M, Liu F, Zhou LY, Liu CY, Yan KW, Dong YH, Wang M, Qian LL, Shan C, Xu S, Wang Q, Zhang YH, Li PF, Zhang J, Wang K.
Circulation. 2019 Mar 5. doi: 10.1161/CIRCULATIONAHA.118.035832.
30.
Cell lineage inference from SNP and scRNA-Seq data.
Ding J, Lin C, Bar-Joseph Z.
Nucleic Acids Res. 2019 Mar 1. pii: gkz146. doi: 10.1093/nar/gkz146.
31.
A general computational approach to predicting synergistic transcriptional cores that determine cell subpopulation identities.
Okawa S, Del Sol A.
Nucleic Acids Res. 2019 Mar 1. pii: gkz147. doi: 10.1093/nar/gkz147.
32.
SQuIRE reveals locus-specific regulation of interspersed repeat expression.
Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH.
Nucleic Acids Res. 2019 Mar 18;47(5):e27. doi: 10.1093/nar/gky1301.
33.
RNA element discovery from germ cell to blastocyst.
Estill MS, Hauser R, Krawetz SA.
Nucleic Acids Res. 2019 Mar 18;47(5):2263-2275. doi: 10.1093/nar/gky1223.
|
