Monthly Letter

1. Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics.
Huang Y, Sheth RU, Kaufman A, Wang HH. Nucleic Acids Res. 2019 Dec 27. pii: gkz1169. doi: 10.1093/nar/gkz1169.

2. Human sperm displays rapid responses to diet.
Nätt D, Kugelberg U, Casas E, Nedstrand E, Zalavary S, Henriksson P, Nijm C, Jäderquist J, Sandborg J, Flinke E, Ramesh R, Örkenby L, Appelkvist F, Lingg T, Guzzi N, Bellodi C, Löf M, Vavouri T, Öst A. PLoS Biol. 2019 Dec 26;17(12):e3000559. doi: 10.1371/journal.pbio.3000559. eCollection 2019 Dec.

3. Molecular Signatures of Dengue Virus-Specific IL-10/IFN-γ Co-producing CD4 T Cells and Their Association with Dengue Disease.
Tian Y, Seumois G, De-Oliveira-Pinto LM, Mateus J, Herrera-de la Mata S, Kim C, Hinz D, Goonawardhana NDS, de Silva AD, Premawansa S, Premawansa G, Wijewickrama A, Balmaseda A, Grifoni A, Vijayanand P, Harris E, Peters B, Sette A, Weiskopf D. Cell Rep. 2019 Dec 24;29(13):4482-4495.e4. doi: 10.1016/j.celrep.2019.11.098.

4. Dysregulation of RNA Splicing in Tauopathies.
Apicco DJ, Zhang C, Maziuk B, Jiang L, Ballance HI, Boudeau S, Ung C, Li H, Wolozin B. Cell Rep. 2019 Dec 24;29(13):4377-4388.e4. doi: 10.1016/j.celrep.2019.11.093.

5. A Spatiomolecular Map of the Striatum.
Märtin A, Calvigioni D, Tzortzi O, Fuzik J, Wärnberg E, Meletis K. Cell Rep. 2019 Dec 24;29(13):4320-4333.e5. doi: 10.1016/j.celrep.2019.11.096.

6. Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins.
Gehring J, Hwee Park J, Chen S, Thomson M, Pachter L. Nat Biotechnol. 2019 Dec 23. doi: 10.1038/s41587-019-0372-z.

7. Transcriptomic signatures related to the obesity paradox in patients with clear cell renal cell carcinoma: a cohort study.
Sanchez A, Furberg H, Kuo F, Vuong L, Ged Y, Patil S, Ostrovnaya I, Petruzella S, Reising A, Patel P, Mano R, Coleman J, Russo P, Liu CH, Dannenberg AJ, Chan TA, Motzer R, Voss MH, Hakimi AA. Lancet Oncol. 2019 Dec 20. pii: S1470-2045(19)30797-1. doi: 10.1016/S1470-2045(19)30797-1.

8. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.
Hafemeister C, Satija R. Genome Biol. 2019 Dec 23;20(1):296. doi: 10.1186/s13059-019-1874-1.

9. 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. 2019 Dec 23;20(1):295. doi: 10.1186/s13059-019-1861-6.

10. Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress.
Ghulam MM, Catala M, Abou Elela S. Nucleic Acids Res. 2019 Dec 21. pii: gkz1183. doi: 10.1093/nar/gkz1183.

11. scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy.
Ocasio J, Babcock B, Malawsky D, Weir SJ, Loo L, Simon JM, Zylka MJ, Hwang D, Dismuke T, Sokolsky M, Rosen EP, Vibhakar R, Zhang J, Saulnier O, Vladoiu M, El-Hamamy I, Stein LD, Taylor MD, Smith KS, Northcott PA, Colaneri A, Wilhelmsen K, Gershon TR. Nat Commun. 2019 Dec 20;10(1):5829. doi: 10.1038/s41467-019-13657-6.

12. Edematous severe acute malnutrition is characterized by hypomethylation of DNA.
Schulze KV, Swaminathan S, Howell S, Jajoo A, Lie NC, Brown O, Sadat R, Hall N, Zhao L, Marshall K, May T, Reid ME, Taylor-Bryan C, Wang X, Belmont JW, Guan Y, Manary MJ, Trehan I, McKenzie CA, Hanchard NA. Nat Commun. 2019 Dec 19;10(1):5791. doi: 10.1038/s41467-019-13433-6.

13. Genotype-free demultiplexing of pooled single-cell RNA-seq.
Xu J, Falconer C, Nguyen Q, Crawford J, McKinnon BD, Mortlock S, Senabouth A, Andersen S, Chiu HS, Jiang L, Palpant NJ, Yang J, Mueller MD, Hewitt AW, Pébay A, Montgomery GW, Powell JE, Coin LJM. Genome Biol. 2019 Dec 19;20(1):290. doi: 10.1186/s13059-019-1852-7.

14. Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging.
Walzer KA, Fradin H, Emerson LY, Corcoran DL, Chi JT. PLoS Genet. 2019 Dec 19;15(12):e1008506. doi: 10.1371/journal.pgen.1008506.

15. Comparison of Reproducibility, Accuracy, Sensitivity, and Specificity of miRNA Quantification Platforms.
Godoy PM, Barczak AJ, DeHoff P, Srinivasan S, Etheridge A, Galas D, Das S, Erle DJ, Laurent LC. Cell Rep. 2019 Dec 17;29(12):4212-4222.e5. doi: 10.1016/j.celrep.2019.11.078.

16. Discrimination of Dormant and Active Hematopoietic Stem Cells by G0 Marker Reveals Dormancy Regulation by Cytoplasmic Calcium.
Fukushima T, Tanaka Y, Hamey FK, Chang CH, Oki T, Asada S, Hayashi Y, Fujino T, Yonezawa T, Takeda R, Kawabata KC, Fukuyama T, Umemoto T, Takubo K, Takizawa H, Goyama S, Ishihama Y, Honda H, Göttgens B, Kitamura T. Cell Rep. 2019 Dec 17;29(12):4144-4158.e7. doi: 10.1016/j.celrep.2019.11.061.

17. Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads.
Tung LH, Shao M, Kingsford C. Genome Biol. 2019 Dec 18;20(1):287. doi: 10.1186/s13059-019-1883-0.

18. Therapeutically targeting head and neck squamous cell carcinoma through synergistic inhibition of LSD1 and JMJD3 by TCP and GSK-J1.
Zhang W, Cheng J, Diao P, Wang D, Zhang W, Jiang H, Wang Y. Br J Cancer. 2019 Dec 18. doi: 10.1038/s41416-019-0680-6.

19. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling.
Liang Q, Dharmat R, Owen L, Shakoor A, Li Y, Kim S, Vitale A, Kim I, Morgan D, Liang S, Wu N, Chen K, DeAngelis MM, Chen R. Nat Commun. 2019 Dec 17;10(1):5743. doi: 10.1038/s41467-019-12917-9.

20. Transcriptome assembly from long-read RNA-seq alignments with StringTie2.
Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1.

21. deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index.
Liu B, Liu Y, Li J, Guo H, Zang T, Wang Y. Genome Biol. 2019 Dec 16;20(1):274. doi: 10.1186/s13059-019-1895-9.

22. Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes.
Henkel J, Saif R, Jagannathan V, Schmocker C, Zeindler F, Bangerter E, Herren U, Posantzis D, Bulut Z, Ammann P, Drögemüller C, Flury C, Leeb T. PLoS Genet. 2019 Dec 16;15(12):e1008536. doi: 10.1371/journal.pgen.1008536.

23. APOBEC3A is a prominent cytidine deaminase in breast cancer.
Cortez LM, Brown AL, Dennis MA, Collins CD, Brown AJ, Mitchell D, Mertz TM, Roberts SA. PLoS Genet. 2019 Dec 16;15(12):e1008545. doi: 10.1371/journal.pgen.1008545.

24. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
Huang Y, McCarthy DJ, Stegle O. Genome Biol. 2019 Dec 13;20(1):273. doi: 10.1186/s13059-019-1865-2.

25. Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program.
Geirsdottir L, David E, Keren-Shaul H, Weiner A, Bohlen SC, Neuber J, Balic A, Giladi A, Sheban F, Dutertre CA, Pfeifle C, Peri F, Raffo-Romero A, Vizioli J, Matiasek K, Scheiwe C, Meckel S, Mätz-Rensing K, van der Meer F, Thormodsson FR, Stadelmann C, Zilkha N, Kimchi T, Ginhoux F, Ulitsky I, Erny D, Amit I, Prinz M. Cell. 2019 Dec 12;179(7):1609-1622.e16. doi: 10.1016/j.cell.2019.11.010.

26. scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data.
Alquicira-Hernandez J, Sathe A, Ji HP, Nguyen Q, Powell JE. Genome Biol. 2019 Dec 12;20(1):264. doi: 10.1186/s13059-019-1862-5.

27. Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation.
Zhang S, Chen F, Bahar I. Nucleic Acids Res. 2019 Dec 12. pii: gkz1102. doi: 10.1093/nar/gkz1102.

28. Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome.
Lau E, Han Y, Williams DR, Thomas CT, Shrestha R, Wu JC, Lam MPY. Cell Rep. 2019 Dec 10;29(11):3751-3765.e5. doi: 10.1016/j.celrep.2019.11.026.

29. A Study of High-Grade Serous Ovarian Cancer Origins Implicates the SOX18 Transcription Factor in Tumor Development.
Lawrenson K, Fonseca MAS, Liu AY, Segato Dezem F, Lee JM, Lin X, Corona RI, Abbasi F, Vavra KC, Dinh HQ, Gill NK, Seo JH, Coetzee S, Lin YG, Pejovic T, Mhawech-Fauceglia P, Rowat AC, Drapkin R, Karlan BY, Hazelett DJ, Freedman ML, Gayther SA, Noushmehr H. Cell Rep. 2019 Dec 10;29(11):3726-3735.e4. doi: 10.1016/j.celrep.2019.10.122.

30. CD36-Mediated Metabolic Rewiring of Breast Cancer Cells Promotes Resistance to HER2-Targeted Therapies.
Feng WW, Wilkins O, Bang S, Ung M, Li J, An J, Del Genio C, Canfield K, DiRenzo J, Wells W, Gaur A, Robey RB, Guo JY, Powles RL, Sotiriou C, Pusztai L, Febbraio M, Cheng C, Kinlaw WB, Kurokawa M. Cell Rep. 2019 Dec 10;29(11):3405-3420.e5. doi: 10.1016/j.celrep.2019.11.008.

31. Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis.
Sun S, Zhu J, Ma Y, Zhou X. Genome Biol. 2019 Dec 10;20(1):269. doi: 10.1186/s13059-019-1898-6.

32. Inactivation of 3-hydroxybutyrate dehydrogenase type 2 promotes proliferation and metastasis of nasopharyngeal carcinoma by iron retention.
Li B, Liao Z, Mo Y, Zhao W, Zhou X, Xiao X, Cui W, Feng G, Zhong S, Liang Y, Du C, Huang G, Li P, Xiao X, Zhou X, Wang R, Zhang Z. Br J Cancer. 2019 Dec 10. doi: 10.1038/s41416-019-0638-8.

33. ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry.
Wang L, Tan TK, Durbin AD, Zimmerman MW, Abraham BJ, Tan SH, Ngoc PCT, Weichert-Leahey N, Akahane K, Lawton LN, Rokita JL, Maris JM, Young RA, Look AT, Sanda T. Nat Commun. 2019 Dec 9;10(1):5622. doi: 10.1038/s41467-019-13515-5.

34. Hic1 Defines Quiescent Mesenchymal Progenitor Subpopulations with Distinct Functions and Fates in Skeletal Muscle Regeneration.
Scott RW, Arostegui M, Schweitzer R, Rossi FMV, Underhill TM. Cell Stem Cell. 2019 Dec 5;25(6):797-813.e9. doi: 10.1016/j.stem.2019.11.004.

35. Antibody Responses to Immunization With HCV Envelope Glycoproteins as a Baseline for B cell-Based Vaccine Development.
Chen F, Nagy K, Chavez D, Willis S, McBride R, Giang E, Honda A, Bukh J, Ordoukhanian P, Zhu J, Frey S, Lanford R, Law M. Gastroenterology. 2019 Dec 3. pii: S0016-5085(19)41871-4. doi: 10.1053/j.gastro.2019.11.282.

36. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses.
Varoquaux N, Cole B, Gao C, Pierroz G, Baker CR, Patel D, Madera M, Jeffers T, Hollingsworth J, Sievert J, Yoshinaga Y, Owiti JA, Singan VR, DeGraaf S, Xu L, Blow MJ, Harrison MJ, Visel A, Jansson C, Niyogi KK, Hutmacher R, Coleman-Derr D, O'Malley RC, Taylor JW, Dahlberg J, Vogel JP, Lemaux PG, Purdom E. Proc Natl Acad Sci U S A. 2019 Dec 5. pii: 201907500. doi: 10.1073/pnas.1907500116.

37. Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis.
Northcutt AJ, Kick DR, Otopalik AG, Goetz BM, Harris RM, Santin JM, Hofmann HA, Marder E, Schulz DJ. Proc Natl Acad Sci U S A. 2019 Dec 5. pii: 201911413. doi: 10.1073/pnas.1911413116.

38. Predictive impact of rare genomic copy number variations in siblings of individuals with autism spectrum disorders.
D'Abate L, Walker S, Yuen RKC, Tammimies K, Buchanan JA, Davies RW, Thiruvahindrapuram B, Wei J, Brian J, Bryson SE, Dobkins K, Howe J, Landa R, Leef J, Messinger D, Ozonoff S, Smith IM, Stone WL, Warren ZE, Young G, Zwaigenbaum L, Scherer SW. Nat Commun. 2019 Dec 5;10(1):5519. doi: 10.1038/s41467-019-13380-2.

39. Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF.
Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB. Cell Rep. 2019 Dec 3;29(10):3147-3159.e12. doi: 10.1016/j.celrep.2019.10.106.

40. Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells.
Magen A, Nie J, Ciucci T, Tamoutounour S, Zhao Y, Mehta M, Tran B, McGavern DB, Hannenhalli S, Bosselut R. Cell Rep. 2019 Dec 3;29(10):3019-3032.e6. doi: 10.1016/j.celrep.2019.10.131.

41. IL-33 Signaling Alters Regulatory T Cell Diversity in Support of Tumor Development.
Li A, Herbst RH, Canner D, Schenkel JM, Smith OC, Kim JY, Hillman M, Bhutkar A, Cuoco MS, Rappazzo CG, Rogers P, Dang C, Jerby-Arnon L, Rozenblatt-Rosen O, Cong L, Birnbaum M, Regev A, Jacks T. Cell Rep. 2019 Dec 3;29(10):2998-3008.e8. doi: 10.1016/j.celrep.2019.10.120.

42. The Escherichia coli transcriptome mostly consists of independently regulated modules.
Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO. Nat Commun. 2019 Dec 4;10(1):5536. doi: 10.1038/s41467-019-13483-w.

43. From single-cell RNA-seq to transcriptional regulation.
La Manno G. Nat Biotechnol. 2019 Dec;37(12):1421-1422. doi: 10.1038/s41587-019-0327-4. No abstract available.

44. Chemoenzymatic Synthesis of O-Mannose Glycans Containing Sulfated or Nonsulfated HNK-1 Epitope.
Gao T, Yan J, Liu CC, Palma AS, Guo Z, Xiao M, Chen X, Liang X, Chai W, Cao H. J Am Chem Soc. 2019 Dec 11;141(49):19351-19359. doi: 10.1021/jacs.9b08964. Epub 2019 Dec 2.

45. Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators.
Farahmand S, O'Connor C, Macoska JA, Zarringhalam K. Nucleic Acids Res. 2019 Dec 16;47(22):11563-11573. doi: 10.1093/nar/gkz1046.

46. Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data.
Cheng C, Easton J, Rosencrance C, Li Y, Ju B, Williams J, Mulder HL, Pang Y, Chen W, Chen X. Nucleic Acids Res. 2019 Dec 16;47(22):e143. doi: 10.1093/nar/gkz826.

47. cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes.
DePasquale EAK, Schnell D, Dexheimer P, Ferchen K, Hay S, Chetal K, Valiente-Alandí Í, Blaxall BC, Grimes HL, Salomonis N. Nucleic Acids Res. 2019 Dec 2;47(21):e138. doi: 10.1093/nar/gkz789.

48. Assessment of kinship detection using RNA-seq data.
Blay N, Casas E, Galván-Femenía I, Graffelman J, de Cid R, Vavouri T. Nucleic Acids Res. 2019 Dec 2;47(21):e136. doi: 10.1093/nar/gkz776.

49. MELK mediates the stability of EZH2 through site-specific phosphorylation in extranodal natural killer/T-cell lymphoma.
Li B, Yan J, Phyu T, Fan S, Chung TH, Mustafa N, Lin B, Wang L, Eichhorn PJA, Goh BC, Ng SB, Kappei D, Chng WJ. Blood. 2019 Dec 5;134(23):2046-2058. doi: 10.1182/blood.2019000381.

50. Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation.
Osborne OG, Ciezarek A, Wilson T, Crayn D, Hutton I, Baker WJ, Turnbull CGN, Savolainen V. Mol Biol Evol. 2019 Dec 1;36(12):2682-2697. doi: 10.1093/molbev/msz166.