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A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes.

Soneson C, Yao Y, Bratus-Neuenschwander A, Patrignani A, Robinson MD, Hussain S.

Nat Commun. 2019 Jul 31;10(1):3359. doi: 10.1038/s41467-019-11272-z.


Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms.

Bick JT, Zeng S, Robinson MD, Ulbrich SE, Bauersachs S.

Database (Oxford). 2019 Jan 1;2019. pii: baz086. doi: 10.1093/database/baz086.


Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish.

D'Agati G, Cabello EM, Frontzek K, Rushing EJ, Klemm R, Robinson MD, White RM, Mosimann C, Burger A.

Dis Model Mech. 2019 Jul 16;12(7). pii: dmm039545. doi: 10.1242/dmm.039545.


Essential guidelines for computational method benchmarking.

Weber LM, Saelens W, Cannoodt R, Soneson C, Hapfelmeier A, Gardner PP, Boulesteix AL, Saeys Y, Robinson MD.

Genome Biol. 2019 Jun 20;20(1):125. doi: 10.1186/s13059-019-1738-8. Review.


Emotion-related variations in motor tremor: Magnitude, time course, and links to emotional temperament.

Klein RJ, Towers C, Robinson MD.

Emotion. 2019 Jun 13. doi: 10.1037/emo0000612. [Epub ahead of print]


CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo.

Chatterjee B, Deng Y, Holler A, Nunez N, Azzi T, Vanoaica LD, Müller A, Zdimerova H, Antsiferova O, Zbinden A, Capaul R, Dreyer JH, Nadal D, Becher B, Robinson MD, Stauss H, Münz C.

PLoS Pathog. 2019 May 30;15(5):e1007748. doi: 10.1371/journal.ppat.1007748. eCollection 2019 May.


diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering.

Weber LM, Nowicka M, Soneson C, Robinson MD.

Commun Biol. 2019 May 14;2:183. doi: 10.1038/s42003-019-0415-5. eCollection 2019.


ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data.

Orjuela S, Huang R, Hembach KM, Robinson MD, Soneson C.

G3 (Bethesda). 2019 Jul 9;9(7):2089-2096. doi: 10.1534/g3.119.400185.


Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp.

Cheng HW, Onder L, Novkovic M, Soneson C, Lütge M, Pikor N, Scandella E, Robinson MD, Miyazaki JI, Tersteegen A, Sorg U, Pfeffer K, Rülicke T, Hehlgans T, Ludewig B.

Nat Commun. 2019 Apr 15;10(1):1739. doi: 10.1038/s41467-019-09728-3.


The Spinal Transcriptome after Cortical Stroke: In Search of Molecular Factors Regulating Spontaneous Recovery in the Spinal Cord.

Kaiser J, Maibach M, Salpeter I, Hagenbuch N, de Souza VBC, Robinson MD, Schwab ME.

J Neurosci. 2019 Jun 12;39(24):4714-4726. doi: 10.1523/JNEUROSCI.2571-18.2019. Epub 2019 Apr 8.


Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34.

Krattinger SG, Kang J, Bräunlich S, Boni R, Chauhan H, Selter LL, Robinson MD, Schmid MW, Wiederhold E, Hensel G, Kumlehn J, Sucher J, Martinoia E, Keller B.

New Phytol. 2019 Jul;223(2):853-866. doi: 10.1111/nph.15815. Epub 2019 Apr 22.


Neuroticism as mental noise: Evidence from a continuous tracking task.

Klein RJ, Robinson MD.

J Pers. 2019 Feb 25. doi: 10.1111/jopy.12469. [Epub ahead of print]


A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.

Soneson C, Love MI, Patro R, Hussain S, Malhotra D, Robinson MD.

Life Sci Alliance. 2019 Jan 17;2(1). pii: e201800175. doi: 10.26508/lsa.201800175. Print 2019 Feb.


TCF/LEF dependent and independent transcriptional regulation of Wnt/β-catenin target genes.

Doumpas N, Lampart F, Robinson MD, Lentini A, Nestor CE, Cantù C, Basler K.

EMBO J. 2019 Jan 15;38(2). pii: e98873. doi: 10.15252/embj.201798873. Epub 2018 Nov 13.


The proto CpG island methylator phenotype of sessile serrated adenomas/polyps.

Parker HR, Orjuela S, Martinho Oliveira A, Cereatti F, Sauter M, Heinrich H, Tanzi G, Weber A, Komminoth P, Vavricka S, Albanese L, Buffoli F, Robinson MD, Marra G.

Epigenetics. 2018;13(10-11):1088-1105. doi: 10.1080/15592294.2018.1543504. Epub 2018 Nov 22.


A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics.

Macey JR, Schulte JAI, Ananjeva NB, Dyke ETV, Wang Y, Orlov N, Shafiei S, Robinson MD, Dujsebayeva T, Freund GS, Fischer CM, Liu D, Papenfuss TJ.

Zootaxa. 2018 Sep 3;4467(1):1-81. doi: 10.11646/zootaxa.4467.1.1.


Treatment of a metabolic liver disease by in vivo genome base editing in adult mice.

Villiger L, Grisch-Chan HM, Lindsay H, Ringnalda F, Pogliano CB, Allegri G, Fingerhut R, Häberle J, Matos J, Robinson MD, Thöny B, Schwank G.

Nat Med. 2018 Oct;24(10):1519-1525. doi: 10.1038/s41591-018-0209-1. Epub 2018 Oct 8.


A systematic performance evaluation of clustering methods for single-cell RNA-seq data.

Duò A, Robinson MD, Soneson C.

Version 2. F1000Res. 2018 Jul 26 [revised 2018 Jan 1];7:1141. doi: 10.12688/f1000research.15666.2. eCollection 2018.


Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity.

Perez-Shibayama C, Gil-Cruz C, Cheng HW, Onder L, Printz A, Mörbe U, Novkovic M, Li C, Lopez-Macias C, Buechler MB, Turley SJ, Mack M, Soneson C, Robinson MD, Scandella E, Gommerman J, Ludewig B.

Sci Immunol. 2018 Aug 10;3(26). pii: eaar4539. doi: 10.1126/sciimmunol.aar4539.


Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression.

Bick JT, Flöter VL, Robinson MD, Bauersachs S, Ulbrich SE.

BMC Genomics. 2018 Aug 6;19(1):590. doi: 10.1186/s12864-018-4954-9.


Hello darkness my old friend: preferences for darkness vary by neuroticism and co-occur with negative affect.

Persich MR, Bair JL, Steinemann B, Nelson S, Fetterman AK, Robinson MD.

Cogn Emot. 2019 Aug;33(5):885-900. doi: 10.1080/02699931.2018.1504746. Epub 2018 Jul 30.


Awareness of Racial Disparities in Diabetes Among Primary Care Residents and Preparedness to Discuss Disparities with Patients.

Taylor YJ, Davis ME, Mohanan S, Robertson S, Robinson MD.

J Racial Ethn Health Disparities. 2019 Apr;6(2):237-244. doi: 10.1007/s40615-018-0518-6. Epub 2018 Jul 23.


Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy.

Krieg C, Nowicka M, Guglietta S, Schindler S, Hartmann FJ, Weber LM, Dummer R, Robinson MD, Levesque MP, Becher B.

Nat Med. 2018 Nov;24(11):1773-1775. doi: 10.1038/s41591-018-0094-7.


Common Features of Regulatory T Cell Specialization During Th1 Responses.

Littringer K, Moresi C, Rakebrandt N, Zhou X, Schorer M, Dolowschiak T, Kirchner F, Rost F, Keller CW, McHugh D, LeibundGut-Landmann S, Robinson MD, Joller N.

Front Immunol. 2018 Jun 13;9:1344. doi: 10.3389/fimmu.2018.01344. eCollection 2018.


Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair.

Savic N, Ringnalda FC, Lindsay H, Berk C, Bargsten K, Li Y, Neri D, Robinson MD, Ciaudo C, Hall J, Jinek M, Schwank G.

Elife. 2018 May 29;7. pii: e33761. doi: 10.7554/eLife.33761.


The Revised Animal Preference Test: An Implicit Probe of Tendencies Toward Psychopathy.

Penzel IB, Bair J, Liu T, Robinson MD.

J Interpers Violence. 2018 May 1:886260518777553. doi: 10.1177/0886260518777553. [Epub ahead of print]


The negative feedback dysregulation effect: losses of motor control in response to negative feedback.

Klein RJ, Robinson MD.

Cogn Emot. 2019 May;33(3):536-547. doi: 10.1080/02699931.2018.1463197. Epub 2018 Apr 19.


ALT-803, an IL-15 superagonist, in combination with nivolumab in patients with metastatic non-small cell lung cancer: a non-randomised, open-label, phase 1b trial.

Wrangle JM, Velcheti V, Patel MR, Garrett-Mayer E, Hill EG, Ravenel JG, Miller JS, Farhad M, Anderton K, Lindsey K, Taffaro-Neskey M, Sherman C, Suriano S, Swiderska-Syn M, Sion A, Harris J, Edwards AR, Rytlewski JA, Sanders CM, Yusko EC, Robinson MD, Krieg C, Redmond WL, Egan JO, Rhode PR, Jeng EK, Rock AD, Wong HC, Rubinstein MP.

Lancet Oncol. 2018 May;19(5):694-704. doi: 10.1016/S1470-2045(18)30148-7. Epub 2018 Apr 5.


Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.

Chevrier S, Crowell HL, Zanotelli VRT, Engler S, Robinson MD, Bodenmiller B.

Cell Syst. 2018 May 23;6(5):612-620.e5. doi: 10.1016/j.cels.2018.02.010. Epub 2018 Mar 28.


Bias, robustness and scalability in single-cell differential expression analysis.

Soneson C, Robinson MD.

Nat Methods. 2018 Apr;15(4):255-261. doi: 10.1038/nmeth.4612. Epub 2018 Feb 26.


Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.

Van den Berge K, Perraudeau F, Soneson C, Love MI, Risso D, Vert JP, Robinson MD, Dudoit S, Clement L.

Genome Biol. 2018 Feb 26;19(1):24. doi: 10.1186/s13059-018-1406-4.


Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen.

Praz CR, Menardo F, Robinson MD, Müller MC, Wicker T, Bourras S, Keller B.

Front Plant Sci. 2018 Jan 30;9:49. doi: 10.3389/fpls.2018.00049. eCollection 2018.


Diversity, distribution and conservation of the terrestrial reptiles of Oman (Sauropsida, Squamata).

Carranza S, Xipell M, Tarroso P, Gardner A, Arnold EN, Robinson MD, Simó-Riudalbas M, Vasconcelos R, de Pous P, Amat F, Šmíd J, Sindaco R, Metallinou M, Els J, Pleguezuelos JM, Machado L, Donaire D, Martínez G, Garcia-Porta J, Mazuch T, Wilms T, Gebhart J, Aznar J, Gallego J, Zwanzig BM, Fernández-Guiberteau D, Papenfuss T, Al Saadi S, Alghafri A, Khalifa S, Al Farqani H, Bait Bilal S, Alazri IS, Al Adhoobi AS, Al Omairi ZS, Al Shariani M, Al Kiyumi A, Al Sariri T, Al Shukaili AS, Al Akhzami SN.

PLoS One. 2018 Feb 7;13(2):e0190389. doi: 10.1371/journal.pone.0190389. eCollection 2018.


High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy.

Krieg C, Nowicka M, Guglietta S, Schindler S, Hartmann FJ, Weber LM, Dummer R, Robinson MD, Levesque MP, Becher B.

Nat Med. 2018 Feb;24(2):144-153. doi: 10.1038/nm.4466. Epub 2018 Jan 8. Erratum in: Nat Med. 2018 Nov;24(11):1773-1775.


Water T2 as an early, global and practical biomarker for metabolic syndrome: an observational cross-sectional study.

Robinson MD, Mishra I, Deodhar S, Patel V, Gordon KV, Vintimilla R, Brown K, Johnson L, O'Bryant S, Cistola DP.

J Transl Med. 2017 Dec 19;15(1):258. doi: 10.1186/s12967-017-1359-5.


An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.

Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C, Frey JE, Robinson MD, Wollscheid B, Ahrens CH.

Genome Res. 2017 Dec;27(12):2083-2095. doi: 10.1101/gr.218255.116. Epub 2017 Nov 15.


Towards unified quality verification of synthetic count data with countsimQC.

Soneson C, Robinson MD.

Bioinformatics. 2018 Feb 15;34(4):691-692. doi: 10.1093/bioinformatics/btx631.


Highly efficient DNA-free gene disruption in the agricultural pest Ceratitis capitata by CRISPR-Cas9 ribonucleoprotein complexes.

Meccariello A, Monti SM, Romanelli A, Colonna R, Primo P, Inghilterra MG, Del Corsano G, Ramaglia A, Iazzetti G, Chiarore A, Patti F, Heinze SD, Salvemini M, Lindsay H, Chiavacci E, Burger A, Robinson MD, Mosimann C, Bopp D, Saccone G.

Sci Rep. 2017 Aug 30;7(1):10061. doi: 10.1038/s41598-017-10347-5.


Electronic Health Record Effects on Work-Life Balance and Burnout Within the I3 Population Collaborative.

Robertson SL, Robinson MD, Reid A.

J Grad Med Educ. 2017 Aug;9(4):479-484. doi: 10.4300/JGME-D-16-00123.1.


stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage.

Van den Berge K, Soneson C, Robinson MD, Clement L.

Genome Biol. 2017 Aug 7;18(1):151. doi: 10.1186/s13059-017-1277-0.


A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription.

Herdman C, Mars JC, Stefanovsky VY, Tremblay MG, Sabourin-Felix M, Lindsay H, Robinson MD, Moss T.

PLoS Genet. 2017 Jul 17;13(7):e1006899. doi: 10.1371/journal.pgen.1006899. eCollection 2017 Jul.


CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.

Nowicka M, Krieg C, Crowell HL, Weber LM, Hartmann FJ, Guglietta S, Becher B, Levesque MP, Robinson MD.

Version 3. F1000Res. 2017 May 26 [revised 2019 Jan 1];6:748. doi: 10.12688/f1000research.11622.3. eCollection 2017.


Male sex in houseflies is determined by Mdmd, a paralog of the generic splice factor gene CWC22.

Sharma A, Heinze SD, Wu Y, Kohlbrenner T, Morilla I, Brunner C, Wimmer EA, van de Zande L, Robinson MD, Beukeboom LW, Bopp D.

Science. 2017 May 12;356(6338):642-645. doi: 10.1126/science.aam5498.


Monitoring the Disassembly of Virus-like Particles by 19F-NMR.

Leung RLC, Robinson MDM, Ajabali AAA, Karunanithy G, Lyons B, Raj R, Raoufmoghaddam S, Mohammed S, Claridge TDW, Baldwin AJ, Davis BG.

J Am Chem Soc. 2017 Apr 19;139(15):5277-5280. doi: 10.1021/jacs.6b11040. Epub 2017 Apr 7.


DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma.

Marinova Z, Maercker A, Küffer A, Robinson MD, Wojdacz TK, Walitza S, Grünblatt E, Burri A.

BMC Med Genet. 2017 Feb 27;18(1):21. doi: 10.1186/s12881-017-0370-2.


DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics.

Nowicka M, Robinson MD.

Version 2. F1000Res. 2016 Jun 13 [revised 2016 Jan 1];5:1356. doi: 10.12688/f1000research.8900.2. eCollection 2016.


Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila.

Sauerwald J, Soneson C, Robinson MD, Luschnig S.

Development. 2017 Feb 15;144(4):657-663. doi: 10.1242/dev.144535. Epub 2017 Jan 13.


Compact NMR relaxometry of human blood and blood components.

Cistola DP, Robinson MD.

Trends Analyt Chem. 2016 Nov;83(A):53-64. doi: 10.1016/j.trac.2016.04.020.


Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data.

Weber LM, Robinson MD.

Cytometry A. 2016 Dec;89(12):1084-1096. doi: 10.1002/cyto.a.23030. Epub 2016 Dec 19.


Linguistic Evidence for the Failure Mindset as a Predictor of Life Span Longevity.

Penzel IB, Persich MR, Boyd RL, Robinson MD.

Ann Behav Med. 2017 Jun;51(3):348-355. doi: 10.1007/s12160-016-9857-x.


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