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Items: 29

1.

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences.

Zhu A, Ibrahim JG, Love MI.

Bioinformatics. 2018 Nov 3. doi: 10.1093/bioinformatics/bty895. [Epub ahead of print]

PMID:
30395178
2.

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.

Love MI, Soneson C, Patro R.

Version 3. F1000Res. 2018 Jun 27 [revised 2018 Jan 1];7:952. doi: 10.12688/f1000research.15398.3. eCollection 2018.

3.

SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data.

Yang Y, Huh R, Culpepper HW, Lin Y, Love MI, Li Y.

Bioinformatics. 2018 Sep 8. doi: 10.1093/bioinformatics/bty793. [Epub ahead of print]

PMID:
30202935
4.

coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers.

van Bömmel A, Love MI, Chung HR, Vingron M.

PLoS Comput Biol. 2018 Aug 24;14(8):e1006372. doi: 10.1371/journal.pcbi.1006372. eCollection 2018 Aug.

5.

Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme.

Pietryk EW, Clement K, Elnagheeb M, Kuster R, Kilpatrick K, Love MI, Ideraabdullah FY.

Reprod Toxicol. 2018 Jun;78:9-19. doi: 10.1016/j.reprotox.2018.03.005. Epub 2018 Mar 10.

PMID:
29535025
6.

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.

7.

Reproductive risk factor associations with lobular and ductal carcinoma in the Carolina Breast Cancer Study.

Williams LA, Nichols HB, Hoadley KA, Tse CK, Geradts J, Bell ME, Perou CM, Love MI, Olshan AF, Troester MA.

Cancer Causes Control. 2018 Jan;29(1):25-32. doi: 10.1007/s10552-017-0977-9. Epub 2017 Nov 9.

PMID:
29124544
8.

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.

Phanstiel DH, Van Bortle K, Spacek D, Hess GT, Shamim MS, Machol I, Love MI, Aiden EL, Bassik MC, Snyder MP.

Mol Cell. 2017 Sep 21;67(6):1037-1048.e6. doi: 10.1016/j.molcel.2017.08.006. Epub 2017 Sep 7.

9.

Salmon provides fast and bias-aware quantification of transcript expression.

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C.

Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6.

10.

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.

Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas-Chollier M, Vingron M, Meijsing SH.

Nucleic Acids Res. 2017 Feb 28;45(4):1805-1819. doi: 10.1093/nar/gkw1163.

11.

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.

Love MI, Hogenesch JB, Irizarry RA.

Nat Biotechnol. 2016 Dec;34(12):1287-1291. doi: 10.1038/nbt.3682. Epub 2016 Sep 26.

12.

Erratum to: A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 Sep 30;17(1):203. No abstract available.

13.

Flexible expressed region analysis for RNA-seq with derfinder.

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE.

Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29.

14.

Erratum to: A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 May 23;17(1):107. No abstract available.

15.

A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 Apr 23;17:74. doi: 10.1186/s13059-016-0940-1. Erratum in: Genome Biol. 2016;17(1):107. Genome Biol. 2016 Sep 30;17 (1):203.

16.

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.

Soneson C, Love MI, Robinson MD.

Version 2. F1000Res. 2015 Dec 30 [revised 2016 Jan 1];4:1521. doi: 10.12688/f1000research.7563.2. eCollection 2015.

17.

RNA-Seq workflow: gene-level exploratory analysis and differential expression.

Love MI, Anders S, Kim V, Huber W.

F1000Res. 2015 Oct 14;4:1070. doi: 10.12688/f1000research.7035.1. eCollection 2015.

18.

Increased STAG2 dosage defines a novel cohesinopathy with intellectual disability and behavioral problems.

Kumar R, Corbett MA, Van Bon BW, Gardner A, Woenig JA, Jolly LA, Douglas E, Friend K, Tan C, Van Esch H, Holvoet M, Raynaud M, Field M, Leffler M, Budny B, Wisniewska M, Badura-Stronka M, Latos-Bieleńska A, Batanian J, Rosenfeld JA, Basel-Vanagaite L, Jensen C, Bienek M, Froyen G, Ullmann R, Hu H, Love MI, Haas SA, Stankiewicz P, Cheung SW, Baxendale A, Nicholl J, Thompson EM, Haan E, Kalscheuer VM, Gecz J.

Hum Mol Genet. 2015 Dec 20;24(25):7171-81. doi: 10.1093/hmg/ddv414. Epub 2015 Oct 6.

PMID:
26443594
19.

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors.

Starick SR, Ibn-Salem J, Jurk M, Hernandez C, Love MI, Chung HR, Vingron M, Thomas-Chollier M, Meijsing SH.

Genome Res. 2015 Jun;25(6):825-35. doi: 10.1101/gr.185157.114. Epub 2015 Feb 26.

20.

X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes.

Hu H, Haas SA, Chelly J, Van Esch H, Raynaud M, de Brouwer AP, Weinert S, Froyen G, Frints SG, Laumonnier F, Zemojtel T, Love MI, Richard H, Emde AK, Bienek M, Jensen C, Hambrock M, Fischer U, Langnick C, Feldkamp M, Wissink-Lindhout W, Lebrun N, Castelnau L, Rucci J, Montjean R, Dorseuil O, Billuart P, Stuhlmann T, Shaw M, Corbett MA, Gardner A, Willis-Owen S, Tan C, Friend KL, Belet S, van Roozendaal KE, Jimenez-Pocquet M, Moizard MP, Ronce N, Sun R, O'Keeffe S, Chenna R, van Bömmel A, Göke J, Hackett A, Field M, Christie L, Boyle J, Haan E, Nelson J, Turner G, Baynam G, Gillessen-Kaesbach G, Müller U, Steinberger D, Budny B, Badura-Stronka M, Latos-Bieleńska A, Ousager LB, Wieacker P, Rodríguez Criado G, Bondeson ML, Annerén G, Dufke A, Cohen M, Van Maldergem L, Vincent-Delorme C, Echenne B, Simon-Bouy B, Kleefstra T, Willemsen M, Fryns JP, Devriendt K, Ullmann R, Vingron M, Wrogemann K, Wienker TF, Tzschach A, van Bokhoven H, Gecz J, Jentsch TJ, Chen W, Ropers HH, Kalscheuer VM.

Mol Psychiatry. 2016 Jan;21(1):133-48. doi: 10.1038/mp.2014.193. Epub 2015 Feb 3.

21.

Orchestrating high-throughput genomic analysis with Bioconductor.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.

22.
23.

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.

Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS.

Genome Biol. 2014;15(12):554.

24.

Deletions of chromosomal regulatory boundaries are associated with congenital disease.

Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN.

Genome Biol. 2014 Sep 4;15(9):423. doi: 10.1186/s13059-014-0423-1.

25.

TRPM2 mediates ischemic kidney injury and oxidant stress through RAC1.

Gao G, Wang W, Tadagavadi RK, Briley NE, Love MI, Miller BA, Reeves WB.

J Clin Invest. 2014 Nov;124(11):4989-5001. doi: 10.1172/JCI76042. Epub 2014 Oct 8.

26.

Airway epithelial miRNA expression is altered in asthma.

Solberg OD, Ostrin EJ, Love MI, Peng JC, Bhakta NR, Hou L, Nguyen C, Solon M, Nguyen C, Barczak AJ, Zlock LT, Blagev DP, Finkbeiner WE, Ansel KM, Arron JR, Erle DJ, Woodruff PG.

Am J Respir Crit Care Med. 2012 Nov 15;186(10):965-74. doi: 10.1164/rccm.201201-0027OC. Epub 2012 Sep 6.

27.

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.

Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA.

Bioinformatics. 2012 Apr 1;28(7):1024-5. doi: 10.1093/bioinformatics/bts064. Epub 2012 Feb 1.

PMID:
22302574
28.

Modeling read counts for CNV detection in exome sequencing data.

Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA.

Stat Appl Genet Mol Biol. 2011 Nov 8;10(1). pii: /j/sagmb.2011.10.issue-1/1544-6115.1732/1544-6115.1732.xml. doi: 10.2202/1544-6115.1732.

29.

Performance of children on the Davis-Eells games and other measures of ability.

LOVE MI, BEACH S.

J Consult Psychol. 1957 Feb;21(1):29-32. No abstract available.

PMID:
13406155

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