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Items: 34


Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level.

Sarkar H, Srivastava A, Patro R.

Bioinformatics. 2019 Jul 15;35(14):i136-i144. doi: 10.1093/bioinformatics/btz351.


Nonparametric expression analysis using inferential replicate counts.

Zhu A, Srivastava A, Ibrahim JG, Patro R, Love MI.

Nucleic Acids Res. 2019 Oct 10;47(18):e105. doi: 10.1093/nar/gkz622.


Alevin efficiently estimates accurate gene abundances from dscRNA-seq data.

Srivastava A, Malik L, Smith T, Sudbery I, Patro R.

Genome Biol. 2019 Mar 27;20(1):65. doi: 10.1186/s13059-019-1670-y.


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.


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.


Common and differential transcriptional responses to different models of traumatic stress exposure in rats.

Jacobson ML, Kim LA, Patro R, Rosati B, McKinnon D.

Transl Psychiatry. 2018 Aug 23;8(1):165. doi: 10.1038/s41398-018-0223-6.


Novel Trichoderma strains isolated from tree barks as potential biocontrol agents and biofertilizers for direct seeded rice.

Swain H, Adak T, Mukherjee AK, Mukherjee PK, Bhattacharyya P, Behera S, Bagchi TB, Patro R, Shasmita, Khandual A, Bag MK, Dangar TK, Lenka S, Jena M.

Microbiol Res. 2018 Sep;214:83-90. doi: 10.1016/j.micres.2018.05.015. Epub 2018 May 23.


Rich Chromatin Structure Prediction from Hi-C Data.

Malik L, Patro R.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Sep-Oct;16(5):1448-1458. doi: 10.1109/TCBB.2018.2851200. Epub 2018 Jun 28.


A space and time-efficient index for the compacted colored de Bruijn graph.

Almodaresi F, Sarkar H, Srivastava A, Patro R.

Bioinformatics. 2018 Jul 1;34(13):i169-i177. doi: 10.1093/bioinformatics/bty292.


Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.

Pandey P, Almodaresi F, Bender MA, Ferdman M, Johnson R, Patro R.

Cell Syst. 2018 Aug 22;7(2):201-207.e4. doi: 10.1016/j.cels.2018.05.021. Epub 2018 Jun 20.


Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis.

Malik L, Almodaresi F, Patro R.

Bioinformatics. 2018 Oct 1;34(19):3265-3272. doi: 10.1093/bioinformatics/bty378.


Squeakr: an exact and approximate k-mer counting system.

Pandey P, Bender MA, Johnson R, Patro R, Berger B.

Bioinformatics. 2018 Feb 15;34(4):568-575. doi: 10.1093/bioinformatics/btx636.


Quark enables semi-reference-based compression of RNA-seq data.

Sarkar H, Patro R.

Bioinformatics. 2017 Nov 1;33(21):3380-3386. doi: 10.1093/bioinformatics/btx428.


Improved data-driven likelihood factorizations for transcript abundance estimation.

Zakeri M, Srivastava A, Almodaresi F, Patro R.

Bioinformatics. 2017 Jul 15;33(14):i142-i151. doi: 10.1093/bioinformatics/btx262.


deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.

Pandey P, Bender MA, Johnson R, Patro R.

Bioinformatics. 2017 Jul 15;33(14):i133-i141. doi: 10.1093/bioinformatics/btx261.


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.


RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes.

Srivastava A, Sarkar H, Gupta N, Patro R.

Bioinformatics. 2016 Jun 15;32(12):i192-i200. doi: 10.1093/bioinformatics/btw277.


TransRate: reference-free quality assessment of de novo transcriptome assemblies.

Smith-Unna R, Boursnell C, Patro R, Hibberd JM, Kelly S.

Genome Res. 2016 Aug;26(8):1134-44. doi: 10.1101/gr.196469.115. Epub 2016 Jun 1.


A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.

Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C.

BMC Bioinformatics. 2016 Apr 8;17:155. doi: 10.1186/s12859-016-1008-7.


AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JW.

New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25.


Data-dependent bucketing improves reference-free compression of sequencing reads.

Patro R, Kingsford C.

Bioinformatics. 2015 Sep 1;31(17):2770-7. doi: 10.1093/bioinformatics/btv248. Epub 2015 Apr 24.


Comparison of conventional, immunological and molecular techniques for the diagnosis of symptomatic congenital human cytomegalovirus infection in neonates and infants.

Choudhary A, Pati SK, Patro RK, Deorari AK, Dar L.

Indian J Med Microbiol. 2015 Feb;33 Suppl:15-9. doi: 10.4103/0255-0857.150874.


Reference-based compression of short-read sequences using path encoding.

Kingsford C, Patro R.

Bioinformatics. 2015 Jun 15;31(12):1920-8. doi: 10.1093/bioinformatics/btv071. Epub 2015 Feb 2.


Identification of alternative topological domains in chromatin.

Filippova D, Patro R, Duggal G, Kingsford C.

Algorithms Mol Biol. 2014 May 3;9:14. doi: 10.1186/1748-7188-9-14. eCollection 2014.


Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.

Patro R, Mount SM, Kingsford C.

Nat Biotechnol. 2014 May;32(5):462-4. doi: 10.1038/nbt.2862. Epub 2014 Apr 20.


Predicting protein interactions via parsimonious network history inference.

Patro R, Kingsford C.

Bioinformatics. 2013 Jul 1;29(13):i237-46. doi: 10.1093/bioinformatics/btt224.


Genotypic diversity and mixed infection in newborn disease and hearing loss in congenital cytomegalovirus infection.

Pati SK, Pinninti S, Novak Z, Chowdhury N, Patro RK, Fowler K, Ross S, Boppana S; NIDCD CHIMES Study Investigators.

Pediatr Infect Dis J. 2013 Oct;32(10):1050-4. doi: 10.1097/INF.0b013e31829bb0b9.


Resolving spatial inconsistencies in chromosome conformation measurements.

Duggal G, Patro R, Sefer E, Wang H, Filippova D, Khuller S, Kingsford C.

Algorithms Mol Biol. 2013 Mar 9;8(1):8. doi: 10.1186/1748-7188-8-8.


Global network alignment using multiscale spectral signatures.

Patro R, Kingsford C.

Bioinformatics. 2012 Dec 1;28(23):3105-14. doi: 10.1093/bioinformatics/bts592. Epub 2012 Oct 9.


Parsimonious reconstruction of network evolution.

Patro R, Sefer E, Malin J, Marçais G, Navlakha S, Kingsford C.

Algorithms Mol Biol. 2012 Sep 19;7(1):25. doi: 10.1186/1748-7188-7-25.


Mixed infection and strain diversity in congenital cytomegalovirus infection.

Ross SA, Novak Z, Pati S, Patro RK, Blumenthal J, Danthuluri VR, Ahmed A, Michaels MG, Sánchez PJ, Bernstein DI, Tolan RW, Palmer AL, Britt WJ, Fowler KB, Boppana SB.

J Infect Dis. 2011 Oct 1;204(7):1003-7. doi: 10.1093/infdis/jir457.


Social snapshot: a system for temporally coupled social photography.

Patro R, Cheuk Yiu Ip, Bista S, Varshney A.

IEEE Comput Graph Appl. 2011 Jan-Feb;31(1):74-84. doi: 10.1109/MCG.2010.107.


Enzyme-linked immunosorbent assay method for detection of cytomegalovirus strain-specific antibody responses.

Novak Z, Ross SA, Patro RK, Pati SK, Reddy MK, Purser M, Britt WJ, Boppana SB.

Clin Vaccine Immunol. 2009 Feb;16(2):288-90. doi: 10.1128/CVI.00281-08. Epub 2008 Nov 26.


Cytomegalovirus strain diversity in seropositive women.

Novak Z, Ross SA, Patro RK, Pati SK, Kumbla RA, Brice S, Boppana SB.

J Clin Microbiol. 2008 Mar;46(3):882-6. doi: 10.1128/JCM.01079-07. Epub 2008 Jan 23.

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