Publications

Articles

Haynes B.H., Brent M.R.. 2009. "Benchmarking regulatory network reconstruction with GRENDEL." Bioinformatics 25(6):801.

Lu D.V., Brown R.H., Arumugam M., Brent M.R.. 2009. "Pairagon: A Highly Accurate, HMM-based cDNA-to-genome Aligner." Bioinformatics :.

Brent MR.. 2007. "How does eukaryotic gene prediction work?." Nature Biotechnology 25(8):883-5.

Keibler E, Arumugam M, Brent MR.. 2007. "The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs." Bioinformatics 23(5):545-54.

Tenney A.E., Wu J.Q., Langton L., Klueh P., Quatrano R., Brent M.R.. 2007. "A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices.." Genome Research 17(2):212-218.

Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Brent MR, Walhout AJ.. 2007. "Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping." Nat Methods 4(8):659-64.

Arumugam, M., Wei, C., Brown, R.H. and M.R. Brent. 2006. "Pairagon+N-SCAN_EST: a model-based gene annotation pipeline." Genome Biology 7(Suppl 1):S5.

Bajic VB, Brent MR, Brown RH, Frankish A, Harrow J, Ohler U, Solovyev VV, Tan SL. 2006. "Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.." Genome biology 7 Suppl 1:S3.1-13.

Flicek P, Brent MR. 2006. "Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.." Genome biology 7 Suppl 1:S8.1-9.

Giannakis M, Stappenbeck TS, Mills JC, Leip DG, Lovett M, Clifton SW, Ippolito JE, Glasscock JI, Arumugam M, Brent MR, Gordon JI. 2006. "Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches.." The Journal of biological chemistry 281(16):11292-300.

Gross SS, Brent MR. 2006. "Using multiple alignments to improve gene prediction.." Journal of computational biology : a journal of computational molecular cell biology 13(2):379-93.

van Baren, M.J. and M.R. Brent. 2006. "Iterative gene prediction and pseudogene removal improves genome annotation.." Genome Research 16(5):678–685.

Wei, C. and Brent, M.R.. 2006. "Using ESTs to improve the accuracy of de novo gene prediction." BMC Bioinformatics 7:327.

Brent MR. 2005. "Genome annotation past, present, and future: how to define an ORF at each locus.." Genome research 15(12):1777-86.

Brown RH, Gross SS, Brent MR. 2005. "Begin at the beginning: predicting genes with 5' UTRs.." Genome research 15(5):742-7.

Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR. 2005. "Gene finding in the chicken genome.." BMC bioinformatics 6:131.

Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW. 2005. "The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.." Science 307(5713):1321-4.

Wei, C., Lamesch, P., Arumugam, M., Rosenberg, J., Hu, P., Vidal, M. and Brent, M.R.. 2005. "Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions." Genome Research 15:577-582.

Ganger J, Brent MR. 2004. "Reexamining the vocabulary spurt.." Developmental psychology 40(4):621-32.

Tenney, A.E., Brown, R.H., Vaske, C., Lodge, J.K., Doering, T.L. and M.R. Brent. 2004. "Gene prediction and verification in a compact genome with numerous small introns." Genome Research 14:2330-2335.

Wu J.Q., Shteynberg D., Arumugam M., Gibbs R.A., and M.R. Brent. 2004. "Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing." Genome Research 14:665-671.

Flicek, P., E. Keibler, P. Hu, I. Korf, and M.R. Brent. 2003. "Leveraging the mouse genome for gene prediction in human: From whole-genome shotgun reads to a global synteny map." Genome Research 13:46-54.

Guigo, R., E.T. Dermitzakis, P. Agarwal, C.P. Ponting, G. Parra, A. Reymond, J.F. Abril, E. Keibler, R. Lyle, C. Ucla, S.E. Antonarakis, and M.R. Brent. 2003. "Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes." Proceedings of the National Academy of Sciences 100:1140-1145.

Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. 2003. "The DNA sequence of human chromosome 7.." Nature 424(6945):157-64.

Hu, P. and M.R. Brent. 2003. "Using Twinscan to Predict Gene Structures in Genomic DNA Sequences." Wiley, New York None:.

Keibler, E. and M.R. Brent. 2003. "Eval: A software package for analysis of genome annotations." Bmc Bioinformatics 4:50.

Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH. 2003. "The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.." PLoS biology 1(2):E45.

Wang M, Buhler J, Brent MR. 2003. "The effects of evolutionary distance on TWINSCAN, an algorithm for pair-wise comparative gene prediction.." Cold Spring Harbor symposia on quantitative biology 68:125-30.

Brent, M.R. 2002. "Predicting full-length transcripts." Trends in Biotechnology 20:273-275.

Korf, I., P. Flicek, D. Duan, and M.R. Brent. 2001. "Integrating genomic homology into gene structure prediction." Bioinformatics 17:S140-148.

Reviews

Brent, M.R and R. Guigo. 2004. "Recent advances in gene structure prediction." Current Opinion in Structural Biology 14:264-272.

Annotations

International Chicken Genome Sequencing Consortium. 2005. "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution." Nature 432:695-716.

Loftus B.J., Fung E., Roncaglia P., Rowley D., Amedeo P., Bruno D., Vamathevan J., Miranda M., Anderson I.J., Fraser J.A., Allen J.E., Bosdet I.E., Brent M.R., Chiu R., Doering T.L., Donlin M.J., D'Souza C.A., Fox D.S., Grinberg V., Fu J., Fukushima M., Haas B.J., Huang J.C., Janbon G., Jones S.J., Koo H.L., Krzywinski M.I., Kwon-Chung J.K., Lengeler K.B., Maiti R., Marra M.A., Marra R.E., Mathewson C.A., Mitchell T.G., Pertea M., Riggs F.R., Salzberg S.L., Schein J.E., Shvartsbeyn A., Shin H., Shumway M., Specht C.A., Suh B.B., Tenney A., Utterback T.R., Wickes B.L., Wortman J.R., Wye N.H., Kronstad J.W., Lodge J.K., Heitman J., Davis R.W., Fraser C.M., and RW Hyman. 2005. "The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus Neoformans." Science None:.

Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. 2003. "The DNA sequence of human chromosome 7." Nature 424:157-164.

Stein L.D., Bao Z., Blasiar D., Blumenthal T., Brent M.R., Chen N., Chinwalla A., Clarke L., Clee C., Coghlan A., Coulson A., D'Eustachio P., Fitch D.H., Fulton L.A., Fulton R.E., Griffiths-Jones S., Harris T.W., Hillier L.W., Kamath R., Kuwabara P.E., Mardis E.R., Marra M.A., Miner T.L., Minx P., Mullikin J.C., Plumb R.W., Rogers J., Schein J.E., Sohrmann M., Spieth J., Stajich J.E., Wei C., Willey D., Wilson R.K., Durbin R., and R.H. Waterston. 2003. "The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics." PLoS Biology 1:E45.

Mouse Genome Sequencing Consortium. 2002. "Initial sequencing and comparative analysis of the mouse genome." Nature 420:520-562.