Skip to content

Publications & Resources

Browse the 871 peer-reviewed publications enabled by 454 Sequencing technology.

Search by Biological Field, Application category or keyword. To refine your search, you may also select any combination of options. Click here to view the complete list.

Biological Fields


Application Category


Keywords (Title, Author or Journal)



Publications within this category

Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae.  Gowda M, Nunes CC, Sailsbery J, Xue M, Chen F, Nelson CA, Brown DE, Oh Y, Meng S, Mitchell T, Hagedorn CH, Dean RA. (7/21/2010) Nucleic Acids Research ePub:
View Publication

High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem.  Martinez G, Donaire L, Llave C, Pallas V, Gomez G. (5/1/2010) Molecular Plant Pathology 11(3): 347-59.
View Publication

Small RNA class transition from siRNA/piRNA to miRNA during pre-implantation mouse development.  Ohnishi Y, Totoki Y, Toyoda A, Watanabe T, Yamamoto Y, Tokunaga K, Sakaki Y, Sasaki H, Hohjoh H. (4/12/2010) Nucleic Acids Research ePub:
View Publication

The MicroRNA Profile of Prostate Carcinoma Obtained by Deep Sequencing.  Szczyrba J, Löprich E, Wach S, Jung V, Unteregger G, Barth S, Grobholz R, Wieland W, Stöhr R, Hartmann A, Wullich B, Grässer F. (3/30/2010) Molecular Cancer Research 8(4): 529-38.
View Publication

Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana.  Vidal EA, Araus V, Lu C, Parry G, Green PJ, Coruzzi GM, Gutiérrez RA. (2/8/2010) PNAS 107(9): 4477-82.
View Publication

Discovery of chicken microRNAs associated with lipogenesis and cell proliferation.  Hicks JA, Trakooljul N, Liu HC. (1/1/2010) Physiological Genomics ePub:
View Publication

MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana.  Grant-Downton R, Le Trionnaire G, Schmid R, Rodriguez-Enriquez J, Hafidh S, Mehdi S, Twell D, Dickinson H. (12/30/2009) BMC Genomics 10(1): 643.
View Publication

Genome-wide profiling of Populus small RNAs.  Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S. (12/20/2009) BMC Genomics 10(1): 620.
View Publication

A Subtle Alternative Splicing Event of the Na(V)1.8 Voltage-Gated Sodium Channel is Conserved in Human, Rat, and Mouse.  Schirmeyer J, Szafranski K, Leipold E, Mawrin C, Platzer M, Heinemann SH. (12/2/2009) Journal of Molecular Neuroscience 41(2): 310-4.
View Publication

Repertoire and evolution of miRNA genes in four divergent nematode species.  de Wit E, Linsen SE, Cuppen E, Berezikov E. (9/15/2009) Genome Research 19(11): 2064-74.
View Publication

Identification and expression analysis of infectious laryngotracheitis virus encoding microRNAs.  Rachamadugu R, Lee JY, Wooming A, Kong BW. (8/29/2009) Virus Genes 39(3): 301-8.
View Publication

Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation.  Ciaudo C, Servant N, Cognat V, Sarazin A, Kieffer E, Viville S, Colot V, Barillot E, Heard E, Voinnet O. (8/28/2009) PLoS Genetics 5(8): e1000620.
View Publication

High-resolution profiling and discovery of planarian small RNAs.  Marc R. Friedländera, Catherine Adamidia, Ting Hanb, Svetlana Lebedevaa, Thomas A. Isenbargerc, Martin Hirstd, Marco Marrad, Chad Nusbaume, William L. Leee, James C. Jenkinf, Alejandro Sánchez Alvaradof, John K. Kimb and Nikolaus Rajewskya (6/29/2009) PNAS 106(28): 11546-51.
View Publication

Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing.  Nygaard S, Jacobsen A, Lindow M, Eriksen J, Balslev E, Flyger H, Tolstrup N, Moller S, Krogh A, Litman T. (6/9/2009) BMC Medical Genomics 2(1): 35.
View Publication

Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.  Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, Fahlman RP. (5/1/2009) Nucleic Acids Research 37(8): 2461-70.
View Publication

Tiny RNAs associated with transcription start sites in animals.  Taft, Glazov, Cloonan, Simons, Stephen, Faulkner, Lassmann , Forrest, Grimmond, Schroder, Irvine, Arakawa, Nakamura, Kubosaki, Hayashida, Kawazu, Murata, Nishiyori, Fukuda, Kawai, Daub, Hume, Suzuki, Orlando, Carninci, Hayashizaki, Mattick. (5/1/2009) Nature Genetics 41(5): 572-8
View Publication

Parallel DNA pyrosequencing unveils new zebrafish microRNAs.  Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MA. (4/27/2009) BMC Genomics 10(1): 195.
View Publication

Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries.  Wyman SK, Parkin RK, Mitchell PS, Fritz BR, O'Briant K, Godwin AK, Urban N, Drescher CW, Knudsen BS, Tewari M. (4/23/2009) PLoS ONE 4(4): e5311
View Publication

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.  Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A. (4/1/2009) Nucleic Acids Research 37(6): e46
View Publication

Identification of novel Epstein-Barr virus microRNA genes from nasopharyngeal carcinomas.  Zhu JY, Pfuhl T, Motsch N, Barth S, Nicholls J, Grässer F, Meister G. (4/1/2009) Journal of Virology 83(7): 3333-41
View Publication

miRNA in situ hybridization in formaldehyde and EDC-fixed tissues.  Pena JT, Sohn-Lee C, Rouhanifard SH, Ludwig J, Hafner M, Mihailovic A, Lim C, Holoch D, Berninger P, Zavolan M, Tuschl T. (2/1/2009) Nature Methods 6(2): 139-41.
View Publication

The deep evolution of metazoan microRNAs.  Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ. (2/1/2009) Evolution & Development 11(1): 50-68
View Publication

MicroRNA Expression in Chicken Embryos.  Hicks JA, Tembhurne P, Liu HC. (11/1/2008) Poultry Science 87: 2335-43
View Publication

Zili is required for germ cell differentiation and meiosis in zebrafish.  Houwing S, Berezikov E, Ketting RF. (10/22/2008) EMBO Journal 27: 2702-11
View Publication

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs.  Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. (10/15/2008) Genes & Development 22: 2773-85
View Publication

TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway.  Bühler M, Spies N, Bartel DP, Moazed D. (10/1/2008) Nature Structural & Molecular Biology 15: 1015-23
View Publication

Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes.  Reid JG, Nagaraja AK, Lynn FC, Drabek RB, Muzny DM, Shaw CA, Weiss MK, Naghavi AO, Khan M, Zhu H, Tennakoon J, Gunaratne GH, Corry DB, Miller J, McManus MT, German MS, Gibbs RA, Matzuk MM, Gunaratne PH. (10/1/2008) Genome Research 18: 1571-81
View Publication

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.  Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T. (10/1/2008) Genome Research 18: 1602-9
View Publication

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains.  Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. (9/1/2008) Genome Research 18: 1456-65
View Publication

MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs.  Umbach JL, Kramer MF, Jurak I, Karnowski HW, Coen DM, Cullen BR. (8/7/2008) Nature 454: 780-783
View Publication

Characterization of unique small RNA populations from rice grain.  Heisel SE, Zhang Y, Allen E, Guo L, Reynolds TL, Yang X, Kovalic D, Roberts JK. (8/6/2008) PLoS ONE 3: e2871
View Publication

Conifers have a unique small RNA silencing signature.  Dolgosheina EV, Morin RD, Aksay G, Sahinalp SC, Magrini V, Mardis ER, Mattsson J, Unrau PJ. (8/1/2008) RNA 14: 1508-15
View Publication

Circulating microRNAs as stable blood-based markers for cancer detection.  Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M. (7/29/2008) PNAS 10513-8: 105
View Publication

Capped small RNAs and MOV10 in human hepatitis delta virus replication  Haussecker D, Cao D, Huang Y, Parameswaran P, Fire AZ, Kay MA (6/15/2008) Nat Struct Mol Biol :
View Publication

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes  Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H. (5/22/2008) Nature 453: 539-543
View Publication

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome  Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (5/7/2008) Current Biology 18: 758-762
View Publication

Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control  Alexei A. Aravin, Ravi Sachidanandam, Angelique Girard, Katalin Fejes-Toth, Gregory J. Hannon* (4/19/2008) Science Express 10:
View Publication

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes  Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ. (4/10/2008) Nature 453: 534-538
View Publication

A Role for Piwi and piRNAs in Germ Cell Maintenance and Transposon Silencing in Zebrafish  Saskia Houwing, Leonie M. Kamminga, Eugene Berezikov, Daniela Cronembold, Angelique Girard, Hans van den Elst, Dmitri V. Filippov, Heiko Blaser, Erez Raz, Cecilia B. Moens, Ronald H.A. Plasterk, Gregory J. Hannon, Bruce W. Draper, and Rene´ F. Ketting (4/6/2008) Cell 129: 69–82
View Publication

RNA-directed RNA polymerase (RdR) 3 from Nicotiana attenuata is required for competitive growth in natural environments  Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ (4/1/2008) Genome Research 18: 571-574
View Publication

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa  Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ (4/1/2008) Genome Research 18: 571-584
View Publication

The birth and death of microRNA genes in Drosophila  Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI.  (3/1/2008) Nature Genetics 40: 351-255
View Publication

PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis  Mosher RA, Schwach F, Studholme D, Baulcombe DC (2/26/2008) PNAS 105: 3145-3150
View Publication

Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA strands in flies  Seitz H, Ghildiyal M, Zamore PD (1/22/2008) Current Biology 18: 147-151
View Publication

Deep Sequencing of Chicken microRNAs  Joan Burnside, Ming Ouyang, Amy Anderson, Erin Bernberg, Cheng Lu, Blake C.Meyers, Pamela J. Green, Milos Markis, Grace Isaacs, Emily Huang, Robin W. Morgan (1/1/2008) BMC Genomics 9:
View Publication

Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci  David M. Tyler, Katsutomo Okamura, Wei-Jen Chung, Joshua W. Hagen, Eugene Berezikov, Gregory J. Hannon and Eric C. Lai (1/1/2008) Genes & Development 22: 26-36
View Publication

Novel and nodulation-regulated microRNAs in soybean roots  Senthil Subramanian, Yan Fu, Ramanjulu Sunkar, W Brad Barbazuk, Jian-Kang Zhu and Oliver Yu (1/1/2008) BMC Genomics 9:
View Publication

Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis  Jin H, Vacic V, Girke T, Lonardi S, Zhu JK. (1/1/2008) BMC Mol Biol 9:
View Publication

Identification of novel and candidate miRNAs in rice by high throughput sequencing  Ramanjulu Sunkar, Xuefeng Zhou, Yun Zheng, Weixiong Zhang, Jian-Kang Zhu (1/1/2008) BMC Plant Biology 8:
View Publication

Conservation and divergence of microRNAs in Populus  Abdelali Barakat*, Kerr P. Wall, Scott DiLoreto, Claude W. dePamphilis, and John E. Carlson (12/31/2007) BMC Genomics 8:
View Publication

Systematic Identification of C. elegans miRISC Proteins, miRNAs, and mRNA Targets by Their Interactions with GW182 Proteins AIN-1 and AIN-2  Liang Zhang, Lei Ding, Tom H. Cheung, Meng-Qiu Dong, Jun Chen, Aileen K. Sewell, Xuedong Liu, John R. Yates III, and Min Han (11/30/2007) Molecular Cell 28: 598–613
View Publication

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells  Calabrese JM, Seila AC, Yeo GW, Sharp PA. (11/13/2007) PNAS 104: 18097-18102
View Publication

Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs  Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC.  (11/7/2007) Genome Research :
View Publication

A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing  Poornima Parameswaran, Roxana Jalili, Li Tao, Shadi Shokralla, Baback Gharizadeh, Mostafa Ronaghi and Andrew Z. Fire (10/11/2007) Nucleic Acids Research :
View Publication

Differential Regulation of microRNAs by p53 Revealed by Massively Parallel Sequencing  Valery Tarasov, Peter Jung, Berlinda Verdoodt, Dmitri Lodygin, Alexey Epanchintsev, Antje Menssen, Gunter Meister, Heiko Hermeking (7/11/2007) Cell Cycle 6:
View Publication

Intronic microRNA precursors that bypass Drosha processing  Ruby JG, Jan CH, Bartel DP.  (7/5/2007) Nature 448: 83-89
View Publication

Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants  Abdelali Barakat, Kerr Wall, Jim Leebens-Mack, Yunjiao J. Wang, John E. Carlson and Claude W. dePamphilis (7/1/2007) The Plant Journal :
View Publication

miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii.   Molnár A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC (6/28/2007) Nature 447: 1126-1129
View Publication

Functions for Diverse Small RNAs of Land Plants  Axtell MJ, Snyder JA, Bartel DP.  (6/1/2007) Plant Cell 19: 1750-1769
View Publication

A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii  Tao Zhao, Guanglin Li, Shijun Mi, Shan Li, Gregory J. Hannon, Xiu-Jie Wang and Yijun Qi (4/3/2007) Genes & Development :
View Publication

Genome-Wide Analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 Pathway in Arabidopsis Reveals Dependency on miRNA- and tasiRNA-Directed Targeting  Miya D. Howell, Noah Fahlgren, Elisabeth J. Chapman, Jason S. Cumbie, Christopher M. Sullivan, Scott A. Givan, Kristin D. Kasschau, and James C. Carrington (3/30/2007) Plant Cell :
View Publication

Role of RNA polymerase IV in plant small RNA metabolism  Xiaoyu Zhang, Ian R. Henderson, Cheng Lu, Pamela J. Green, and Steven E. Jacobsen (3/13/2007) PNAS 104: 4536–4541
View Publication

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs  Kristin D. Kasschau, Noah Fahlgren, Elisabeth J. Chapman, Christopher M. Sullivan, Jason S. Cumbie, Scott A. Givan, James C. Carrington (3/1/2007) PLoS Biology 5:
View Publication

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila  Julius Brennecke, Alexei A. Aravin, Alexander Stark, Monica Dus, Manolis Kellis, Ravi Sachidanandam, and Gregory J. Hannon (3/1/2007) Cell 128: 1089-1103
View Publication

High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes  Noah Fahlgren, Miya D. Howell, Kristin D. Kasschau, Elisabeth J. Chapman, Christopher M. Sullivan, Jason S. Cumbie, Scott A. Givan, Theresa F. Law, Sarah R. Grant, Jeffery L. Dangl, James C. Carrington (2/1/2007) PLoS ONE 2:
View Publication

Cloning and characterization of microRNAs from wheat (Triticum aestivum L.)   Yingyin Yao, Ganggang Guo, Zhongfu Ni, Ramanjulu Sunkar, JinkunDu, Jian-Kang Zhu, Qixin Sun (1/1/2007) Genome Biology 8:
View Publication

A novel class of bacteria-induced small RNAs in Arabidopsis  Surekha Katiyar-Agarwal, Shang Gao, Adam Vivian-Smith and Hailing Jin (1/1/2007) Genes & Development 21: 3123-3134
View Publication

A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana  Ramya Rajagopalan, Hervé Vaucheret, Jerry Trejo and David P. Bartel (12/16/2006) Genes & Development 20: 3407-3425
View Publication

Large-Scale Sequencing Reveals 21U-RNAs and Additional MicroRNAs and Endogenous siRNAs in C. elegans  J. Graham Ruby, Calvin Jan, Christopher Player, Michael J. Axtell, William Lee, Chad Nusbaum, Hui Ge, and David P. Bartel (12/15/2006) Cell 127: 1193–1207
View Publication

CSRDB: a small RNA integrated database and browser resource for cereals  Cameron Johnson, Lewis Bowman, Alex T. Adai, Vicki Vance and Venkatesan Sundaresan (12/14/2006) Nucleic Acids Research :
View Publication

A Two-Hit Trigger for siRNA Biogenesis in Plants  Michael J. Axtell, Calvin Jan, Ramya Rajagopalan, and David P. Bartel (11/3/2006) Cell 127: 565-577
View Publication

Diversity of microRNAs in Human and Chimpanzee Brain  Eugene Berezikov, Fritz Thuemmler, Linda W van Laake, Ivanela Kondova, Ronald Bontrop, Edwin Cuppen and Ronald H A Plasterk (10/29/2006) Nature Genetics 38: 1375-1377
View Publication

MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant   Cheng Lu, Karthik Kulkarni, Frédéric F. Souret, Ramesh MuthuValliappan, Shivakundan Singh Tej, R. Scott Poethig, Ian R. Henderson, Steven E. Jacobsen, Wenzhong Wang, Pamela J. Green and Blake C. Meyers (10/1/2006) Genome Research 16: 1276–1288
View Publication

Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation  Yijun Qi, Xingyue He, Xiu-Jie Wang, Oleksiy Kohany, Jerzy Jurka & Gregory J. Hannon (9/24/2006) Nature 443: 1008-1012
View Publication

Marek's Disease Virus Encodes MicroRNAs That Map to meq and the Latency-Associated Transcript  Joan Burnside, Erin Bernberg, Amy Anderson, Cheng Lu, Blake C. Meyers, Pamela J. Green, Neeta Jain, Grace Isaacs, and Robin W. Morgan (9/1/2006) Journal of Virology 80: 8778-8786
View Publication

Characterization of the piRNA Complex from Rat Testes  Nelson C. Lau, Anita G. Seto, Jinkuk Kim, Satomi Kuramochi-Miyagawa, Toru Nakano, David P. Bartel, Robert E. Kingston (7/21/2006) Science 313: 363-367
View Publication

A germline-specific class of small RNAs binds mammalian Piwi proteins  Angélique Girard, Ravi Sachidanandam, Gregory J. Hannon and Michelle A. Carmell (7/13/2006) Nature 442: 119-202
View Publication

Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning  Ian R Henderson, Xiaoyu Zhang, Cheng Lu, Lianna Johnson, Blake C Meyers, Pamela J Green & Steven E Jacobsen (6/1/2006) Nature Genetics 38: 721-725
View Publication