Publications

Li W, Wang W, Uren PJ, Penalva LO and Smith AD
Riborex: Fast and flexible identification of differential translation from Ribo-seq data.
Bioinformatics btx047 [PDF][Publisher Site]

Chen H, Smith AD and Chen T (2016)
WALT: fast and accurate read mapping for bisulfite sequencing.
Bioinformatics 32(22):3507-3509 [PDF][Publisher Site]

Ennajdaoui H, Howard JM, Sterne-Weiler T, Jahanbani F, Coyne DJ, Uren PJ, Dargyte M, Katzman S, Draper JM, Wallace A, Cazarez O, Burns SC, Qiao M, Hinck L, Smith AD, Toloue MM, Blencowe BJ, Penalva LOF, Sanford JR (2016)
IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC.
Cell Reports, 15(9):1876–1883 [PDF][Publisher Site]

Uren PJ, Bahrami-Samani E, de Araujo PR, Vogel C, Qiao M, Burns SC, Smith AD, Penalva LOF
High-throughput analyses of hnRNP H1 dissects its multi-functional aspect
RNA Biology 13(4):400-411 [PDF][Publisher Site]

Mangul S, Yang HT, Strauli N, Gruhl F, Daley T, Christenson S, Andersen AW, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N
Dumpster diving in RNA-sequencing to find the source of every last read
bioRxiv, preprint 053041 [PDF][Publisher Site]

Deng C and Smith AD (2016)
Estimating the number of species to attain sufficient representation in a random sample
arXiv, preprint arXiv:1607.02804 [PDF][Publisher Site]

Kaaij LJ, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond AS, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD, Ketting RF (2016)
Enhancers reside in a unique epigenetic environment during early zebrafish development
Genome Biology, 17(1):1 [PDF][Publisher Site]

Larson EL, Vanderpool D, Keeble S, Zhou M, Sarver BAJ, Smith AD, Dean MD and Good JM (2016)
Contrasting Levels of Molecular Evolution on the Mouse X Chromosome
Genetics 203(4):1841-1857; [PDF][Publisher Site]

Daley T and Smith AD (2016)
What’s the value in more moments?
arXiv, preprint arXiv:1605.03294 [PDF][Publisher Site]

Wasik K, Gurtowski J, Zhou X, Mendivil Ramos O, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ and Schatz M (2015)
Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignin
PNAS, 112(40):12462-7. [PDF][Publisher Site]

Aston KI, Uren PJ, Jenkins TG, Horsager A, Cairns BR, Smith AD and Carrel DT (2015)
Aberrant sperm DNA methylation predicts male fertility status and embryo quality
Fertility and Sterility, 104(6):1388-97.e1-5 [PDF][Publisher Site]

Deng C, Daley T and Smith AD (2015)
Applications of species accumulation curves in large-scale biological data analysis
Quantitative Biology, 3(3):135-144 [PDF][Publisher Site]

Uren PJ, Vo DT, de Araujo PR, Potschke R, Burns SC, Bahrami-Samani E, Qiao M, de Sousa Abreau R, Nakaya HI, Correa BR, Kuhnol C, Ule J, Martindale JL, Abdelmohsen K, Gorospe M, Smith AD, Penalva LOF (2015)
The RNA-binding protein Musashi1 is a central regulator of adhesion pathways in glioblastoma
Molecular and Cellular Biology, 35(17):2965-78 [PDF][Publisher Site]

dos Santos CO, Dolzhenko E, Hodges E, Smith AD and Hannon GJ (2015)
An epigenetic memory of pregnancy in the mouse mammary gland
Cell Reports, 11:1102-1109 [PDF][Publisher Site]

Wagenblast E, Soto M, Gutiérrez-Ángel S, Hartl CA, Gable AL, Maceli AR, Erard N, Williams AM, Kim SY, Dickopf S, Harrell JC, Smith AD, Perou CM, Wilkinson JE, Hannon GJ and Knott SRV (2015)
A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis
Nature, 520:358–362 [PDF][Publisher Site]

Chatterjee R, He X, Huang D, Fitzgerald P, Smith AD and Vinson C (2014)
High resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes
Epigenetics & Chromatin, 7:35 [PDF][Publisher Site]

He X, Chatterjee R, Tillo D, Smith AD, Fitzgerald P and Vinson C (2014)
Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes
Epigenetics & Chromatin, 7:34 [PDF][Publisher Site]

Bahrami-Samani E, Penalva LOF, Smith AD and Uren PJ (2014)
Leveraging cross-link modification events in CLIP-seq for motif discovery
Nucleic Acids Research, 43(1):95-103 [PDF][Publisher Site]

Bahrami-Samani E, Vo DT, Araujo PR, Vogel C, Smith AD, Penalva LOF and Uren PJ (2014)
Computational challenges, tools and resources for analyzing co- and post-transcriptional events in high throughput
Wiley Interdisciplinary Reviews: RNA [PDF][Publisher Site]

Uren PJ, Lee JT, Doroudchi MM, Smith AD and Horsager A (2014)
A profile of transcriptomic changes in the rd10 mouse model of retinitis pigmentosa
Molecular Vision, 20:1612-1628 [PDF][Publisher Site]

Dines J, Otárola-Castillo E, Ralph P, Alas J, Daley T, Smith AD and Dean MD (2014)
Sexual selection targets cetacean pelvic bones
Evolution, 68 (11): 3296–3306 [PDF][Publisher Site]

Daley T and Smith AD (2014)
Modeling genome coverage in single cell sequencing
Bioinformatics, 30 (22): 3159-3165 [PDF][Publisher Site]

Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD and Hannon GJ (2014)
Two waves of de novo methylation during mouse germ cell development
Genes & Development, 28: 1544-1549 [PDF][Publisher Site]

Behnam E and Smith AD (2014)
The Amordad database engine for metagenomics
Bioinformatics, 30 (20): 2949-2955 [PDF][Publisher Site]

Dolzhenko E and Smith AD (2014)
Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments
BMC Bioinformatics, 15:215 [PDF][Publisher Site]

Orozco LD, Rubbi L, Martin LJ, Fang F, Hormozdiari F, Che N, Smith AD, Lusis AJ and Pellegrini M (2014)
Intergenerational genomic DNA methylation patterns in mouse hybrid strains
Genome Biology, 15:R68 [PDF][Publisher Site]

Tamim S, Vo DT, Uren PJ, Qiao M, Bindewald E, Kasprzak WK, Shapiro BA, Nakaya HI, Burns SC, Araujo PR, Nakano I, Radek AJ, Kuersten S, Smith AD and Penalva LOF (2014)
Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells
PLoS ONE, 9 (1): e85591 [PDF][Publisher Site]

Eggeling R,  Gohr A, Keilwagen J, Mohr M, Posch S, Smith AD and Grosse I (2014)
On the value of intra-motif dependencies of human insulator protein CTCF
PLoS ONE 9 (1): e85629 [PDF][Publisher Site][Press Release]

Song Q, Decato B, Hong E, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J and Smith AD (2013)
A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics
PLoS ONE, 8 (12): e81148 [PDF][Publisher Site]

Qu J, Zhou M, Song Q, Hong EE and Smith AD (2013)
MLML: Consistent simultaneous estimates of DNA methylation and hydroxymethylation
Bioinformatics, 29 (20): 2645-2646 [PDF][Publisher Site]

Behnam E, Waterman MS and Smith AD (2013)
A geometric interpretation for local alignment-free sequence comparison
Journal of Computational Biology, 20 (7): 471-85 [PDF][Publisher Site]

Schlesinger F, Smith AD, Gingeras TR, Hannon GJ and Hodges E (2013)
De novo demethylation and non-coding transcription define active intergenic regulatory elements
Genome Research, 23: 1601-1614 [PDF][Publisher Site]

Veluchamy A, Lin X, Maumus F, Rivarola M, Bhavsar J, Creasy T, O’Brien K, Sengamalay NA, Tallon LJ, Smith AD, Rayko E, Ahmed I, Le Crom S, Farrant GK, Sgro JY, Olson SA, Splinter Bondurant S, Allen A, Rabinowicz PD, Sussman MR, Bowler C and la Tirichine L (2013)
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum
Nature Communications 4, Article number: 2091 [PDF][Publisher Site]

Regulski M, Lu Z, Kendall J, Reinders J, Llaca V, Deschamps S, Smith AD, Levy D, McCombie WR, Tingey S, Rafalski A, Hicks J, Ware D and Martienssen R (2013)
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
Genome Research 23: 1651-1662 [PDF][Publisher Site]

Main BJ, Smith AD, Jang H and Nuzhdin SV (2013)
Transcription Start Site Evolution in Drosophila
Molecular Biology and Evolution, 30 (8): 1966-1974 [PDF][Publisher Site]

Kaaij LJT, van der Wetering M, Fang F, Decato B, Molaro A, Harmen JG, van der Werken H, van Es JH, Schuijers J, de Wit E, de Laat W, Hannon GJ, Clevers HC, Smith AD and Ketting RF (2013)
DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus
Genome Biology, 14:R50 [PDF][Publisher Site]

Hong EE, Okitsu CY, Smith AD and Hsieh CL (2013)
Regionally-specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA
Molecular and Cellular Biology, 33 (14): 2683-2690 [PDF][Publisher Site]

dos Santos CO, Rebbeck C, Rozhkova E, Valentine A, Samuels A, Kadiri L, Osten P, Harris EY, Uren PJ, Smith AD and Hannon GJ (2013)
Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells
PNAS 110 (18): 7123-30 [PDF][Publisher Site]

Daley T and Smith AD (2013)
Predicting the molecular complexity of sequencing libraries
Nature Methods, 10: 325-327 [PDF][Publisher Site]

Penalva LOF, Vo DT, Boutz D, Smith AD (2013)
Post-transcriptional gene neworks
Encyclopedia of Systems Biology, 2013: 1725-1728 [Publisher Site]

Zhang MQ, Smith AD (2013)
Topics in computational genomics
Basics of Bioinformatics, 2013: 69-100 [Publisher Site]

Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LOF and Smith AD (2012)
Site identification in high-throughput RNA-protein interaction data
Bioinformatics, 28 (23): 3013–3020 [PDF][Publisher Site]

Vo DT, Subramaniam D, Remke M, Burton TL, Uren PJ, Gelfond JA, Abreu RdS, Burns SC, Qiao M, Suresh U, Korshunov A, Dubuc AM, Northcott PA, Smith AD, Pfister SM, Taylor MD, Janga SC, Anant S, Vogel C and Penalva LOF (2012)
The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis
The American Journal of Pathology, 181 (5): 1762-1772 [PDF][Publisher Site]

Fang F, Hodges E, Molaro A, Dean MD, Hannon GJ and Smith AD (2012)
The genomic landscape of human allele-specific DNA methylation
PNAS, 109 (19): 7332-7 [PDF][Publisher Site]

Araujo PR, Yoon K, Ko D, Smith AD, Qiao M, Suresh U, Burns SC, Penalva LOF (2012)
Before it gets started: regulating translation at the 5′ UTR
International Journal of Genomics, 2012:475731 [PDF][Publisher Site]

Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ and Smith AD (2011)
Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
Cell, 146 (6): 1029-1041 [PDF][Publisher Site]

Hodges E, Molaro A, dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD and Hannon GJ (2011)
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment
Molecular Cell, 44: 1-12 [PDF][Publisher Site]

Uren PJ, Burns SC, Sandhu D, Ruan J, Singh KK, Smith AD and Penalva LOF (2011)
Genomic analyses of the RNA binding protein Hu Antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites
Journal of Biological Chemistry, 286 (43): 37063-37066 [PDF][Publisher Site]

Vo DT, Qiao M, Smith AD, Burns SC, Brenner AJ and Penalva LOF (2011)
The oncogenic RNA binding protein Musashi1 is regulated by tumor suppressor miRNAs
RNA Biology, 8 (5): 817-828 [PDF][Publisher Site]

Song Q and Smith AD (2011)
Identifying dispersed epigenomic domains from ChIP-seq data
Bioinformatics 27 (6): 870-871 [PDF][Publisher Site]

Peng Q and Smith AD (2010)
Multiple sequence assembly from reads alignable to a common reference genome
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (5): 1283-1295 [PDF][Publisher Site]

Karginov F, Cheloufi S, Stark A, Smith AD and Hannon GJ (2010)
Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases
Molecular Cell, 38 (6): 781-788 [PDF][Publisher Site]

Zhang MQ and Smith AD (2010)
Challenges in understanding genome-wide DNA methylation
Journal of Computer Science and Technology, 25 (1): 1860-4749 [PDF][Publisher Site]

Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z and Zhang MQ (2009)
Updates to the RMAP short-read mapping software
Bioinformatics 25 (21): 2841-2842 [PDF][Publisher Site]

Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie RW, Wigler M, Hannon GJ and Hicks JB (2009)
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
Genome Research, 19: 1593-1605 [PDF][Publisher Site]

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC and Xavier RJ (2009)
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia
Nucleic Acids Research, 37 (14): 4587-4602 [PDF][Publisher Site]

Niida A, Smith AD, Imoto S, Aburatani H, Zhang MQ and Akiyama T (2009)
Gene set-based module discovery in the breast cancer transcriptome
BMC Bioinformatics, 10:71 [PDF][Publisher Site]

Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ and Akiyama T (2008)
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
BMC Bioinformatics, 9:404 [PDF][Publisher Site]

Smith AD, Xuan Z and Zhang MQ (2008)
Using quality scores and longer reads improves accuracy of Solexa read mapping
BMC Bioinformatics, 9:128 [PDF] [Publisher Site]

Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD and Ren B (2008)
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
Genome Research, 18: 46-59 [PDF][Publisher Site]

Kim TH, Abdullaev Z, Smith AD, Ching KA, Loukinow D, Green RD, Zhang MQ, Lobanenkov V and Ren B (2007)
Analysis of the vertebrate insulator protein CTCF binding sites in the human genome
Cell, 128: 1231-1245 [PDF][Publisher Site]

Schones DE, Smith AD and Zhang MQ (2007)
Statistical significance of cis-regulatory modules
BMC Bioinformatics, 8:19 [PDF][Publisher Site]

Smith AD, Sumazin P and Zhang MQ (2007)
Tissue-specific regulatory elements in mammalian promoters
Molecular Systems Biology, 3:73 [PDF][Publisher Site]

Martinez MJ, Smith AD, Li B, Zhang MQ and Harrod KS (2007)
Computational prediction of novel components of lung transcriptional networks
Bioinformatics, 23:21-29 [PDF][Publisher Site]

Smith AD, Sumazin P, Xuan Z and Zhang MQ (2006)
DNA motifs in human and mouse proximal promoters predict tissue specific expression
PNAS, 103(16):6275-6280 [PDF][Publisher Site]

Smith AD, Sumazin P, Das D and Zhang MQ (2005)
Mining ChIP-chip data for transcription factor and cofactor binding sites
Bioinformatics, 21 (Suppl 1): i403-i412 [PDF][Publisher Site]
Presented at the 13th International Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, MI, 2005

Smith AD, Sumazin P and Zhang MQ (2005)
Identifying tissue-specific transcription factor binding sites in vertebrate promoters
PNAS, 102(5):1560 – 1565 [PDF][Publisher Site]
This article was highlighted in Nature Review Genetics

Sumazin P, Chen G, Hata N, Smith AD, Zhang T and Zhang MQ (2005)
DWE: Discriminating Word Enumerator
Bioinformatics 21 (1): 31-38 [PDF][Publisher Site]

Pang A, Smith AD, Nuin PAS and Tillier ERM (2005)
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
BMC Bioinformatics, 6:236 [PDF][Publisher Site]

Smith AD, Lui TWH and Tillier ERM (2004)
Empirical models for substitution in ribosomal RNA
Molecular Biology and Evolution, 21 (3): 419-427 [PDF][Publisher Site]

Veerassamy S, Smith AD and Tillier ERM (2003)
A transition probability model for amino acid substitutions from BLOCKS
Journal of Computational Biology, 10 (6): 997-1010 [PDF][Publisher Site]

Evans PA and Smith AD (2003)
Complexity of approximating closest substring problems
Proceedings of the 14th International Symposium on Fundamentals of Computation Theory (FCT),
LNCS 2751: 210-221 [PDF][Publisher Site]

Evans PA and Smith AD (2003)
Toward optimal motif enumeration
Proceedings of the 8th International Workshop on Algorithms And Data Structures (WADS),
LNCS 2748: 47-58 [PDF][Publisher Site]

Evans PA, Smith AD and Wareham HT (2003)
On the complexity of finding common approximate substrings
Theoretical Computer Science, 306 (1-3): 407-430 [PDF][Publisher Site]