Andrew D. Smith

发表

Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

Michael Q. Zhang, Tae Hoon Kim, R. Green, 2007, Cell.

Molecular Heterogeneity in Large-Scale Biological Data: Techniques and Applications

Andrew D. Smith, C. Deng, Timothy P Daley, 2019, Annual Review of Biomedical Data Science.

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Ryan D. Hernandez, R. Ophoff, E. Eskin, 2018, Genome Biology.

Comprehensive analysis of RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Ryan D. Hernandez, R. Ophoff, E. Eskin, 2016, bioRxiv.

Title : Dumpster diving in RNA-sequencing to find the source of every last read Authors :

Ryan D. Hernandez, R. Ophoff, E. Eskin, 2016 .

Dumpster diving in RNA-sequencing to find the source of every last read

Ryan D. Hernandez, R. Ophoff, E. Eskin, 2016 .

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

Tyler H. Garvin, Elizabeth E. Hong, Meng Zhou, 2013, PloS one.

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

Michael Q. Zhang, Kenny Q. Ye, J. Kendall, 2009 .

Genomic analyses of early responses to radiation inglioblastoma reveal new alterations at transcription,splicing, and translation levels

Xiu-fen Lei, L. Penalva, S. Choudhary, 2020, Scientific Reports.

Integrated analyses of early responses to radiation in glioblastoma identify new alterations in RNA processing and candidate target genes to improve treatment outcomes

L. Penalva, S. Choudhary, S. Burns, 2019, bioRxiv.

Conserved and Divergent Features of Mesenchymal Progenitor Cell Types within the Cortical Nephrogenic Niche of the Human and Mouse Kidney.

A. Ransick, A. McMahon, L. Baskin, 2018, Journal of the American Society of Nephrology : JASN.

DNA motifs in human and mouse proximal promoters predict tissue-specific expression.

Michael Q. Zhang, Z. Xuan, Pavel Sumazin, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Tissue-specific Regulatory Elements in Mammalian Promoters: Supplementary Information 1 Transcripts and Promoters under Tissue-specific Regulation

Michael Q. Zhang, Pavel Sumazin, Andrew D. Smith, 2022 .

Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment.

S. Rafii, G. Hannon, W. McCombie, 2011, Molecular cell.

Computational challenges, tools, and resources for analyzing co‐ and post‐transcriptional events in high throughput

C. Vogel, L. Penalva, Andrew D. Smith, 2015, Wiley interdisciplinary reviews. RNA.

Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium

Michael D. Lee, Fei-xue Fu, D. Hutchins, 2020, Molecular biology and evolution.

Increased accuracy and speed in whole genome bisulfite read mapping using a two-letter alphabet

Andrew D. Smith, G. Brandine, 2020 .

ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions.

E. Hodges, Andrew D. Smith, B. Decato, 2020, Molecular cell.

Genomic landscape of human allele-specific DNA methylation

Matthew D Dean, G. Hannon, E. Hodges, 2012, Proceedings of the National Academy of Sciences.

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs.

Michael Q. Zhang, Leah Barrera, R. Green, 2007, Genome research.

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia

Michael Q. Zhang, Hirotoshi Kikuchi, Ramnik J. Xavier, 2009, Nucleic acids research.

Before It Gets Started: Regulating Translation at the 5′ UTR

Kihoon Yoon, Daijin Ko, Luiz O. F. Penalva, 2012, Comparative and functional genomics.

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*

Jianhua Ruan, Andrew D Smith, Jianhua Ruan, 2011, The Journal of Biological Chemistry.

Leveraging cross-link modification events in CLIP-seq for motif discovery

Philip J. Uren, L. Penalva, Andrew D. Smith, 2014, Nucleic acids research.

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Nuno R. Faria, N. Loman, J. Quick, 2017, Nature Protocols.

Reverse engineering mammalian transcriptional regulatory networks

Pavel Sumazin, Andrew D. Smith, 2007 .

An evolutionarily conserved gene family encodes proton-selective ion channels

E. Liman, Andrew D. Smith, H. Turner, 2018, Science.

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

W. Richard McCombie, Gregory J. Hannon, Qiang Song, 2011, Cell.

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases.

Gregory J. Hannon, Fedor V. Karginov, Alexander Stark, 2010, Molecular cell.

RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma

J. Ule, Kotb Abdelmohsen, M. Gorospe, 2015, Molecular and Cellular Biology.

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano

Osama El Demerdash, M. Schatz, G. Hannon, 2015, Proceedings of the National Academy of Sciences.

Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies

Sean M. Hasso, A. McMahon, B. Ren, 2018, PLoS genetics.

Characterization of universal features of partially methylated domains across tissues and species

G. Hannon, Andrew D. Smith, S. Knott, 2020, Epigenetics & chromatin.

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Trevor Bedford, Karthik Gangavarapu, Allison Black, 2017, Nature Protocols.

Spatial Transcriptional Mapping of the Human Nephrogenic Program

Rachel S. G. Sealfon, O. Troyanskaya, Jian Zhou, 2020, bioRxiv.

An epigenetic memory of pregnancy in the mouse mammary gland.

G. Hannon, E. Hodges, Camila O. dos Santos, 2015, Cell reports.

Biogeographic conservation of the cytosine epigenome in the globally important marine, nitrogen‐fixing cyanobacterium Trichodesmium

Michael D. Lee, Fei-xue Fu, D. Hutchins, 2017, Environmental microbiology.

Establishing a stable, repeatable platform for measuring changes in sperm DNA methylation

Alan Horsager, D. Carrell, Andrew D. Smith, 2018, Clinical Epigenetics.

Associations between Maternal Tobacco Smoke Exposure and the Cord Blood CD4+ DNA Methylome

Michelle R. Campbell, D. Bell, G. Pittman, 2019, Environmental health perspectives.

DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta

Matthew D Dean, Andrew D. Smith, B. Decato, 2017, Molecular biology and evolution.

SMURF-seq: efficient copy number profiling on long-read sequencers

Rishvanth K. Prabakar, Andrew D. Smith, Liya Xu, 2019, Genome Biology.

Contrasting Levels of Molecular Evolution on the Mouse X Chromosome

Matthew D Dean, J. Good, Meng Zhou, 2016, Genetics.

Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells

P. Osten, G. Hannon, Lolahon R. Kadiri, 2013, Proceedings of the National Academy of Sciences.

Sexual selection targets cetacean pelvic bones

Peter L. Ralph, Andrew D. Smith, Timothy P Daley, 2014, Evolution; international journal of organic evolution.

In Vivo Developmental Trajectories of Human Podocyte Inform In Vitro Differentiation of Pluripotent Stem Cell-Derived Podocytes.

A. Ransick, A. McMahon, J. Peti-Peterdi, 2019, Developmental cell.

Progressive Recruitment of Mesenchymal Progenitors Reveals a Time-Dependent Process of Cell Fate Acquisition in Mouse and Human Nephrogenesis.

Andrew P McMahon, Andrew D Smith, A. Ransick, 2018, Developmental cell.

Two waves of de novo methylation during mouse germ cell development

S. Rafii, G. Hannon, A. Aravin, 2014, Genes & development.

development Two waves of de novo methylation during mouse germ cell Material

S. Rafii, G. Hannon, A. Aravin, 2014 .

Subtype classification and functional annotation of L1Md retrotransposon promoters

Meng Zhou, Andrew D. Smith, 2019, Mobile DNA.

Tumorigenesis and Neoplastic Progression The RNA-Binding Protein Musashi 1 Affects Medulloblastoma Growth via a Network of Cancer-Related Genes and Is an Indicator of Poor Prognosis

P. Northcott, S. Pfister, C. Vogel, 2012 .

Modulates the Interaction of Invasion-Associated Transcripts with

B. Blencowe, Sol Katzman, L. Penalva, 2016 .

Author Correction: SMURF-seq: efficient copy number profiling on long-read sequencers

Rishvanth K. Prabakar, Andrew D. Smith, Liya Xu, 2020, Genome Biology.

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum.

Jaysheel D. Bhavsar, Gregory K. Farrant, T. Creasy, 2013, Nature Communications.

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Jaysheel D. Bhavsar, Gregory K. Farrant, T. Creasy, 2013, Nature Communications.

A profile of transcriptomic changes in the rd10 mouse model of retinitis pigmentosa

M. M. Doroudchi, Alan Horsager, Andrew D. Smith, 2014, Molecular vision.

Global translational landscape of the Candida albicans morphological transition

S. Choudhary, Andrew D. Smith, D. Kadosh, 2020, G3.

Falco: high-speed FastQC emulation for quality control of sequencing data.

Andrew D. Smith, Guilherme De Sena Brandine, Andrew D. Smith, 2019, F1000Research.

Aberrant sperm DNA methylation predicts male fertility status and embryo quality.

B. Cairns, Alan Horsager, K. Aston, 2015, Fertility and sterility.

Gene set-based module discovery in the breast cancer transcriptome

Michael Q. Zhang, Andrew D. Smith, Atsushi Niida, 2009, BMC Bioinformatics.

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells

Michael Q. Zhang, Andrew D. Smith, Atsushi Niida, 2008, BMC Bioinformatics.

Better lower bounds for missing species: improved non-parametric moment-based estimation for large experiments

Andrew D. Smith, Timothy P. Daley, 2016 .

Identifying tissue-selective transcription factor binding sites in vertebrate promoters.

Michael Q. Zhang, Pavel Sumazin, Michael Q Zhang, 2005, Proceedings of the National Academy of Sciences of the United States of America.

lncRNA requirements for mouse acute myeloid leukemia and normal differentiation

David R. Kelley, J. Rinn, G. Hannon, 2017, eLife.

Site identification in high-throughput RNA-protein interaction data

Andrew D. Smith, Mei Qiao, Emad Bahrami Samani, 2012, Bioinform..

Genomic analyses of early responses to radiation inglioblastoma reveal new alterations at transcription,splicing, and translation levels

Xiu-fen Lei, L. Penalva, S. Choudhary, 2020, Scientific Reports.

Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet

Andrew D. Smith, Guilherme de Sena Brandine, 2020, bioRxiv.

Evolutionary expansion of DNA hypomethylation in the mammalian germline genome

Matthew D Dean, Emily Hodges, Jianghan Qu, 2018, Genome research.

Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes

D. Tillo, R. Chatterjee, Ximiao He, 2014, Epigenetics & Chromatin.

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

T. Gingeras, G. Hannon, F. Schlesinger, 2013, Genome research.

active intergenic regulatory elements De novo DNA demethylation and non-coding transcription define

T. Gingeras, G. Hannon, F. Schlesinger, 2013 .

High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes

R. Chatterjee, Ximiao He, C. Vinson, 2014, Epigenetics & Chromatin.

DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus

G. Hannon, R. Ketting, H. Clevers, 2013, Genome Biology.

Using quality scores and longer reads improves accuracy of Solexa read mapping

Michael Q. Zhang, Andrew D. Smith, Zhenyu Xuan, 2008, BMC Bioinformatics.

Accurate detection of short and long active ORFs using Ribo-seq data

Saket Choudhary, Wenzheng Li, Andrew D Smith, 2019, Bioinform..

IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC.

B. Blencowe, Sol Katzman, L. Penalva, 2016, Cell reports.

Challenges in Understanding Genome-Wide DNA Methylation

Michael Q. Zhang, Andrew D. Smith, Andrew D. Smith, 2010, Journal of Computer Science and Technology.

capture and single molecule bisulfite sequencing High definition profiling of mammalian DNA methylation by array Material Supplemental

Michael Q. Zhang, Kenny Q. Ye, J. Kendall, 2009 .

Bioinformatics Applications Note Gene Expression Identifying Dispersed Epigenomic Domains from Chip-seq Data

Andrew D. Smith, Qiang Song, Andrew D. Smith, 2022 .

Genomic Analyses Reveal Broad Impact of miR-137 on Genes Associated with Malignant Transformation and Neuronal Differentiation in Glioblastoma Cells

S. Kuersten, L. Penalva, H. Nakaya, 2014, PloS one.

BMC Bioinformatics Methodology article Statistical significance of cis-regulatory modules

Michael Q. Zhang, Andrew D. Smith, Dustin E. Schones, 2007 .

Applications of species accumulation curves in large-scale biological data analysis

Timothy Daley, Andrew Smith, Chao Deng, 2015, Quantitative Biology.

Riborex: fast and flexible identification of differential translation from Ribo‐seq data

Weili Wang, Andrew D. Smith, Wenzheng Li, 2017, Bioinform..

SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

Andrew D. Smith, Elisabeth R. M. Tillier, Paulo A. S. Nuin, 2005, BMC Bioinformatics.

Regionally Specific and Genome-Wide Analyses Conclusively Demonstrate the Absence of CpG Methylation in Human Mitochondrial DNA

Elizabeth E. Hong, C. Hsieh, Andrew D. Smith, 2013, Molecular and Cellular Biology.

Resource An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland Graphical

G. Hannon, E. Hodges, Andrew D. Smith, 2015 .

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments

Andrew D. Smith, E. Dolzhenko, 2014, BMC Bioinformatics.

Updates to the RMAP short-read mapping software

Michael Q. Zhang, Andrew D. Smith, Zhenyu Xuan, 2009, Bioinform..

A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis

Steffen Dickopf, Annika L. Gable, C. Perou, 2015, Nature.

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments

Andrew D. Smith, Egor Dolzhenko, Andrew D. Smith, 2014, BMC Bioinformatics.

The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis.

P. Northcott, S. Pfister, C. Vogel, 2012, The American journal of pathology.

High-throughput analyses of hnRNP H1 dissects its multi-functional aspect

C. Vogel, L. Penalva, S. Burns, 2016, RNA biology.

SMURF-seq for fast, multiplexed copy number profiling with long-read sequencers

Andrew D. Smith, Rishvanth K. Prabakar, James W. Hicks, 2018, bioRxiv.

The oncogenic RNA-binding protein Musashi1 is regulated by tumor suppressor miRNAs

L. Penalva, A. Brenner, S. Burns, 2011, RNA biology.

Circulating tumor cells exhibit metastatic tropism and reveal brain metastasis drivers.

J. Hicks, A. Bardia, D. Juric, 2019, Cancer discovery.

Modeling genome coverage in single-cell sequencing

Timothy Daley, Andrew D. Smith, Andrew D. Smith, 2014, Bioinform..

WALT: fast and accurate read mapping for bisulfite sequencing

Ting Chen, Haifeng Chen, Andrew D. Smith, 2016, Bioinform..

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Andrew D Smith, Ji Hyun Choi, David Stoddart, 2020, bioRxiv.

Intergenerational genomic DNA methylation patterns in mouse hybrid strains

F. Hormozdiari, M. Pellegrini, A. Lusis, 2014, Genome Biology.

Mining ChIP-chip data for transcription factor and cofactor binding sites

Michael Q. Zhang, Andrew D. Smith, Debopriya Das, 2005, ISMB.

DWE: Discriminating Word Enumerator

Michael Q. Zhang, Andrew D. Smith, Gengxin Chen, 2005, Bioinform..

Topics in Computational Genomics

Michael Q. Zhang, Andrew D. Smith, Michael Q. Zhang, 2013 .

CREAD: Comprehensive Regulatory Element Analysis and Detection

Michael Q. Zhang, Pavel Sumazin, Andrew D. Smith, 2005 .

Computational prediction of novel components of lung transcriptional networks

Michael Q. Zhang, Andrew D. Smith, Kevin S. Harrod, 2007, Bioinform..

Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era

N. Loman, J. Quick, G. Dougan, 2023, Microbial genomics.

The Amordad database engine for metagenomics

Andrew D. Smith, Ehsan Behnam, Andrew D. Smith, 2014, Bioinform..

Molecular characterization of the transition from acute to chronic kidney injury following ischemia/reperfusion

A. McMahon, Meng Li, Andrew D. Smith, 2017, JCI insight.

Falco: high-speed FastQC emulation for quality control of sequencing data

Andrew D. Smith, Guilherme de Sena Brandine, 2021, F1000Research.

Subtype classification and functional annotation of L1Md retrotransposon promoters

Meng Zhou, Andrew D. Smith, 2019, Mobile DNA.

IGF 2 BP 3 Modulates the In teraction of Invasion-Associated Transcripts with RISC Graphical Abstract Highlights

B. Blencowe, Sol Katzman, L. Penalva, 2016 .

Before It Gets Started: Regulating Translation at the 5′ UTR

U. Suresh, L. Penalva, S. Burns, 2012, Comparative and Functional Genomics.

MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation

Meng Zhou, Andrew D. Smith, Qiang Song, 2013, Bioinform..

Predicting the molecular complexity of sequencing libraries

Timothy Daley, Andrew D Smith, Andrew D. Smith, 2013, Nature Methods.

Transcription Start Site Evolution in Drosophila

Bradley J. Main, S. Nuzhdin, Andrew D. Smith, 2013, Molecular biology and evolution.

Multiple Sequence Assembly from Reads Alignable to a Common Reference Genome

Andrew D. Smith, Qian Peng, Andrew D. Smith, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Establishing a stable, repeatable platform for measuring changes in sperm DNA methylation

Alan Horsager, D. Carrell, Andrew D. Smith, 2018, Clinical Epigenetics.

Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments

Chao Deng, Timothy Daley, Jie Ren, 2019, J. Comput. Biol..

Global effects of identity and aging on the human sperm methylome

K. Aston, Andrew D. Smith, Guilherme de Sena Brandine, 2023, bioRxiv.

Paternal germ line aging: DNA methylation age prediction from human sperm

B. Cairns, K. Aston, D. Carrell, 2018, BMC Genomics.

Gene set-based module discovery in the breast cancer transcriptome

Michael Q. Zhang, H. Aburatani, A. Niida, 2009 .

Bioinformatics Original Paper Computational Prediction of Novel Components of Lung Transcriptional Networks

Michael Ruogu Zhang, Andrew D. Smith, K. Harrod, 2022 .

Molecular Systems Biology 3; Article number 73; doi:10.1038/msb4100114 Citation: Molecular Systems Biology 3:73

Michael Q. Zhang, Pavel Sumazin, Andrew D. Smith, 2022 .

DWE: Discriminating Word Enumerator

Michael Q. Zhang, Pavel Sumazin, Gengxin Chen, 2005, Bioinform..

Paternal germ line aging: DNA methylation age prediction from human sperm

B. Cairns, K. Aston, D. Carrell, 2018, BMC Genomics.

Gene set-based module discovery in the breast cancer transcriptome.

Michael Q. Zhang, H. Aburatani, A. Niida, 2009, BMC bioinformatics.

Title : Dumpster diving in RNA-sequencing to find the source of every last read

R. Ophoff, E. Eskin, F. Gruhl, 2016 .

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia

Michael Q. Zhang, R. Xavier, Yair Benita, 2009, Nucleic acids research.

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases.

Fedor V. Karginov, G. Hannon, Sihem Cheloufi, 2010, Molecular cell.

Gene set-based module discovery in the breast cancer transcriptome

Michael Q. Zhang, H. Aburatani, A. Niida, 2009, BMC Bioinformatics.

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.

Michael Q. Zhang, Kenny Q. Ye, J. Kendall, 2009, Genome research.

Title: An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1) target

R. Xavier, Yair Benita, D. Chung, 2022 .

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*

Jianhua Ruan, L. Penalva, S. Burns, 2011, The Journal of Biological Chemistry.

Multiple Sequence Assembly from Reads Alignable to a Common Reference Genome

Andrew D. Smith, Qian Peng, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Increased accuracy and speed in whole genome bisulﬁte read mapping using a two-letter alphabet

Andrew D. Smith, Guilherme de, Sena Brandine, 2020 .