Michael Snyder

发表

Classifying Non-Small Cell Lung Cancer Histopathology Types and Transcriptomic Subtypes using Convolutional Neural Networks

Russ B. Altman, Isaac S. Kohane, Kun-Hsing Yu, 2019, bioRxiv.

Course 19-108 Stretch, Snip, Sculpt, or Replace? Master Course in Complex Iris Repair and Prosthesis Cases

Michael Snyder, 2015 .

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.

Yijun Ruan, Chia-Lin Wei, Mark B Gerstein, 2007, Genome research.

ProCAT: a data analysis approach for protein microarrays

Mark Gerstein, Michael Snyder, M. Gerstein, 2006, Genome Biology.

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

Raymond K. Auerbach, Kevin Y Yip, Zhi John Lu, 2011, Genome research.

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.

Mark Gerstein, Tara A Gianoulis, Michael Snyder, 2007, Genes & development.

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.

Mark Gerstein, Zhi John Lu, Mihail Sarov, 2011, Genome research.

High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution

Yehudit Hasin, Tsviya Olender, Miriam Khen, 2008, PLoS genetics.

Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing

Mark Gerstein, Lukas Habegger, Michael Snyder, 2013, G3: Genes, Genomes, Genetics.

Dynamic and complex transcription factor binding during an inducible response in yeast.

Mark B Gerstein, Michael Snyder, Can Bruce, 2009, Genes & development.

A major epigenetic programming mechanism guided by piRNAs.

Michael Snyder, Sarah Sweeney, M. Snyder, 2013, Developmental cell.

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.

Deyou Zheng, Mark B Gerstein, Alexander E Urban, 2007, Genome research.

The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics

Tara A Gianoulis, Mark B Gerstein, Michael Snyder, 2011, Genome Biology.

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

Mark Gerstein, Justin Jee, Michael R. Seringhaus, 2008, BMC Genomics.

Global analysis of gene expression in yeast

Christine E. Horak, Michael Snyder, M. Snyder, 2002, Functional & Integrative Genomics.

Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms

Mark Gerstein, Alexej Abyzov, Michael Snyder, 2011, PloS one.

Global changes in STAT target selection and transcription regulation upon interferon treatments.

Mark Gerstein, Paul Bertone, Thomas E. Royce, 2005, Genes & development.

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.

Zhiping Weng, Yutao Fu, Mark B Gerstein, 2007, Genome research.

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

Mark Gerstein, Edward J Oakeley, Thomas E. Royce, 2004, Proceedings of the National Academy of Sciences of the United States of America.

ChIP-chip: a genomic approach for identifying transcription factor binding sites.

Michael Snyder, M. Snyder, C. Horak, 2002, Methods in enzymology.

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).

Jonghwan Kim, Vishwanath R Iyer, Michael Snyder, 2007, Genome research.

MSB: a mean-shift-based approach for the analysis of structural variation in the genome.

Mark Gerstein, Lu-Yong Wang, Alexej Abyzov, 2008, Genome research.

Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool

Mark Gerstein, Haiyuan Yu, Michael Snyder, 2006, Nucleic acids research.

Target hub proteins serve as master regulators of development in yeast.

Mark Gerstein, Haiyuan Yu, Paul Bertone, 2006, Genes & development.

High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays.

Alexander Eckehart Urban, Mark B Gerstein, Todd Richmond, 2006, Proceedings of the National Academy of Sciences of the United States of America.

CREB Binds to Multiple Loci on Human Chromosome 22

Mark Gerstein, Paul Bertone, Thomas E Royce, 2004, Molecular and Cellular Biology.

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

Mark Gerstein, Joel Rozowsky, Alexander E Urban, 2008, Genome Biology.

Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing

Enrique Blanco, Michael Snyder, Albert Carbonell, 2011, Nucleic acids research.

in the human genome Systematic prediction and validation of breakpoints associated with copy-number variants

Alexander Eckehart Urban, Thomas E. Royce, Mark B Gerstein, 2007 .

Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.

Mark Gerstein, Haiyuan Yu, Lixia Jiang, 2005, Genes & development.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.

Mark Gerstein, Paul Bertone, Thomas E. Royce, 2005, Trends in genetics : TIG.

Lessons learned? Chemical plant safety since Bhopal.

Mark Gerstein, Michael Snyder, E. Hood, 2004, Environmental health perspectives.

Tilescope: online analysis pipeline for high-density tiling microarray data

Mark Gerstein, Hugo Y. K. Lam, Joel Rozowsky, 2007, Genome Biology.

Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes.

Mark Gerstein, Haiyuan Yu, Philip M. Kim, 2011, Genes & development.

Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

Raymond K. Auerbach, Mark Gerstein, Anthony A. Hyman, 2010, PLoS genetics.

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms

Mark Gerstein, Michael R. Seringhaus, Anthony R. Borneman, 2007, Functional & Integrative Genomics.

A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans

Anthony A. Hyman, Mihail Sarov, A. Francis Stewart, 2012, Cell.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

Raymond K. Auerbach, Mark Gerstein, Joel Rozowsky, 2009 .

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.

Zhiping Weng, Richard M Myers, Anason S. Halees, 2007, Genome research.

Comparative annotation of functional regions in the human genome using epigenomic data

Wei Wang, Tao Wang, Bing Ren, 2013, Nucleic acids research.

Genomics. Defining genes in the genomics era.

Mark Gerstein, Michael Snyder, M. Gerstein, 2003, Science.

Quantifying environmental adaptation of metabolic pathways in metagenomics

Jan O. Korbel, Peer Bork, Ivica Letunic, 2009, Proceedings of the National Academy of Sciences.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Mark Gerstein, Kevin Struhl, Zhiping Weng, 2008, Genome research.

Personal phenotypes to go with personal genomes

Mark Gerstein, Sherman Weissman, Michael Snyder, 2009, Molecular systems biology.

Evidence against a genomic code for nucleosome positioning Reply to “Nucleosome sequence preferences influence in vivo nucleosome organization”

Kevin Struhl, Yong Zhang, X Shirley Liu, 2010, Nature Structural &Molecular Biology.

Divergence of transcription factor binding sites across related yeast species.

Mark Gerstein, Haiyuan Yu, Michael R. Seringhaus, 2007, Science.

Distribution of NF-kappaB-binding sites across human chromosome 22.

Mark Gerstein, Paul Bertone, Thomas E. Royce, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Defining Genes in the Genomics Era

Mark Gerstein, Michael Snyder, M. Gerstein, 2003, Science.

A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.

Mark Gerstein, Nathaniel Echols, Ning Lan, 2002, Journal of molecular biology.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

Philipp Kapranov, Jennifer Harrow, Roderic Guigó, 2007, Genome research.