Genomic Instability and Cancer Genetics Program, CINJ

Research Output 1973 2020

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2017
2 Citations (Scopus)

Polyadenylation site-based analysis of transcript expression by 3′READS+

Zheng, D. & Tian, B., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 65-77 13 p. (Methods in Molecular Biology; vol. 1648).

Research output: Chapter in Book/Report/Conference proceedingChapter

Polyadenylation
Gene Expression Profiling
Ligation
High-Throughput Nucleotide Sequencing
Messenger RNA

The translationally controlled tumor protein and the cellular response to ionizing radiation-induced DNA damage

Zhang, J., Shim, G., de Toledo, S. M. & Azzam, E., Jan 1 2017, Results and Problems in Cell Differentiation. Springer Verlag, p. 227-253 27 p. (Results and Problems in Cell Differentiation; vol. 64).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ionizing Radiation
DNA Damage
DNA
DNA End-Joining Repair
Double-Stranded DNA Breaks
2014
15 Citations (Scopus)

Accurate mapping of cleavage and polyadenylation sites by 3′ region extraction and deep sequencing

Hoque, M., Li, W. & Tian, B., Jan 1 2014, Methods in Molecular Biology. Humana Press Inc., p. 119-129 11 p. (Methods in Molecular Biology; vol. 1125).

Research output: Chapter in Book/Report/Conference proceedingChapter

High-Throughput Nucleotide Sequencing
Polyadenylation
RNA
Gene Expression
Reverse Transcription

Regulation of pericentric heterochromatin by ncRNA in Schizosaccharomyces pombe

Zaratiegui, M., Mar 1 2014, Fungal RNA Biology. Springer International Publishing, p. 315-345 31 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Untranslated RNA
Heterochromatin
Schizosaccharomyces
Chromatin
Tandem Repeat Sequences
2013

DNA Helicases: Hexameric Enzyme Action

Sen, D. & Patel, S. S., Feb 15 2013, Encyclopedia of Biological Chemistry: Second Edition. Elsevier Inc., p. 21-27 7 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA Helicases
Nucleic Acids
Enzymes
Hydrolysis
Nucleoside-Triphosphatase

Ethnic differences in fertility and assisted reproduction: Ethnic disparity in stem cell availability and research

Lu, C. W., Seita, Y., Treff, N. & Roth, M. J., Mar 1 2013, Ethnic Differences in Fertility and Assisted Reproduction. Springer New York, p. 213-226 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Stem Cell Research
Pluripotent Stem Cells
Reproduction
Fertility
Stem Cells
2 Citations (Scopus)

Helicase unwinding at the replication fork

Nandakumar, D. & Patel, S., Jan 1 2013, Molecular Biophysics for the Life Sciences. Springer New York, p. 291-312 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nucleoside-Triphosphatase
DNA Primase
Bacteriophage T7
DNA-binding proteins
DNA-directed DNA polymerase

Heterochromatin

Zaratiegui, M. & Martienssen, R. A., Feb 27 2013, Brenner's Encyclopedia of Genetics: Second Edition. Elsevier Inc., p. 438-441 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Heterochromatin
heterochromatin
Chromatin
chromatin
Histone Code

Revisiting mutagenesis in the age of high-throughput sequencing

De, S. & Ward, R. M., Nov 1 2013, Stress-Induced Mutagenesis. Springer New York, p. 257-270 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutagenesis
Throughput
Technology
Biological Phenomena
Microbiology
7 Citations (Scopus)

The ionizing radiation-induced bystander effect: Evidence, mechanism, and significance

Azzam, E. I., De Toledo, S. M., Harris, A. L., Ivanov, V., Zhou, H., Amundson, S. A., Lieberman, H. B. & Hei, T. K., Jan 1 2013, Pathobiology of Cancer Regimen-Related Toxicities. Springer New York, p. 35-61 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Bystander Effect
Ionizing Radiation
Second Primary Neoplasms
Gap Junctions
DNA Repair
2012

Computational analysis of alternative polyadenylation in embryonic stem cells and induced pluripotent cells

Ji, Z., Hoque, M. & Tian, B., Dec 1 2012, Computational Biology of Embryonic Stem Cells. Bentham Science Publishers Ltd., p. 133-146 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polyadenylation
3' Untranslated Regions
Embryonic Stem Cells
Stem cells
Induced Pluripotent Stem Cells

Generation of DNA circles in yeast by inducible site-specific recombination

Gartenberg, M. R., Jan 20 2012, Chromatin Remodeling: Methods and Protocols. Morse, R. H. (ed.). p. 103-113 11 p. (Methods in Molecular Biology; vol. 833).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genetic Recombination
Yeasts
Gene Rearrangement
DNA
Masks
2010

Predicting Cancer Survival Using Expression Patterns

Reddy, A., Kronek, L. P., Brannon, A. R., Seiler, M., Ganesan, S., Rathmell, W. K. & Bhanot, G., Jul 19 2010, Medical Biostatistics for Complex Diseases. Wiley-VCH, p. 305-323 19 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Renal Cell Carcinoma
Neoplasms
2009
10 Citations (Scopus)

Model-based global analysis of heterogeneous experimental data using gfit

Levin, M. K., Hingorani, M. M., Holmes, R. M., Patel, S. S. & Carson, J. H., Dec 1 2009, Systems Biology. Maly, I. (ed.). 1 ed. p. 335-359 25 p. (Methods in Molecular Biology; vol. 500, no. 1).

Research output: Chapter in Book/Report/Conference proceedingChapter

Regression Analysis
Information Systems
Software
Datasets

Quantum Chromodynamics on the BlueGene/L Supercomputer

Vranas, P. M. & Bhanot, G., Dec 9 2009, Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications. John Wiley & Sons, Inc., p. 131-148 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Supercomputers
2 Citations (Scopus)

Viral helicases

Rajagopal, V. & Patel, S., Jan 1 2009, Viral Genome Replication. Springer US, p. 429-466 38 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nucleic Acids
Recombinational DNA Repair
Chromatin Assembly and Disassembly
Protein Biosynthesis
Hydrolysis
2008
13 Citations (Scopus)

Identification of mRNA Polyadenylation Sites in Genomes Using cDNA Sequences, Expressed Sequence Tags, and Trace

Lee, J. Y., Park, J. Y. & Tian, B., Dec 1 2008, Post-Transcriptional Gene Regulation. Wilusz, J. (ed.). p. 23-37 15 p. (Methods in Molecular Biology; vol. 419).

Research output: Chapter in Book/Report/Conference proceedingChapter

Polyadenylation
Expressed Sequence Tags
Poly A
Complementary DNA
Genome
4 Citations (Scopus)

Synapsis, double-strand breaks, and domains of crossover control in drosophila females

Mehrotra, S., Hawley, R. S. & McKim, K., Jan 1 2008, Recombination and Meiosis: Crossing-Over and Disjunction. Egel, R. & Lankenau, D-H. (eds.). p. 125-151 27 p. (Genome Dynamics and Stability; vol. 2).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chromosome Pairing
Drosophila
Chromosome Structures
Genetic Recombination
Cell Biology
3 Citations (Scopus)

Tumor Suppressor Genes

Levine, A. J., Hu, W. & Feng, Z., Dec 1 2008, The Molecular Basis of Cancer. Elsevier Inc., p. 31-38 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Tumor Suppressor Genes
2007

High-throughput genotyping of single nucleotide polymorphisms with high sensitivity

Li, H., Wang, H. Y., Cui, X., Luo, M., Hu, G., Greenawalt, D. M., Tereshchenko, I. V., Li, J. Y., Chu, Y. & Gao, R., Nov 1 2007, Comparative Genomics. Nicholas, B. H. (ed.). p. 281-294 14 p. (Methods in Molecular Biology; vol. 396).

Research output: Chapter in Book/Report/Conference proceedingChapter

Single Nucleotide Polymorphism
Single-Stranded DNA
Polymerase Chain Reaction
Haploidy
Genetic Markers
11 Citations (Scopus)

Mammalian homologous recombination repair and cancer intervention

Shen, Z. & Nickoloff, J. A., Jan 1 2007, DNA Repair, Genetic Instability, and Cancer. World Scientific Publishing Co., p. 119-156 38 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Recombinational DNA Repair
Homologous Recombination
homologous recombination
Repair
neoplasms
2005
4 Citations (Scopus)

Alteration and Analyses of Viral Entry with Library-Derived Peptides

Bupp, K. & Roth, M. J., Dec 1 2005, Advances in Virus Research. Maramorosch, K. & Shatkin, A. (eds.). p. 147-172 26 p. (Advances in Virus Research; vol. 65).

Research output: Chapter in Book/Report/Conference proceedingChapter

Peptide Library
Peptides
Viruses
Dependovirus
Genetic Therapy
2003
10 Citations (Scopus)

Phylogenetics and Functions of the Double-Stranded RNA-Binding Motif: A Genomic Survey

Tian, B. & Mathews, M. B., Dec 1 2003, Progress in Nucleic Acid Research and Molecular Biology. p. 123-158 36 p. (Progress in Nucleic Acid Research and Molecular Biology; vol. 74).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteins
Plant Viruses
Protein Array Analysis
Amino Acid Motifs
Archaea
2001

Assays for retroviral RNase H

Snyder, C. S. & Roth, M. J., Jan 1 2001, Methods in Enzymology. Academic Press Inc., p. 440-452 13 p. (Methods in Enzymology; vol. 341).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ribonuclease H
Assays