Introduction to Bioinformatics.

How the scientific community looks at molecular biology today is very different from that 50 years ago. During this time technological developments have led to many significant findings that have shook one of the most important foundations of molecular biology: the central dogma. In this chapter, we will mention how these changes occurred and gave birth to a very important field of today's science, bioinformatics. We will also mention briefly the newest topics of molecular biology regarding bioinformatics technologies and skills.

[1]  D. Cacchiarelli,et al.  A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA , 2011, Cell.

[2]  F. Crick Central Dogma of Molecular Biology , 1970, Nature.

[3]  J. Joseph,et al.  A review of the basics of mitochondrial bioenergetics, metabolism, and related signaling pathways in cancer cells: Therapeutic targeting of tumor mitochondria with lipophilic cationic compounds , 2017, Redox biology.

[4]  Arne Klungland,et al.  A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation , 2015, Genes & development.

[5]  E. Birney,et al.  Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans , 2010, Science.

[6]  C. Allis,et al.  Micronuclei of Tetrahymena contain two types of histone H3. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Zhike Lu,et al.  m6A-dependent regulation of messenger RNA stability , 2013, Nature.

[8]  Xuemei Chen,et al.  Regulation of small RNA stability: methylation and beyond , 2012, Cell Research.

[9]  Sharmistha Banerjee,et al.  Cytosine methylation by DNMT2 facilitates stability and survival of HIV-1 RNA in the host cell during infection. , 2017, The Biochemical journal.

[10]  Elizabeth T. Cirulli,et al.  The Characterization of Twenty Sequenced Human Genomes , 2010, PLoS genetics.

[11]  D. Bartel MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[12]  A. Razin,et al.  In vitro methylation of the hamster adenine phosphoribosyltransferase gene inhibits its expression in mouse L cells. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[13]  M. Kupiec,et al.  Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq , 2012, Nature.

[14]  P. Pandolfi,et al.  A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? , 2011, Cell.

[15]  Pao-Yang Chen,et al.  Profiling genome-wide DNA methylation , 2016, Epigenetics & Chromatin.

[16]  A. Pasquinelli MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship , 2012, Nature Reviews Genetics.

[17]  Tao Pan,et al.  RNA modifications and structures cooperate to guide RNA–protein interactions , 2017, Nature Reviews Molecular Cell Biology.

[18]  P. Shannon,et al.  Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing , 2010, Science.

[19]  E. Stedman,et al.  Cell Specificity of Histones , 1950, Nature.

[20]  Howard Y. Chang,et al.  Unique features of long non-coding RNA biogenesis and function , 2015, Nature Reviews Genetics.

[21]  Gideon Rechavi,et al.  The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA , 2016, Nature.

[22]  Yi Xing,et al.  m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome , 2016, Nature Methods.

[23]  U. Schibler,et al.  The 5'-termini of heterogeneous nuclear RNA: a comparison among molecules of different sizes and ages. , 1977, Nucleic acids research.

[24]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[25]  Ferdinando Di Cunto,et al.  Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs , 2011, Cell.

[26]  A. Mirsky,et al.  ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[28]  Schraga Schwartz,et al.  High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis , 2013, Cell.

[29]  Christopher E. Mason,et al.  Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome , 2015, Nature Methods.

[30]  Chengqi Yi,et al.  Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. , 2016, Nature chemical biology.

[31]  Olivier Elemento,et al.  5′ UTR m6A Promotes Cap-Independent Translation , 2015, Cell.

[32]  Jörn Walter,et al.  DNA-methylation analysis by the bisulfite-assisted genomic sequencing method. , 2002, Methods in molecular biology.

[33]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[34]  A. Razin,et al.  Clonal inheritance of the pattern of DNA methylation in mouse cells. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[35]  D. L. Nanney,et al.  EPIGENETIC CONTROL SYSTEMS. , 1958, Proceedings of the National Academy of Sciences of the United States of America.

[36]  M. Grunstein,et al.  Yeast histone H4 N-terminal sequence is required for promoter activation in vivo , 1991, Cell.

[37]  Chuan He,et al.  N 6 -methyladenosine Modulates Messenger RNA Translation Efficiency , 2015, Cell.

[38]  P. Pandolfi,et al.  The Epitranscriptome of Noncoding RNAs in Cancer. , 2017, Cancer discovery.

[39]  Tao Pan,et al.  Dynamic RNA Modifications in Gene Expression Regulation , 2017, Cell.

[40]  R. Micura,et al.  Long non-coding RNAs as targets for cytosine methylation , 2013, RNA biology.

[41]  Claus Emmeche,et al.  Aspects of Complexity in Life and Science. , 1997, Philosophica.

[42]  Helmut Gernsheim,et al.  W. H. Fox Talbot and the history of photography , 1977 .

[43]  O. Elemento,et al.  Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons , 2012, Cell.

[44]  Phillip A Sharp,et al.  MicroRNA sponges: progress and possibilities. , 2010, RNA.

[45]  Ulrik Brandes,et al.  Biological Networks , 2013, Handbook of Graph Drawing and Visualization.

[46]  J. Wallis,et al.  Histone H2B genes of yeast encode two different proteins , 1980, Cell.

[47]  Nian Liu,et al.  Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA , 2013, RNA.

[48]  H. Cedar,et al.  Active gene sequences are undermethylated. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[49]  R. Kornberg,et al.  Chromatin structure; oligomers of the histones. , 1974, Science.

[50]  P. Pandolfi,et al.  A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.

[51]  R. Martienssen,et al.  The expanding world of small RNAs in plants , 2015, Nature Reviews Molecular Cell Biology.