Alessandro Guffanti - Academia.edu (original) (raw)

Papers by Alessandro Guffanti

Methods in molecular medicine, 2004

DNA microarray is an innovative technology for obtaining information on gene function. Because it... more DNA microarray is an innovative technology for obtaining information on gene function. Because it is a high-throughput method, computational tools are essential in data analysis and mining to extract the knowledge from experimental results. Filtering procedures and statistical approaches are frequently combined to identify differentially expressed genes. However, obtaining a list of differentially expressed genes is only the starting point because an important step is the integration of differential expression profiles in a biological context, which is a hot topic in data mining. In this chapter an integrated approach of filtering and statistical validation to select trustable differentially expressed genes is described together with a brief introduction on data mining focusing on the classification of co-regulated genes on the basis of their biological function.

Cell Death and Differentiation, 2014

Epigenetic changes on DNA and chromatin are implicated in cell differentiation and organogenesis.... more Epigenetic changes on DNA and chromatin are implicated in cell differentiation and organogenesis. For the heart, distinct histone methylation profiles were recently linked to stage-specific gene expression programs during cardiac differentiation in vitro. However, the enzymes catalyzing these modifications and the genes regulated by them remain poorly defined. We therefore decided to identify the epigenetic enzymes that are potentially involved in cardiomyogenesis by analyzing the expression profile of the 85 genes encoding the epigenetic-related proteins in mouse cardiomyocytes (CMs), and then study how they affect gene expression during differentiation and maturation of this cell type. We show here with gene expression screening of epigenetic enzymes that the highly expressed H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) drives a transitional pattern of di-methylation on H3 lysine 79 (H3K79) in CMs at different stages of differentiation in vitro and in vivo. Through a genome-wide chromatin-immunoprecipitation DNA-sequencing approach, we found H3K79me2 enriched at genes expressed during cardiac differentiation. Moreover, knockdown of Dot1L affected the expression of H3K79me2-enriched genes. Our results demonstrate that histone methylation, and in particular DOT1L-mediated H3K79me2 modification, drives cardiomyogenesis through the definition of a specific transcriptional landscape.Cell Death and Differentiation advance online publication, 19 December 2014; doi:10.1038/cdd.2014.199.

BMC Cancer, 2014

Rhabdomyosarcoma (RMS) is a highly malignant tumour accounting for nearly half of soft tissue sar... more Rhabdomyosarcoma (RMS) is a highly malignant tumour accounting for nearly half of soft tissue sarcomas in children. MicroRNAs (miRNAs) represent a class of short, non-coding, regulatory RNAs which play a critical role in different cellular processes. Altered miRNA levels have been reported in human cancers, including RMS.

Briefings in Functional Genomics, 2014

Different ChIP-Seq protocols may have a significant impact on the final outcome in terms of quali... more Different ChIP-Seq protocols may have a significant impact on the final outcome in terms of quality, number and distribution of called peaks. Sample DNA undergoes a long procedure before the final sequencing step, and damaged DNA can result in excessive mismatches in the alignment with reference genome. In this letter, we present the effect of well-defined modifications (timing of formaldehyde crosslink reversal, brand of the sonicator) of standard ChIP-Seq protocol on parallel samples derived from the same cell line correlating the initial DNA quality control metrics to the final bioinformatics analysis results.

Trends in Genetics, 1997

nificant number of sequences for the quety and target organisms'. Among model organisms, the frui... more nificant number of sequences for the quety and target organisms'. Among model organisms, the fruit fly I Cdii, F. and Galas, D. (1993) Sckrce262,43-46 2 Fasman, K.H. et al. (1%) Nucleic Acrds Res. 24. 57-63 3 http://gdbwww.gdb.org/ Contributed by Amy K. Vokz (avoltz@gdb.org) and Thomas C. Emmel ftom@gdb.org).

RNA, 2012

In order to understand the role of microRNAs (miRNAs) in vascular physiopathology, we took advant... more In order to understand the role of microRNAs (miRNAs) in vascular physiopathology, we took advantage of deep-sequencing techniques to accurately and comprehensively profile the entire miRNA population expressed by endothelial cells exposed to hypoxia. SOLiD sequencing of small RNAs derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% % O 2 or normoxia for 24 h yielded more than 22 million reads per library. A customized bioinformatic pipeline identified more than 400 annotated microRNA/microRNA* species with a broad abundance range: miR-21 and miR-126 totaled almost 40% % of all miRNAs. A complex repertoire of isomiRs was found, displaying also 59 variations, potentially affecting target recognition. Highstringency bioinformatic analysis identified microRNA candidates, whose predicted pre-miRNAs folded into a stable hairpin. Validation of a subset by qPCR identified 18 high-confidence novel miRNAs as detectable in independent HUVEC cultures and associated to the RISC complex. The expression of two novel miRNAs was significantly down-modulated by hypoxia, while miR-210 was significantly induced. Gene ontology analysis of their predicted targets revealed a significant association to hypoxiainducible factor signaling, cardiovascular diseases, and cancer. Overexpression of the novel miRNAs in hypoxic endothelial cells affected cell growth and confirmed the biological relevance of their down-modulation. In conclusion, deep-sequencing accurately profiled known, variant, and novel microRNAs expressed by endothelial cells in normoxia and hypoxia.

Proceedings of the National Academy of Sciences, 2013

Cardiac hypertrophy, initially an adaptive response of the myocardium to stress, can progress to ... more Cardiac hypertrophy, initially an adaptive response of the myocardium to stress, can progress to heart failure. The epigenetic signature underlying this phenomenon is poorly understood. Here, we report on the genome-wide distribution of seven histone modifications in adult mouse cardiomyocytes subjected to a prohypertrophy stimulus in vivo. We found a set of promoters with an epigenetic pattern that distinguishes specific functional classes of genes regulated in hypertrophy and identified 9,207 candidate active enhancers whose activity was modulated. We also analyzed the transcriptional network within which these genetic elements act to orchestrate hypertrophy gene expression, finding a role for myocyte enhancer factor (MEF)2C and MEF2A in regulating enhancers. We propose that the epigenetic landscape is a key determinant of gene expression reprogramming in cardiac hypertrophy and provide a basis for understanding the role of chromatin in regulating this phenomenon.

Nucleic Acids Research, 2004

The identification and study of evolutionarily conserved genomic sequences that surround disease-... more The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better elucidate the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human-mouse conserved genomic sequences that are localized within or in the vicinity of human disease-related genes. CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp. The database contains CST data relative to over 1088 genes responsible for monogenetic human genetic diseases or involved in the susceptibility to multifactorial/polygenic diseases. DG-CST is accessible via the internet at http://dgcst.ceinge.unina.it/ and may be searched using both simple and complex queries. A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts.

Nature, 2002

per sample area) were measured as dependent variable and treatment means, sample sizes and varian... more per sample area) were measured as dependent variable and treatment means, sample sizes and variance estimates were reported. Included were two experiments on macroalgae (this study), five experiments with periphyton in freshwater, brackish and marine ecosystems 27,28 , two experiments with salt marsh plants 29 , and one with lake phytoplankton 30 , including subtropical and temperate climates in North America and Europe. We analysed data from sampling dates when species richness reached the seasonal peak, which was usually in late spring or summer. Data were standardized using the common meta-analysis metric of standardized effect size, Hedges's d (ref. 21). This is a measure of the difference between experimental and control means, divided by a pooled standard deviation and multiplied by a correction factor to account for small sample sizes. Homogeneity of effect sizes was tested using the Q-statistic 21 . As we detected significant heterogeneity among effect sizes we split the data set into low-productivity (oligotrophic and mesotrophic) and high-productivity (eutrophic) sites, based on information provided in the publications.

Journal of Virology, 2014

Human Molecular Genetics, 2014

In recent years considerable advances have been made in our understanding of genetics of mammalia... more In recent years considerable advances have been made in our understanding of genetics of mammalian gonad development; however, the underlying genetic aetiology in the majority of patients with 46,XY Disorders of Sex Development (DSD) still remains unknown. Using whole exome sequencing we identified missense mutations in the gene Friend of GATA 2, currently named as ZFMP2 zinc finger protein, FOG family member 2 (FOG2/ZFPM2), in two patients with 46,XY gonadal dysgenesis. One patient carried a heterozygous p.S402R non-synonymous mutation, whilst the other patient carried one heterozygous p.R260Q and one homozygous p.M544I non-synonymous mutation. Failure of testis development in these cases is explained by the impaired ability of the mutant FOG2 proteins to interact with a known regulator of early testis development, GATA4. This is the first example of mutations in the coding sequence of FOG2 associated with 46,XY DSD in human. 46,XY gonadal dysgenesis | FOG2/ZFPM2 | Disorders of Sex Development

Genomics, 1997

strategy for cross-species gene identification. It is now The Drosophila lark gene encodes an ess... more strategy for cross-species gene identification. It is now The Drosophila lark gene encodes an essential RNApossible, for example, to search expressed sequence tag binding protein of the RNA recognition motif (RRM) (EST) databases (Boguski et al., 1993) with a given class that is required during embryonic development. query sequence to identify similar genes and/or pro-Genetic analysis demonstrates that it also functions as teins in several different mammalian and invertebrate a molecular element of a circadian clock output pathspecies quickly. This has permitted large-scale crossway, mediating the temporal regulation of adult emerspecies comparisons of sequences representing differgence in the fruitfly. We now report the molecular ent model organisms, and such comparisons, using characterization of a human gene with significant simknown Drosophila gene sequences, have now identified ilarity to lark. Based on fluorescence in situ hybridizamany potential human and mouse homologues (Banfi tion and radiation hybrid mapping, the human gene et al., 1996).

Genomics, 1997

pounds (Bergner and Shapiro, 1988; Roy, l970). Eight We recently reported the isolation of two ne... more pounds (Bergner and Shapiro, 1988; Roy, l970). Eight We recently reported the isolation of two new memdistinct inherited disorders resulting from specific sulbers of the sulfatase gene family, arylsulfatase D fatase deficiencies have been described (Franco et al., (ARSD) and E (ARSE), located approximately 50 kb . Sequence analysis has refrom each other in the Xp22.3 region. Mutation analyvealed a high degree of homology among these proteins. sis indicated ARSE as the gene responsible for X-Four of the previously described human sulfatases, linked recessive chondrodysplasia punctata. Expresknown as arylsulfatases A, B, C, and E (ARSA, ARSB, sion of the ARSE gene in COS cells resulted in a heat-ARSC, and ARSE), are able to hydrolyze sulfated artilabile arylsulfatase activity that was inhibited by ficial substrates containing a phenolic ring, such as pwarfarin. At the same time, we detected the presence nitrocatechol sulfate or 4-methylumbelliferyl sulfate of a 1.2-kb fragment located at Ç60 kb from ARSD and (4-MU sulfate) (Kolodny and Fluharty, 1995). ARSA ARSE with significant homology to these two genes, and ARSB are lysosomal in their subcellular localizasuggesting the existence of another sulfatase gene, artion and have acidic pH optima, while ARSC (also ylsulfatase F (ARSF), in Xp22.3. We have used a comknown as steroid sulfatase, STS) is microsomal and bined approach of long-range genomic sequencing and screening of cDNA libraries to isolate the ARSF gene. has a neutral to alkaline pH optimum (Kawano et al., Expression of the ARSF cDNA in COS cells resulted in 1989).

BMC Genomics, 2009

The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qua... more The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qualitative changes in gene expression linked to the disease status. An increasing number of "unconventional" transcripts, such as novel isoforms, non-coding RNAs, somatic gene fusions and deletions have been associated with the tumoral state. Massively parallel sequencing techniques provide a framework for exploring the transcriptional complexity inherent to cancer with a limited laboratory and financial effort. We developed a deep sequencing and bioinformatics analysis protocol to investigate the molecular composition of a breast cancer poly(A) + transcriptome. This method utilizes a cDNA library normalization step to diminish the representation of highly expressed transcripts and biology-oriented bioinformatic analyses to facilitate detection of rare and novel transcripts.

BMC Genomics, 2008

Background: Although the overlap of transcriptional units occurs frequently in eukaryotic genomes... more Background: Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm).

BMC Bioinformatics, 2005

The BITS2005 Conference brought together about 200 Italian scientists working in the field of

Bioinformatics, 1999

TargetFinder is a new software tool to search a database of annotated sequences for transcription... more TargetFinder is a new software tool to search a database of annotated sequences for transcription factor binding sites located in context with other important transcription regulatory signals and regions, like the TATA element, the promoter, and so on, thereby greatly reducing the background usually associated with this kind of search. Availability: The TargetFinder Web service is available at

Methods in molecular medicine, 2004

DNA microarray is an innovative technology for obtaining information on gene function. Because it... more DNA microarray is an innovative technology for obtaining information on gene function. Because it is a high-throughput method, computational tools are essential in data analysis and mining to extract the knowledge from experimental results. Filtering procedures and statistical approaches are frequently combined to identify differentially expressed genes. However, obtaining a list of differentially expressed genes is only the starting point because an important step is the integration of differential expression profiles in a biological context, which is a hot topic in data mining. In this chapter an integrated approach of filtering and statistical validation to select trustable differentially expressed genes is described together with a brief introduction on data mining focusing on the classification of co-regulated genes on the basis of their biological function.

Cell Death and Differentiation, 2014

Epigenetic changes on DNA and chromatin are implicated in cell differentiation and organogenesis.... more Epigenetic changes on DNA and chromatin are implicated in cell differentiation and organogenesis. For the heart, distinct histone methylation profiles were recently linked to stage-specific gene expression programs during cardiac differentiation in vitro. However, the enzymes catalyzing these modifications and the genes regulated by them remain poorly defined. We therefore decided to identify the epigenetic enzymes that are potentially involved in cardiomyogenesis by analyzing the expression profile of the 85 genes encoding the epigenetic-related proteins in mouse cardiomyocytes (CMs), and then study how they affect gene expression during differentiation and maturation of this cell type. We show here with gene expression screening of epigenetic enzymes that the highly expressed H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) drives a transitional pattern of di-methylation on H3 lysine 79 (H3K79) in CMs at different stages of differentiation in vitro and in vivo. Through a genome-wide chromatin-immunoprecipitation DNA-sequencing approach, we found H3K79me2 enriched at genes expressed during cardiac differentiation. Moreover, knockdown of Dot1L affected the expression of H3K79me2-enriched genes. Our results demonstrate that histone methylation, and in particular DOT1L-mediated H3K79me2 modification, drives cardiomyogenesis through the definition of a specific transcriptional landscape.Cell Death and Differentiation advance online publication, 19 December 2014; doi:10.1038/cdd.2014.199.

BMC Cancer, 2014

Rhabdomyosarcoma (RMS) is a highly malignant tumour accounting for nearly half of soft tissue sar... more Rhabdomyosarcoma (RMS) is a highly malignant tumour accounting for nearly half of soft tissue sarcomas in children. MicroRNAs (miRNAs) represent a class of short, non-coding, regulatory RNAs which play a critical role in different cellular processes. Altered miRNA levels have been reported in human cancers, including RMS.

Briefings in Functional Genomics, 2014

Different ChIP-Seq protocols may have a significant impact on the final outcome in terms of quali... more Different ChIP-Seq protocols may have a significant impact on the final outcome in terms of quality, number and distribution of called peaks. Sample DNA undergoes a long procedure before the final sequencing step, and damaged DNA can result in excessive mismatches in the alignment with reference genome. In this letter, we present the effect of well-defined modifications (timing of formaldehyde crosslink reversal, brand of the sonicator) of standard ChIP-Seq protocol on parallel samples derived from the same cell line correlating the initial DNA quality control metrics to the final bioinformatics analysis results.

Trends in Genetics, 1997

nificant number of sequences for the quety and target organisms'. Among model organisms, the frui... more nificant number of sequences for the quety and target organisms'. Among model organisms, the fruit fly I Cdii, F. and Galas, D. (1993) Sckrce262,43-46 2 Fasman, K.H. et al. (1%) Nucleic Acrds Res. 24. 57-63 3 http://gdbwww.gdb.org/ Contributed by Amy K. Vokz (avoltz@gdb.org) and Thomas C. Emmel ftom@gdb.org).

RNA, 2012

In order to understand the role of microRNAs (miRNAs) in vascular physiopathology, we took advant... more In order to understand the role of microRNAs (miRNAs) in vascular physiopathology, we took advantage of deep-sequencing techniques to accurately and comprehensively profile the entire miRNA population expressed by endothelial cells exposed to hypoxia. SOLiD sequencing of small RNAs derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% % O 2 or normoxia for 24 h yielded more than 22 million reads per library. A customized bioinformatic pipeline identified more than 400 annotated microRNA/microRNA* species with a broad abundance range: miR-21 and miR-126 totaled almost 40% % of all miRNAs. A complex repertoire of isomiRs was found, displaying also 59 variations, potentially affecting target recognition. Highstringency bioinformatic analysis identified microRNA candidates, whose predicted pre-miRNAs folded into a stable hairpin. Validation of a subset by qPCR identified 18 high-confidence novel miRNAs as detectable in independent HUVEC cultures and associated to the RISC complex. The expression of two novel miRNAs was significantly down-modulated by hypoxia, while miR-210 was significantly induced. Gene ontology analysis of their predicted targets revealed a significant association to hypoxiainducible factor signaling, cardiovascular diseases, and cancer. Overexpression of the novel miRNAs in hypoxic endothelial cells affected cell growth and confirmed the biological relevance of their down-modulation. In conclusion, deep-sequencing accurately profiled known, variant, and novel microRNAs expressed by endothelial cells in normoxia and hypoxia.

Proceedings of the National Academy of Sciences, 2013

Cardiac hypertrophy, initially an adaptive response of the myocardium to stress, can progress to ... more Cardiac hypertrophy, initially an adaptive response of the myocardium to stress, can progress to heart failure. The epigenetic signature underlying this phenomenon is poorly understood. Here, we report on the genome-wide distribution of seven histone modifications in adult mouse cardiomyocytes subjected to a prohypertrophy stimulus in vivo. We found a set of promoters with an epigenetic pattern that distinguishes specific functional classes of genes regulated in hypertrophy and identified 9,207 candidate active enhancers whose activity was modulated. We also analyzed the transcriptional network within which these genetic elements act to orchestrate hypertrophy gene expression, finding a role for myocyte enhancer factor (MEF)2C and MEF2A in regulating enhancers. We propose that the epigenetic landscape is a key determinant of gene expression reprogramming in cardiac hypertrophy and provide a basis for understanding the role of chromatin in regulating this phenomenon.

Nucleic Acids Research, 2004

The identification and study of evolutionarily conserved genomic sequences that surround disease-... more The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better elucidate the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human-mouse conserved genomic sequences that are localized within or in the vicinity of human disease-related genes. CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp. The database contains CST data relative to over 1088 genes responsible for monogenetic human genetic diseases or involved in the susceptibility to multifactorial/polygenic diseases. DG-CST is accessible via the internet at http://dgcst.ceinge.unina.it/ and may be searched using both simple and complex queries. A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts.

Nature, 2002

per sample area) were measured as dependent variable and treatment means, sample sizes and varian... more per sample area) were measured as dependent variable and treatment means, sample sizes and variance estimates were reported. Included were two experiments on macroalgae (this study), five experiments with periphyton in freshwater, brackish and marine ecosystems 27,28 , two experiments with salt marsh plants 29 , and one with lake phytoplankton 30 , including subtropical and temperate climates in North America and Europe. We analysed data from sampling dates when species richness reached the seasonal peak, which was usually in late spring or summer. Data were standardized using the common meta-analysis metric of standardized effect size, Hedges's d (ref. 21). This is a measure of the difference between experimental and control means, divided by a pooled standard deviation and multiplied by a correction factor to account for small sample sizes. Homogeneity of effect sizes was tested using the Q-statistic 21 . As we detected significant heterogeneity among effect sizes we split the data set into low-productivity (oligotrophic and mesotrophic) and high-productivity (eutrophic) sites, based on information provided in the publications.

Journal of Virology, 2014

Human Molecular Genetics, 2014

In recent years considerable advances have been made in our understanding of genetics of mammalia... more In recent years considerable advances have been made in our understanding of genetics of mammalian gonad development; however, the underlying genetic aetiology in the majority of patients with 46,XY Disorders of Sex Development (DSD) still remains unknown. Using whole exome sequencing we identified missense mutations in the gene Friend of GATA 2, currently named as ZFMP2 zinc finger protein, FOG family member 2 (FOG2/ZFPM2), in two patients with 46,XY gonadal dysgenesis. One patient carried a heterozygous p.S402R non-synonymous mutation, whilst the other patient carried one heterozygous p.R260Q and one homozygous p.M544I non-synonymous mutation. Failure of testis development in these cases is explained by the impaired ability of the mutant FOG2 proteins to interact with a known regulator of early testis development, GATA4. This is the first example of mutations in the coding sequence of FOG2 associated with 46,XY DSD in human. 46,XY gonadal dysgenesis | FOG2/ZFPM2 | Disorders of Sex Development

Genomics, 1997

strategy for cross-species gene identification. It is now The Drosophila lark gene encodes an ess... more strategy for cross-species gene identification. It is now The Drosophila lark gene encodes an essential RNApossible, for example, to search expressed sequence tag binding protein of the RNA recognition motif (RRM) (EST) databases (Boguski et al., 1993) with a given class that is required during embryonic development. query sequence to identify similar genes and/or pro-Genetic analysis demonstrates that it also functions as teins in several different mammalian and invertebrate a molecular element of a circadian clock output pathspecies quickly. This has permitted large-scale crossway, mediating the temporal regulation of adult emerspecies comparisons of sequences representing differgence in the fruitfly. We now report the molecular ent model organisms, and such comparisons, using characterization of a human gene with significant simknown Drosophila gene sequences, have now identified ilarity to lark. Based on fluorescence in situ hybridizamany potential human and mouse homologues (Banfi tion and radiation hybrid mapping, the human gene et al., 1996).

Genomics, 1997

pounds (Bergner and Shapiro, 1988; Roy, l970). Eight We recently reported the isolation of two ne... more pounds (Bergner and Shapiro, 1988; Roy, l970). Eight We recently reported the isolation of two new memdistinct inherited disorders resulting from specific sulbers of the sulfatase gene family, arylsulfatase D fatase deficiencies have been described (Franco et al., (ARSD) and E (ARSE), located approximately 50 kb . Sequence analysis has refrom each other in the Xp22.3 region. Mutation analyvealed a high degree of homology among these proteins. sis indicated ARSE as the gene responsible for X-Four of the previously described human sulfatases, linked recessive chondrodysplasia punctata. Expresknown as arylsulfatases A, B, C, and E (ARSA, ARSB, sion of the ARSE gene in COS cells resulted in a heat-ARSC, and ARSE), are able to hydrolyze sulfated artilabile arylsulfatase activity that was inhibited by ficial substrates containing a phenolic ring, such as pwarfarin. At the same time, we detected the presence nitrocatechol sulfate or 4-methylumbelliferyl sulfate of a 1.2-kb fragment located at Ç60 kb from ARSD and (4-MU sulfate) (Kolodny and Fluharty, 1995). ARSA ARSE with significant homology to these two genes, and ARSB are lysosomal in their subcellular localizasuggesting the existence of another sulfatase gene, artion and have acidic pH optima, while ARSC (also ylsulfatase F (ARSF), in Xp22.3. We have used a comknown as steroid sulfatase, STS) is microsomal and bined approach of long-range genomic sequencing and screening of cDNA libraries to isolate the ARSF gene. has a neutral to alkaline pH optimum (Kawano et al., Expression of the ARSF cDNA in COS cells resulted in 1989).

BMC Genomics, 2009

The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qua... more The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qualitative changes in gene expression linked to the disease status. An increasing number of "unconventional" transcripts, such as novel isoforms, non-coding RNAs, somatic gene fusions and deletions have been associated with the tumoral state. Massively parallel sequencing techniques provide a framework for exploring the transcriptional complexity inherent to cancer with a limited laboratory and financial effort. We developed a deep sequencing and bioinformatics analysis protocol to investigate the molecular composition of a breast cancer poly(A) + transcriptome. This method utilizes a cDNA library normalization step to diminish the representation of highly expressed transcripts and biology-oriented bioinformatic analyses to facilitate detection of rare and novel transcripts.

BMC Genomics, 2008

Background: Although the overlap of transcriptional units occurs frequently in eukaryotic genomes... more Background: Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm).

BMC Bioinformatics, 2005

The BITS2005 Conference brought together about 200 Italian scientists working in the field of

Bioinformatics, 1999

TargetFinder is a new software tool to search a database of annotated sequences for transcription... more TargetFinder is a new software tool to search a database of annotated sequences for transcription factor binding sites located in context with other important transcription regulatory signals and regions, like the TATA element, the promoter, and so on, thereby greatly reducing the background usually associated with this kind of search. Availability: The TargetFinder Web service is available at