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List of works by Manuela Helmer-Citterich

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures

scientific article published on 8 May 2007

A Proteome-wide Domain-centric Perspective on Protein Phosphorylation

scientific article

A neural strategy for the inference of SH3 domain-peptide interaction specificity

scientific article

A novel approach to represent and compare RNA secondary structures

scientific article published on 21 April 2014

A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications

scientific article

A simple protocol for the inference of RNA global pairwise alignments

scientific article published in January 2015

A structural study for the optimisation of functional motifs encoded in protein sequences

scientific article

A structure filter for the Eukaryotic Linear Motif Resource

scientific article

AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation

scientific article published on December 2014

Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani

scientific article

Alternative splicing tends to avoid partial removals of protein-protein interaction sites

scientific article

B-Pred, a structure based B-cell epitopes prediction server

scientific article

BEAM web server: A tool for structural RNA motif discovery

scientific article published on 31 October 2017

BRIO: a web server for RNA sequence and structure motif scan

scientific article published on 01 July 2021

Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics

scientific article

Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics.

scientific article published on 8 March 2007

Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics.

scientific article published on 26 March 2008

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics ⬇️

scientific article published on March 28, 2012

COVID-19 and Genetic Variants of Protein Involved in the SARS-CoV-2 Entry into the Host Cells

scientific article published on 27 August 2020

Computational methods for analysis and inference of kinase/inhibitor relationships

scientific article

Convergent evolution of enzyme active sites is not a rare phenomenon

scientific article published on 14 June 2007

Correlated mutations contain information about protein-protein interaction 1 1Edited by A. R. Fersht ⬇️

scientific article published on August 29, 1997

Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite proliferation and viability

scientific article

DBATE: database of alternative transcripts expression

scientific article published on 9 July 2013

Deciphering a global network of functionally associated post-translational modifications

scientific article

Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information

scientific article

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

scientific article

ELM: the status of the 2010 eukaryotic linear motif resource

scientific article

Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound

scientific article published on 16 May 2013

Erratum: Corrigendum: AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation

scholarly article published in Nature Cell Biology

Escher: A new docking procedure applied to the reconstruction of protein tertiary structure ⬇️

scientific article published on August 1, 1997

Experimental and computational methods for the analysis and modeling of signaling networks

scientific article

Exploiting holistic approaches to model specificity in protein phosphorylation

scientific article

Exploring the diversity of SPRY/B30.2-mediated interactions

scientific article published on 17 November 2012

False occurrences of functional motifs in protein sequences highlight evolutionary constraints

scientific article published in March 2007

From sequence to structural analysis in protein phosphorylation motifs

scientific article published on January 2011

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures

scientific article (publication date: 26 March 2008)

Functional annotation by identification of local surface similarities: a novel tool for structural genomics

scientific article

Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells.

scientific article published on 24 March 2016

HMG1 interacts with HOX proteins and enhances their DNA binding and transcriptional activation

scientific article

Homology modeling of Neurospora crassa geranylgeranyl pyrophosphate synthase: structural interpretation of mutant phenotypes

scientific article published on 01 September 1997

Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses

scientific article

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities

scientific article

Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity

scientific article

Kinome-wide decoding of network-attacking mutations rewiring cancer signaling

scientific article

Kinome-wide identification of phosphorylation networks in eukaryotic proteomes

scientific article published on 01 February 2019

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites

scientific article published on 8 March 2007

MINT: a Molecular INTeraction database

scientific article (publication date: 20 February 2002)

Mapping the human phosphatome on growth pathways

scientific article

Modeling cancer drug response through drug-specific informative genes

scientific article published on 23 October 2019

Modeling gene regulatory network motifs using Statecharts

scientific article

Modular architecture of nucleotide-binding pockets.

scientific article

Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages Ff (fd, f1, M13), If1 and IKe

scientific article

Next Generation Sequencing and Linkage Analysis for the Molecular Diagnosis of a Novel Overlapping Syndrome Characterized by Hypertrophic Cardiomyopathy and Typical Electrical Instability of Brugada Syndrome

scientific article published on 09 March 2016

Nucleos: a web server for the identification of nucleotide-binding sites in protein structures

scientific article

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society.

scientific article

PUZZLE: a new method for automated protein docking based on surface shape complementarity.

scientific article

Peamaclein--a new peach allergenic protein: similarities, differences and misleading features compared to Pru p 3.

scientific article

PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae

scientific article

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

scientific article

Phosphate binding sites identification in protein structures

scientific article

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites

scientific article

Phospho3D: a database of three-dimensional structures of protein phosphorylation sites

scientific article

Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif

scientific article published on 11 June 2013

Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics

scientific article published on June 2015

Query3d: a new method for high-throughput analysis of functional residues in protein structures

scientific article published in December 2005

Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends

scientific article

Revealing protein-lncRNA interaction

scientific article published on 02 June 2015

Role of CTCF protein in regulating FMR1 locus transcription

scientific article (publication date: 2013)

SH3-Hunter: discovery of SH3 domain interaction sites in proteins

scientific article

SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family.

scientific article

SURFACE: a database of protein surface regions for functional annotation

scientific article published on January 2004

Searching the MINT database for protein interaction information

scientific article published on 01 August 2003

Seq2Struct: a resource for establishing sequence-structure links

scientific article published on 28 September 2004

Structural motifs recurring in different folds recognize the same ligand fragments

scientific article

Structural studies on an inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition

scientific article

Structure-based function prediction: approaches and applications.

scientific article

Superpose3D: a local structural comparison program that allows for user-defined structure representations

scientific article

The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation

scientific article

The human rs1050286 polymorphism alters LOX-1 expression through modifying miR-24 binding.

scientific article published on 6 November 2015

Three-dimensional profiles: a new tool to identify protein surface similarities.

scientific article

Tools and data services registry: a community effort to document bioinformatics resources

scientific article

Web-Beagle: a web server for the alignment of RNA secondary structures

scientific article published on 14 May 2015

What has proteomics taught us about Leishmania development?

scientific article published on 28 February 2012

c-MYC inhibition impairs hypoxia response in glioblastoma multiforme

scientific article published on 22 April 2016

iSPOT: A web tool to infer the interaction specificity of families of protein modules

scientific article

pdbFun: mass selection and fast comparison of annotated PDB residues

scientific article

webPDBinder: a server for the identification of ligand binding sites on protein structures

scientific article (publication date: July 2013)

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