Alessandro Vullo

Publication Activity (10 Years)

Years Active: 2001-2021
Publications (10 Years): 9

Top Topics

Phylogenetic Trees

Gene Prediction

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Publications

Fergus Simpson, Ian Davies, Vidhi Lalchand, Alessandro Vullo, Nicolas Durrande, Carl Edward Rasmussen
Kernel Identification Through Transformers. NeurIPS (2021)
Fergus Simpson, Ian Davies, Vidhi Lalchand, Alessandro Vullo, Nicolas Durrande, Carl E. Rasmussen
Kernel Identification Through Transformers. CoRR (2021)
Andrew D. Yates, Premanand Achuthan, Wasiu A. Akanni, James E. Allen, Jamie Allen, Jorge Álvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Andrey G. Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, José Carlos Marugán, Carla A. Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Reham Fatima, Astrid Gall, Carlos García-Girón, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Mike P. Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, Thomas Maurel, Mark D. McDowall, Aoife McMahon, Shamika Mohanan, Benjamin Moore, Michael Nuhn, Denye N. Oheh, Anne Parker, Andrew Parton, Mateus Patricio, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, Mira Sycheva, Marek Szuba, Kieron R. Taylor, Anja Thormann, Glen Threadgold, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Bethany Flint, Adam Frankish, Sarah E. Hunt, Garth IIsley, Myrto Kostadima, Nick Langridge, Jane E. Loveland, Fergal J. Martin, Joannella Morales, Jonathan M. Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, Stephen J. Trevanion, Fiona Cunningham, Kevin L. Howe, Daniel R. Zerbino, Paul Flicek
Ensembl 2020. Nucleic Acids Res. 48 (Database-Issue) (2020)
Fiona Cunningham, Premanand Achuthan, Wasiu A. Akanni, James E. Allen, M. Ridwan Amode, Irina M. Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla A. Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Astrid Gall, Carlos García-Girón, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Mike P. Kay, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, José Carlos Marugán, Thomas Maurel, Aoife C. McMahon, Benjamin Moore, Joannella Morales, Jonathan M. Mudge, Michael Nuhn, Denye N. Ogeh, Anne Parker, Andrew Parton, Mateus Patricio, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Daniel Sheppard, Helen Sparrow, Eloise Stapleton, Marek Szuba, Kieron R. Taylor, Glen Threadgold, Anja Thormann, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nick Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek
Ensembl 2019. Nucleic Acids Res. 47 (Database-Issue) (2019)
Daniel R. Zerbino, Premanand Achuthan, Wasiu A. Akanni, M. Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla A. Cummins, Astrid Gall, Carlos García-Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, Thomas Maurel, William M. McLaren, Benjamin Moore, Jonathan M. Mudge, Daniel N. Murphy, Victoria Newman, Michael Nuhn, Denye N. Ogeh, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Helen Schuilenburg, Daniel Sheppard, Helen Sparrow, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Amonida Zadissa, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Fiona Cunningham, Andrew D. Yates, Paul Flicek
Ensembl 2018. Nucleic Acids Res. 46 (Database-Issue) (2018)
Paul Julian Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu, Thomas Maurel, Benjamin Moore, Mark D. McDowall, Uma Maheswari, Guy Naamati, Victoria Newman, Chuang Kee Ong, Michael Paulini, Helder Pedro, Emily Perry, Matthew Russell, Helen Sparrow, Electra Tapanari, Kieron R. Taylor, Alessandro Vullo, Gareth Williams, Amonida Zadissa, Andrew Olson, Joshua C. Stein, Sharon Wei, Marcela K. Tello-Ruiz, Doreen Ware, Aurelien Luciani, Simon C. Potter, Robert D. Finn, Martin Urban, Kim E. Hammond-Kosack, Dan M. Bolser, Nishadi De Silva, Kevin L. Howe, Nicholas Langridge, Gareth Maslen, Daniel Michael Staines, Andrew D. Yates
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res. 46 (Database-Issue) (2018)
Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew R. Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel M. Staines, Kieron R. Taylor, Alessandro Vullo, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. Database J. Biol. Databases Curation 2017 (2017)
Bronwen L. Aken, Premanand Achuthan, Wasiu A. Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla A. Cummins, Peter Clapham, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Thomas Juettemann, Stephen Keenan, Matthew R. Laird, Ilias Lavidas, Thomas Maurel, William M. McLaren, Benjamin Moore, Daniel N. Murphy, Rishi Nag, Victoria Newman, Michael Nuhn, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Daniel Sheppard, Helen Sparrow, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Steven P. Wilder, Amonida Zadissa, Myrto Kostadima, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Fiona Cunningham, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek
Ensembl 2017. Nucleic Acids Res. 45 (Database-Issue) (2017)
Andrew D. Yates, Wasiu A. Akanni, M. Ridwan Amode, Daniel Barrell, Konstantinos Billis, Denise Carvalho-Silva, Carla A. Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Stephen Keenan, Ilias Lavidas, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Michael Nuhn, Anne Parker, Mateus Patricio, Miguel Pignatelli, Matthew Rahtz, Harpreet Singh Riat, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Jennifer L. Harrow, Matthieu Muffato, Emily Perry, Magali Ruffier, Giulietta Spudich, Stephen J. Trevanion, Fiona Cunningham, Bronwen L. Aken, Daniel R. Zerbino, Paul Flicek
Ensembl 2016. Nucleic Acids Res. 44 (Database-Issue) (2016)
Andrew D. Yates, Kathryn Beal, Stephen Keenan, William M. McLaren, Miguel Pignatelli, Graham R. S. Ritchie, Magali Ruffier, Kieron R. Taylor, Alessandro Vullo, Paul Flicek
The Ensembl REST API: Ensembl Data for Any Language. Bioinform. 31 (1) (2015)
Fiona Cunningham, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Andreas K. Kähäri, Stephen Keenan, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Anne Parker, Mateus Patricio, Emily Perry, Miguel Pignatelli, Harpreet Singh Riat, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Jennifer L. Harrow, Rhoda Kinsella, Matthieu Muffato, Magali Ruffier, Stephen M. J. Searle, Giulietta Spudich, Stephen J. Trevanion, Andy Yates, Daniel R. Zerbino, Paul Flicek
Ensembl 2015. Nucleic Acids Res. 43 (Database-Issue) (2015)
Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Nathan Johnson, Thomas Juettemann, Andreas Kähäri, Stephen Keenan, Eugene Kulesha, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet Singh Riat, Magali Ruffier, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Stephen J. Trevanion, Alessandro Vullo, Steven P. Wilder, Mark Wilson, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Rhoda Kinsella, Matthieu Muffato, Anne Parker, Giulietta Spudich, Andy Yates, Daniel R. Zerbino, Stephen M. J. Searle
Ensembl 2014. Nucleic Acids Res. 42 (Database-Issue) (2014)
Ian Walsh, Alberto J. M. Martin, Tomás Di Domenico, Alessandro Vullo, Gianluca Pollastri, Silvio C. E. Tosatto
CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Ian Walsh, Alessandro Vullo, Gianluca Pollastri
An adaptive model for learning molecular endpoints. Similarity-based learning on structures (2009)
Ian Walsh, Alessandro Vullo, Gianluca Pollastri
Recursive Neural Networks for Undirected Graphs for Learning Molecular Endpoints. PRIB (2009)
Ian Walsh, Alberto J. M. Martin, Catherine Mooney, Enrico Rubagotti, Alessandro Vullo, Gianluca Pollastri
Ab initio and homology based prediction of protein domains by recursive neural networks. BMC Bioinform. 10 (2009)
Alberto J. M. Martin, Alessandro Vullo, Gianluca Pollastri
Neural Network Pairwise Interaction Fields for Protein Model Quality Assessment. LION (2009)
Alessandro Vullo, Andrea Passerini, Paolo Frasconi, Fabrizio Costa, Gianluca Pollastri
On the Convergence of Protein Structure and Dynamics. Statistical Learning Studies of Pseudo Folding Pathways. EvoBIO (2008)
Alberto J. M. Martin, Davide Baù, Alessandro Vullo, Ian Walsh, Gianluca Pollastri
Long-Range Information and Physicality Constraints Improve predicted protein Contact Maps. J. Bioinform. Comput. Biol. 6 (5) (2008)
Gianluca Pollastri, Alberto J. M. Martin, Catherine Mooney, Alessandro Vullo
Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information. BMC Bioinform. 8 (2007)
Gianluca Pollastri, Alessandro Vullo, Paolo Frasconi, Pierre Baldi
Modular DAG-RNN Architectures for Assembling Coarse Protein Structures. J. Comput. Biol. 13 (3) (2006)
Alessandro Vullo, Ian Walsh, Gianluca Pollastri
A two-stage approach for improved prediction of residue contact maps. BMC Bioinform. 7 (2006)
Catherine Mooney, Alessandro Vullo, Gianluca Pollastri
Space Leads to Improved Secondary Structure Prediction. J. Comput. Biol. 13 (8) (2006)
Alessio Ceroni, Andrea Passerini, Alessandro Vullo, Paolo Frasconi
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Alessandro Vullo, Oscar Bortolami, Gianluca Pollastri, Silvio C. E. Tosatto
Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Davide Baù, Alberto J. M. Martin, Catherine Mooney, Alessandro Vullo, Ian Walsh, Gianluca Pollastri
Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. BMC Bioinform. 7 (2006)
Alessandro Vullo, Paolo Frasconi
Disulfide connectivity prediction using recursive neural networks and evolutionary information. Bioinform. 20 (5) (2004)
Pierre Baldi, Jianlin Cheng, Alessandro Vullo
Large-Scale Prediction of Disulphide Bond Connectivity. NIPS (2004)
Alessio Ceroni, Paolo Frasconi, Alessandro Vullo
-Sheet Motifs and Secondary Structure. WIRN (2004)
Alessio Ceroni, Paolo Frasconi, Andrea Passerini, Alessandro Vullo
A Combination of Support Vector Machines and Bidirectional Recurrent Neural Networks for Protein Secondary Structure Prediction. AI*IA (2003)
Alessandro Vullo, Paolo Frasconi
A Recursive Connectionist Approach for Predicting Disulfide Connectivity in Proteins. SAC (2003)
Alessio Ceroni, Paolo Frasconi, Andrea Passerini, Alessandro Vullo
Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines. J. VLSI Signal Process. 35 (3) (2003)
Alessandro Vullo, Paolo Frasconi
Prediction of Protein Coarse Contact Maps. J. Bioinform. Comput. Biol. 1 (2) (2003)
Gianluca Pollastri, Pierre Baldi, Alessandro Vullo, Paolo Frasconi
Prediction of Protein Topologies Using Generalized IOHMMS and RNNs. NIPS (2002)
Paolo Frasconi, Andrea Passerini, Alessandro Vullo
A two-stage SVM architecture for predicting the disulfide bonding state of cysteines. NNSP (2002)
Paolo Frasconi, Giovanni Soda, Alessandro Vullo
Hidden Markov Models for Text Categorization in Multi-Page Documents. J. Intell. Inf. Syst. 18 (2-3) (2002)
Alessandro Vullo, Paolo Frasconi
A Bi-Recursive Neural Network Architecture for the Prediction of Protein Coarse Contact Maps. CSB (2002)
Paolo Frasconi, Giovanni Soda, Alessandro Vullo
Text categorization for multi-page documents: a hybrid naive Bayes HMM approach. JCDL (2001)