TY  - JOUR
AU  - Perović, Vladimir R.
AU  - Leclercq, Jeremy Y
AU  - Šumonja, Neven
AU  - Richard, Francois D
AU  - Veljković, Nevena V.
AU  - Kajava, Andrey V.
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8997
AB  - Motivation: Proteins containing tandem repeats (TRs) are abundant, frequently fold in elongated non-globular structures and perform vital functions. A number of computational tools have been developed to detect TRs in protein sequences. A blurred boundary between imperfect TR motifs and non-repetitive sequences gave rise to necessity to validate the detected TRs. Results: Tally-2.0 is a scoring tool based on a machine learning (ML) approach, which allows to validate the results of TR detection. It was upgraded by using improved training datasets and additional ML features. Tally-2.0 performs at a level of 93% sensitivity, 83% specificity and an area under the receiver operating characteristic curve of 95%.
T2  - Bioinformatics
T1  - Tally-2.0: upgraded validator of tandem repeat detection in protein sequences
VL  - 36
IS  - 10
SP  - 3260
EP  - 3262
DO  - 10.1093/bioinformatics/btaa121
ER  - 

@article{
author = "Perović, Vladimir R. and Leclercq, Jeremy Y and Šumonja, Neven and Richard, Francois D and Veljković, Nevena V. and Kajava, Andrey V.",
year = "2020",
abstract = "Motivation: Proteins containing tandem repeats (TRs) are abundant, frequently fold in elongated non-globular structures and perform vital functions. A number of computational tools have been developed to detect TRs in protein sequences. A blurred boundary between imperfect TR motifs and non-repetitive sequences gave rise to necessity to validate the detected TRs. Results: Tally-2.0 is a scoring tool based on a machine learning (ML) approach, which allows to validate the results of TR detection. It was upgraded by using improved training datasets and additional ML features. Tally-2.0 performs at a level of 93% sensitivity, 83% specificity and an area under the receiver operating characteristic curve of 95%.",
journal = "Bioinformatics",
title = "Tally-2.0: upgraded validator of tandem repeat detection in protein sequences",
volume = "36",
number = "10",
pages = "3260-3262",
doi = "10.1093/bioinformatics/btaa121"
}

Perović, V. R., Leclercq, J. Y., Šumonja, N., Richard, F. D., Veljković, N. V.,& Kajava, A. V.. (2020). Tally-2.0: upgraded validator of tandem repeat detection in protein sequences. in Bioinformatics, 36(10), 3260-3262.
https://doi.org/10.1093/bioinformatics/btaa121

Perović VR, Leclercq JY, Šumonja N, Richard FD, Veljković NV, Kajava AV. Tally-2.0: upgraded validator of tandem repeat detection in protein sequences. in Bioinformatics. 2020;36(10):3260-3262.
doi:10.1093/bioinformatics/btaa121 .

Perović, Vladimir R., Leclercq, Jeremy Y, Šumonja, Neven, Richard, Francois D, Veljković, Nevena V., Kajava, Andrey V., "Tally-2.0: upgraded validator of tandem repeat detection in protein sequences" in Bioinformatics, 36, no. 10 (2020):3260-3262,
https://doi.org/10.1093/bioinformatics/btaa121 . .

TY  - JOUR
AU  - Hatos, András
AU  - Hajdu-Soltész, Borbála
AU  - Monzon, Alexander M
AU  - Palopoli, Nicolas
AU  - Álvarez, Lucía
AU  - Aykac-Fas, Burcu
AU  - Bassot, Claudio
AU  - Benítez, Guillermo I
AU  - Bevilacqua, Martina
AU  - Chasapi, Anastasia
AU  - Chemes, Lucia
AU  - Davey, Norman E
AU  - Davidović, Radoslav S.
AU  - Dunker, A Keith
AU  - Elofsson, Arne
AU  - Gobeill, Julien
AU  - Foutel, Nicolás S González
AU  - Sudha, Govindarajan
AU  - Guharoy, Mainak
AU  - Horvath, Tamas
AU  - Iglesias, Valentin
AU  - Kajava, Andrey V.
AU  - Kovacs, Orsolya P
AU  - Lamb, John
AU  - Lambrughi, Matteo
AU  - Lazar, Tamas
AU  - Leclercq, Jeremy Y
AU  - Leonardi, Emanuela
AU  - Macedo-Ribeiro, Sandra
AU  - Macossay-Castillo, Mauricio
AU  - Maiani, Emiliano
AU  - Manso, José A
AU  - Marino-Buslje, Cristina
AU  - Martínez-Pérez, Elizabeth
AU  - Mészáros, Bálint
AU  - Mičetić, Ivan
AU  - Minervini, Giovanni
AU  - Murvai, Nikoletta
AU  - Necci, Marco
AU  - Ouzounis, Christos A
AU  - Pajkos, Mátyás
AU  - Paladin, Lisanna
AU  - Pancsa, Rita
AU  - Papaleo, Elena
AU  - Parisi, Gustavo
AU  - Pasche, Emilie
AU  - Barbosa Pereira, Pedro J
AU  - Promponas, Vasilis J
AU  - Pujols, Jordi
AU  - Quaglia, Federica
AU  - Ruch, Patrick
AU  - Salvatore, Marco
AU  - Schad, Eva
AU  - Szabo, Beata
AU  - Szaniszló, Tamás
AU  - Tamana, Stella
AU  - Tantos, Agnes
AU  - Veljković, Nevena V.
AU  - Ventura, Salvador
AU  - Vranken, Wim
AU  - Dosztányi, Zsuzsanna
AU  - Tompa, Peter
AU  - Tosatto, Silvio C E
AU  - Piovesan, Damiano
PY  - 2019
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8799
AB  - The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the ‘dark’ proteome.
T2  - Nucleic Acids Research
T1  - DisProt: intrinsic protein disorder annotation in 2020
VL  - 48
IS  - D1
SP  - D269
EP  - D276
DO  - 10.1093/nar/gkz975
ER  - 

@article{
author = "Hatos, András and Hajdu-Soltész, Borbála and Monzon, Alexander M and Palopoli, Nicolas and Álvarez, Lucía and Aykac-Fas, Burcu and Bassot, Claudio and Benítez, Guillermo I and Bevilacqua, Martina and Chasapi, Anastasia and Chemes, Lucia and Davey, Norman E and Davidović, Radoslav S. and Dunker, A Keith and Elofsson, Arne and Gobeill, Julien and Foutel, Nicolás S González and Sudha, Govindarajan and Guharoy, Mainak and Horvath, Tamas and Iglesias, Valentin and Kajava, Andrey V. and Kovacs, Orsolya P and Lamb, John and Lambrughi, Matteo and Lazar, Tamas and Leclercq, Jeremy Y and Leonardi, Emanuela and Macedo-Ribeiro, Sandra and Macossay-Castillo, Mauricio and Maiani, Emiliano and Manso, José A and Marino-Buslje, Cristina and Martínez-Pérez, Elizabeth and Mészáros, Bálint and Mičetić, Ivan and Minervini, Giovanni and Murvai, Nikoletta and Necci, Marco and Ouzounis, Christos A and Pajkos, Mátyás and Paladin, Lisanna and Pancsa, Rita and Papaleo, Elena and Parisi, Gustavo and Pasche, Emilie and Barbosa Pereira, Pedro J and Promponas, Vasilis J and Pujols, Jordi and Quaglia, Federica and Ruch, Patrick and Salvatore, Marco and Schad, Eva and Szabo, Beata and Szaniszló, Tamás and Tamana, Stella and Tantos, Agnes and Veljković, Nevena V. and Ventura, Salvador and Vranken, Wim and Dosztányi, Zsuzsanna and Tompa, Peter and Tosatto, Silvio C E and Piovesan, Damiano",
year = "2019",
abstract = "The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the ‘dark’ proteome.",
journal = "Nucleic Acids Research",
title = "DisProt: intrinsic protein disorder annotation in 2020",
volume = "48",
number = "D1",
pages = "D269-D276",
doi = "10.1093/nar/gkz975"
}

Hatos, A., Hajdu-Soltész, B., Monzon, A. M., Palopoli, N., Álvarez, L., Aykac-Fas, B., Bassot, C., Benítez, G. I., Bevilacqua, M., Chasapi, A., Chemes, L., Davey, N. E., Davidović, R. S., Dunker, A. K., Elofsson, A., Gobeill, J., Foutel, N. S. G., Sudha, G., Guharoy, M., Horvath, T., Iglesias, V., Kajava, A. V., Kovacs, O. P., Lamb, J., Lambrughi, M., Lazar, T., Leclercq, J. Y., Leonardi, E., Macedo-Ribeiro, S., Macossay-Castillo, M., Maiani, E., Manso, J. A., Marino-Buslje, C., Martínez-Pérez, E., Mészáros, B., Mičetić, I., Minervini, G., Murvai, N., Necci, M., Ouzounis, C. A., Pajkos, M., Paladin, L., Pancsa, R., Papaleo, E., Parisi, G., Pasche, E., Barbosa Pereira, P. J., Promponas, V. J., Pujols, J., Quaglia, F., Ruch, P., Salvatore, M., Schad, E., Szabo, B., Szaniszló, T., Tamana, S., Tantos, A., Veljković, N. V., Ventura, S., Vranken, W., Dosztányi, Z., Tompa, P., Tosatto, S. C. E.,& Piovesan, D.. (2019). DisProt: intrinsic protein disorder annotation in 2020. in Nucleic Acids Research, 48(D1), D269-D276.
https://doi.org/10.1093/nar/gkz975

Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović RS, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljković NV, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt: intrinsic protein disorder annotation in 2020. in Nucleic Acids Research. 2019;48(D1):D269-D276.
doi:10.1093/nar/gkz975 .

Hatos, András, Hajdu-Soltész, Borbála, Monzon, Alexander M, Palopoli, Nicolas, Álvarez, Lucía, Aykac-Fas, Burcu, Bassot, Claudio, Benítez, Guillermo I, Bevilacqua, Martina, Chasapi, Anastasia, Chemes, Lucia, Davey, Norman E, Davidović, Radoslav S., Dunker, A Keith, Elofsson, Arne, Gobeill, Julien, Foutel, Nicolás S González, Sudha, Govindarajan, Guharoy, Mainak, Horvath, Tamas, Iglesias, Valentin, Kajava, Andrey V., Kovacs, Orsolya P, Lamb, John, Lambrughi, Matteo, Lazar, Tamas, Leclercq, Jeremy Y, Leonardi, Emanuela, Macedo-Ribeiro, Sandra, Macossay-Castillo, Mauricio, Maiani, Emiliano, Manso, José A, Marino-Buslje, Cristina, Martínez-Pérez, Elizabeth, Mészáros, Bálint, Mičetić, Ivan, Minervini, Giovanni, Murvai, Nikoletta, Necci, Marco, Ouzounis, Christos A, Pajkos, Mátyás, Paladin, Lisanna, Pancsa, Rita, Papaleo, Elena, Parisi, Gustavo, Pasche, Emilie, Barbosa Pereira, Pedro J, Promponas, Vasilis J, Pujols, Jordi, Quaglia, Federica, Ruch, Patrick, Salvatore, Marco, Schad, Eva, Szabo, Beata, Szaniszló, Tamás, Tamana, Stella, Tantos, Agnes, Veljković, Nevena V., Ventura, Salvador, Vranken, Wim, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C E, Piovesan, Damiano, "DisProt: intrinsic protein disorder annotation in 2020" in Nucleic Acids Research, 48, no. D1 (2019):D269-D276,
https://doi.org/10.1093/nar/gkz975 . .