| T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension P Di Tommaso, S Moretti, I Xenarios, M Orobitg, A Montanyola, JM Chang, ... Nucleic acids research 39 (suppl_2), W13-W17, 2011 | 1394 | 2011 |
| The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome Biology 20, 244, 2019 | 527 | 2019 |
| Multiple sequence alignment modeling: methods and applications M Chatzou, C Magis, JM Chang, C Kemena, G Bussotti, I Erb, ... Briefings in bioinformatics 17 (6), 1009-1023, 2016 | 322 | 2016 |
| TADs are 3D structural units of higher-order chromosome organization in Drosophila Q Szabo, D Jost, JM Chang, DI Cattoni, GL Papadopoulos, B Bonev, ... Science advances 4 (2), eaar8082, 2018 | 295 | 2018 |
| Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development Y Ogiyama, B Schuettengruber, GL Papadopoulos, JM Chang, G Cavalli Molecular Cell 71 (1), 73-88, 2018 | 264 | 2018 |
| TCS: A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction JM Chang, P Di Tommaso, C Notredame Molecular biology and evolution 31 (6), 1625-1637, 2014 | 231 | 2014 |
| Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions DI Cattoni, AM Cardozo Gizzi, M Georgieva, M Di Stefano, A Valeri, ... Nature communications 8 (1), 1753, 2017 | 171 | 2017 |
| Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee JM Chang, P Di Tommaso, JF Taly, C Notredame BMC Bioinformatics 13 (Suppl 4), S1, 2012 | 147 | 2012 |
| Alignathon: A competitive assessment of whole genome alignment methods D Earl, NK Nguyen, G Hickey, RS Harris, S Fitzgerald, K Beal, I Seledtsov, ... Genome Research 24, 2077-2089, 2014 | 137 | 2014 |
| Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures JF Taly, C Magis, G Bussotti, JM Chang, P Di Tommaso, I Erb, ... Nature protocols 6 (11), 1669-1682, 2011 | 125 | 2011 |
| Constrained multiple sequence alignment tool development and its application to RNase family alignment CY Tang, CL Lu, MDT Chang, YT Tsai, YJ Sun, KM Chao, JM Chang, ... Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society, 127-137, 2002 | 99 | 2002 |
| T-Coffee: Tree-based consistency objective function for alignment evaluation C Magis, JF Taly, G Bussotti, JM Chang, P Di Tommaso, I Erb, ... Multiple Sequence Alignment Methods, 117-129, 2013 | 86 | 2013 |
| PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases EW Floden, PD Tommaso, M Chatzou, C Magis, C Notredame, JM Chang Nucleic acids research 44 (W1), W339-W343, 2016 | 82 | 2016 |
| HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence HN Lin, JM Chang, KP Wu, TY Sung, WL Hsu Bioinformatics 21 (15), 3227-3233, 2005 | 68 | 2005 |
| TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction JM Chang, P Di Tommaso, V Lefort, O Gascuel, C Notredame Nucleic acids research 43 (W1), W3–W6, 2015 | 66 | 2015 |
| PSLDoc: protein subcellular localization prediction based on gapped‐dipeptides and probabilistic latent semantic analysis JM Chang, ECY Su, A Lo, HS Chiu, TY Sung, WL Hsu Proteins: Structure, Function, and Bioinformatics 72 (2), 693-710, 2008 | 64 | 2008 |
| Expression divergence of chemosensory genes between Drosophila sechellia and its sibling species and its implications for host shift MS Shiao, JM Chang, WL Fan, MYJ Lu, C Notredame, S Fang, R Kondo, ... Genome biology and evolution 7 (10), 2843-2858, 2015 | 52 | 2015 |
| MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks YM Lin, CT Chen, JM Chang BMC genomics 20 (Suppl 9), 906, 2019 | 41 | 2019 |
| HYPROSP: a hybrid protein secondary structure prediction algorithm—a knowledge-based approach KP Wu, HN Lin, JM Chang, TY Sung, WL Hsu Nucleic Acids Research 32 (17), 5059-5065, 2004 | 37 | 2004 |
| Topological screen identifies hundreds of Cp190-and CTCF-dependent Drosophila chromatin insulator elements TG Kahn, M Savitsky, C Kuong, C Jacquier, G Cavalli, JM Chang, ... Science Advances 9 (5), eade0090, 2023 | 32 | 2023 |
Cedric NotredameCentre for Genomic Regulation, SpainVerified email at crg.eu
