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Structure determination of genomic domains by satisfaction of spatial restraints.
- Published in:
- Chromosome Research, 2011, v. 19, n. 1, p. 25, doi. 10.1007/s10577-010-9167-2
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- Publication type:
- Article
ModView, visualization of multiple protein sequences and structures.
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- Bioinformatics, 2003, v. 19, n. 1, p. 165, doi. 10.1093/bioinformatics/19.1.165
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- Article
EVA: continuous automatic evaluation of protein structure prediction servers.
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- Bioinformatics, 2001, v. 17, n. 12, p. 1242, doi. 10.1093/bioinformatics/17.12.1242
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- Article
Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.
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- Life Science Alliance, 2024, v. 7, n. 2, p. 1, doi. 10.26508/lsa.202302154
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- Article
Challenges for visualizing three-dimensional data in genomic browsers.
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- FEBS Letters, 2017, v. 591, n. 17, p. 2505, doi. 10.1002/1873-3468.12778
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- Article
On the demultiplexing of chromosome capture conformation data.
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- FEBS Letters, 2015, v. 589, n. 20PartA, p. 3005, doi. 10.1016/j.febslet.2015.05.049
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- Publication type:
- Article
Restraint-based three-dimensional modeling of genomes and genomic domains.
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- FEBS Letters, 2015, v. 589, n. 20PartA, p. 2987, doi. 10.1016/j.febslet.2015.05.012
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- Publication type:
- Article
Alignment of multiple protein structures based on sequence and structure features.
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- PEDS: Protein Engineering, Design & Selection, 2009, v. 22, n. 9, p. 569, doi. 10.1093/protein/gzp040
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- Article
Variable gap penalty for protein sequence–structure alignment.
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- PEDS: Protein Engineering, Design & Selection, 2006, v. 19, n. 3, p. 129, doi. 10.1093/protein/gzj005
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- Publication type:
- Article
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.
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- Nature Reviews Genetics, 2013, v. 14, n. 6, p. 390, doi. 10.1038/nrg3454
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- Article
Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.
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- Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01962-x
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- Article
Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae.
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- Nature Communications, 2017, v. 8, n. 3, p. 14665, doi. 10.1038/ncomms14665
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- Publication type:
- Article
Quantifying the relationship between sequenceand three-dimensional structure conservation inRNA.
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- BMC Bioinformatics, 2010, v. 11, p. 322, doi. 10.1186/1471-2105-11-322
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- Article
Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast.
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- Genetics, 2020, v. 214, n. 3, p. 651, doi. 10.1534/genetics.119.302978
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- Article
A Kernel for Open Source Drug Discovery in Tropical Diseases.
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- PLoS Neglected Tropical Diseases, 2009, v. 3, n. 4, p. 1, doi. 10.1371/journal.pntd.0000418
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- Article
A Kernel for Open Source Drug Discovery in Tropical Diseases.
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- PLoS Neglected Tropical Diseases, 2009, v. 3, n. 4, p. 1, doi. 10.1371/journal.pntd.0000418
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- Publication type:
- Article
N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon.
- Published in:
- Protein Science: A Publication of the Protein Society, 2011, v. 20, n. 1, p. 179, doi. 10.1002/pro.551
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- Article
Localization of binding sites in protein structures by optimization of a composite scoring function.
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- Protein Science: A Publication of the Protein Society, 2006, v. 15, n. 10, p. 2366, doi. 10.1110/ps.062247506
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- Article
A composite score for predicting errors in protein structure models.
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- Protein Science: A Publication of the Protein Society, 2006, v. 15, n. 7, p. 1653, doi. 10.1110/ps.062095806
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- Publication type:
- Article
Alignment of protein sequences by their profiles.
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- Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 4, p. 1071, doi. 10.1110/ps.03379804
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- Publication type:
- Article
The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.
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- Nature Structural & Molecular Biology, 2011, v. 18, n. 1, p. 107, doi. 10.1038/nsmb.1936
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- Article
The C-type lectin fold as an evolutionary solution for massive sequence variation.
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- Nature Structural & Molecular Biology, 2005, v. 12, n. 10, p. 886, doi. 10.1038/nsmb992
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- Article
Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution.
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- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09907-2
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- Article
Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains.
- Published in:
- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05912-z
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- Article
A kernel for the Tropical Disease Initiative.
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- 2009
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- Publication type:
- Letter
Prediction of enzyme function by combining sequence similarity and protein interactions.
- Published in:
- BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-249
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- Publication type:
- Article
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
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- BMC Bioinformatics, 2007, v. 8, p. S4, doi. 10.1186/1471-2105-8-S4-S4
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- Publication type:
- Article
Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze.
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- PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004157
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- Article
Target Prediction for an Open Access Set of Compounds Active against <i>Mycobacterium tuberculosis</i>.
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- PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003253
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- Article
Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization.
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- PLoS Computational Biology, 2011, v. 7, n. 7, p. 1, doi. 10.1371/journal.pcbi.1002125
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- Article
Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions.
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- PLoS Computational Biology, 2007, v. 3, n. 9, p. 1761, doi. 10.1371/journal.pcbi.0030178
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- Publication type:
- Article
The impact of chromosomal fusions on 3D genome folding and recombination in the germ line.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23270-1
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- Article
Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-020-20849-y
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- Publication type:
- Article
Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology.
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- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-19999-w
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- Article
3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?
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- WIREs: Computational Molecular Science, 2017, v. 7, n. 5, p. n/a, doi. 10.1002/wcms.1308
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- Article
Software for predicting the 3D structure of RNA molecules.
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- WIREs: Computational Molecular Science, 2015, v. 5, n. 1, p. 56, doi. 10.1002/wcms.1198
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- Article
Polar/Ionizable Residues in Transmembrane Segments: Effects on Helix-Helix Packing.
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- PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0044263
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- Article
The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity.
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- PLoS Pathogens, 2023, v. 18, n. 3, p. 1, doi. 10.1371/journal.ppat.1011224
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- Article
Rational design of non-resistant targeted cancer therapies.
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- Scientific Reports, 2017, p. 46632, doi. 10.1038/srep46632
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- Article
Biological insertion of computationally designed short transmembrane segments.
- Published in:
- Scientific Reports, 2016, p. 23397, doi. 10.1038/srep23397
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- Article
Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.
- Published in:
- Proteins, 2006, v. 63, n. 4, p. 986, doi. 10.1002/prot.20881
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- Publication type:
- Article
Identification of chromatin loops from Hi-C interaction matrices by CTCF–CTCF topology classification.
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- NAR Genomics & Bioinformatics, 2022, v. 4, n. 1, p. 1, doi. 10.1093/nargab/lqac021
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- Article
Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform.
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- GigaScience, 2020, v. 9, n. 8, p. 1, doi. 10.1093/gigascience/giaa087
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- Article
Parallel sequencing lives, or what makes large sequencing projects successful.
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- GigaScience, 2017, v. 6, n. 11, p. 1, doi. 10.1093/gigascience/gix100
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- Article
Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion.
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- Nucleic Acids Research, 2022, v. 50, n. 7, p. 3892, doi. 10.1093/nar/gkac226
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- Publication type:
- Article
STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells.
- Published in:
- Nucleic Acids Research, 2021, v. 49, n. 19, p. 11005, doi. 10.1093/nar/gkab864
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- Article
Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana.
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- Nucleic Acids Research, 2021, v. 49, n. 4, p. 1840, doi. 10.1093/nar/gkaa1275
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- Article
Hierarchical chromatin organization detected by TADpole.
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- Nucleic Acids Research, 2020, v. 48, n. 7, p. e39, doi. 10.1093/nar/gkaa087
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- Article
OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. 8, p. 1, doi. 10.1093/nar/gky064
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- Article
Assessing the limits of restraint-based 3D modeling of genomes and genomic domains.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. 7, p. 3465, doi. 10.1093/nar/gkv221
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- Publication type:
- Article