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Efficient iterative Hi-C scaffolder based on N-best neighbors

Dengfeng Guan, Shane A. McCarthy, Zemin Ning, Guohua Wang, Yadong Wang, Richard Durbin
2021 BMC Bioinformatics  
Results We design and develop a novel Hi-C based scaffolding tool, pin_hic, which takes advantage of contact information from Hi-C reads to construct a scaffolding graph iteratively based on N-best neighbors  ...  Conclusions Pin_hic is an efficient Hi-C based scaffolding tool, which can be useful for building chromosome-scale assemblies.  ...  Programming language: C. Other requirements: gcc. License MIT Any restrictions to use by non-academics: None.  ... 
doi:10.1186/s12859-021-04453-5 pmid:34837944 pmcid:PMC8627104 fatcat:hqiv2xzbqzhaviyrmwus6rypoe

Whole-Genome Restriction Mapping by "Subhaploid"-Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding

Jinzhuang Dou, Huaiqian Dou, Chuang Mu, Lingling Zhang, Yangping Li, Jia Wang, Tianqi Li, Yuli Li, Xiaoli Hu, Shi Wang, Zhenmin Bao
2017 Genetics  
RadMap outperforms BioNano and Hi-C when input assembly is highly fragmented (contig N50 = 54 kb).  ...  RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies.  ...  Genome scaffolding of A. thaliana by BioNano and Hi-C Scaffolding the WGS assemblies of A. thaliana by BioNano (optical mapping) and Hi-C was conducted for comparison with RadMap.  ... 
doi:10.1534/genetics.117.200303 pmid:28468906 pmcid:PMC5500127 fatcat:4lhzkjotgvdpzmlsus7uic3eda

Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

Bin Huang, Guozheng Wei, Bing Wang, Fusong Ju, Yi Zhong, Zhuozheng Shi, Shiwei Sun, Dongbo Bu
2021 BMC Bioinformatics  
Results We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps.  ...  increasing searching efficiency.  ...  Acknowledgements We greatly appreciate Xuan Li for providing experimental optical maps data and appreciate Wei Shen for his helps to performing Hi-C scaffolding and analysis.  ... 
doi:10.1186/s12859-021-04448-2 pmid:34717539 fatcat:axg7xivkl5apzdorqaxumcndmy

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho (+1 others)
2020 Genome Biology  
Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies.  ...  Because few robust programs are available for this type of data, we developed instaGRAAL, a complete overhaul of the GRAAL program, which has adapted the latter to allow efficient assembly of large genomes  ...  Peer review information Andrew Cosgrove was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.  ... 
doi:10.1186/s13059-020-02041-z pmid:32552806 fatcat:f3pvheaiy5fghg2r73nbi4stve

Accurate, scalable and integrative haplotype estimation

Olivier Delaneau, Jean-François Zagury, Matthew R. Robinson, Jonathan L. Marchini, Emmanouil T. Dermitzakis
2019 Nature Communications  
The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required.  ...  We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.  ...  Code availability SHAPEIT4 is available on the GitHub webpage (https://odelaneau.github.io/shapeit4/).  ... 
doi:10.1038/s41467-019-13225-y pmid:31780650 pmcid:PMC6882857 fatcat:t76r6oqv7rd5bjoxm3d2iyomtm

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data

Gregory K. Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Erwan Corre, Laurence Garczarek
2015 BMC Bioinformatics  
This software was tested on the newly sequenced marine cyanobacterium Synechococcus sp.  ...  A number of automatic scaffolders were recently released, which improved the global quality of genomes published in the last few years. Yet, none of them reach the efficiency of manual scaffolding.  ...  Florian Humily and Morgane Ratin for strain purification and DNA extraction, the Roscoff Culture Collection for maintaining the Synechococcus strain used in this study as well as Christophe Caron for his  ... 
doi:10.1186/s12859-015-0705-y pmid:26335184 pmcid:PMC4559175 fatcat:s5bby5ew45dcxcf6zmtn2yyjbi

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Zev N Kronenberg, Arang Rhie, Sergey Koren, Gregory T Concepcion, Paul Peluso, Katherine M Munson, David Porubsky, Kristen Kuhn, Kathryn A Mueller, Wai Yee Low, Stefan Hiendleder, Olivier Fedrigo (+9 others)
2021 Nature Communications  
To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold  ...  FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing.  ...  M i;j :¼ M i;j z i þ z j ð1Þ We designed an algorithm to extend phasing between haplotig phase blocks based on Hi-C read pair mapping.  ... 
doi:10.1038/s41467-020-20536-y pmid:33911078 fatcat:esjjluxvhnasdgcoydjshqvxby

Idea2Data: Towards a New Paradigm for Drug Discovery

Christos A Nicolaou, Christine Humblet, Hong Hu, Eva-Marie Martín de la Nava, Frank C. Dorsey, Thomas M. Castle, Keith Ian Burton, Haitao Hu, Jorg Hendle, Michael J. Hickey, Joel Duerksen, Jibo Wang (+1 others)
2019 ACS Medicinal Chemistry Letters  
Hit identification can be carried out through large compound collection screening and often involves the generation and testing of many hypotheses based on available knowledge.  ...  Since its introduction, I2D has positively impacted several portfolio efforts through identification of new chemical scaffolds and functionalization of existing scaffolds.  ...  , such as CC bond cross coupling, CN bond formation, oxidation, reduction, and heterocyclic formation.  ... 
doi:10.1021/acsmedchemlett.8b00488 pmid:30891127 pmcid:PMC6421544 fatcat:k5tax75o5jds5ifymiblgf3u3m

MOLER: Incorporate Molecule-Level Reward to Enhance Deep Generative Model for Molecule Optimization

Tianfan Fu, Cao Xiao, Lucas Glass, Jimeng Sun
2021 IEEE Transactions on Knowledge and Data Engineering  
Empirical studies show that MOLER achieves up to 20.2% relative improvement in success rate over the best baseline method on several properties, including QED, DRD2 and LogP.  ...  Policy gradient technique is introduced to optimize reward-based objectives with small computational overhead.  ...  N (u) represents the set of all the neighbor nodes of the node u. m uv and m vu are the hidden variables representing the message from node u to node v and vice versa.  ... 
doi:10.1109/tkde.2021.3052150 fatcat:abgfwzytrnbuxigrnp4bwziofi

PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

Sean P. Gordon, Joshua J. Levy, John P. Vogel
2019 BMC Genomics  
In theory, existing methods for assigning sequences to individual species from metagenome samples could be used to separate subgenomes in polyploid organisms, however, these methods rely on differences  ...  Optionally, merge the binned fragments back together based on their scaffold of origin (or bin the entire original scaffold based on the total counts of differential repetitive sequence).  ...  In order to both provide a comprehensive analysis of N. tabacum subgenomes and to show that polyCRACKER works efficiently and accurately on fragmented draft assemblies, we repeated our analysis on the  ... 
doi:10.1186/s12864-019-5828-5 pmid:31299888 pmcid:PMC6626429 fatcat:vsasn32ywvhxzllrwq65wxrroy

Multi-Objective De Novo Drug Design with Conditional Graph Generative Model [article]

Yibo Li, Liangren Zhang, Zhenming Liu
2018 arXiv   pre-print
This method offers higher flexibility compared to previous fine-tuning based approach and is suitable for generation based on multiple objectives.  ...  In this work, a new de novo molecular design framework is proposed based on a type sequential graph generators that do not use atom level recurrent units.  ...  Acknowledgements We would like to thank Xiaodong Dou for his help on the discussion of generated inhibitors of JNK3 and GSK3β. Thanks to Bo Yang who helped with the profiling of Supplementary Text 8.  ... 
arXiv:1801.07299v3 fatcat:krtf3ppkhvchvog65unfqjyrs4

Ranbow: A fast and accurate method for polyploid haplotype reconstruction

M-Hossein Moeinzadeh, Jun Yang, Evgeny Muzychenko, Giuseppe Gallone, David Heller, Knut Reinert, Stefan Haas, Martin Vingron, Alexander Schönhuth
2020 PLoS Computational Biology  
Specifically, Ranbow is one order of magnitude faster than the next best method.  ...  The efficiency and accuracy of Ranbow makes whole genome haplotype reconstruction of complex genome with higher ploidy feasible.  ...  These distant connections can be obtained via paired-end, Hi-C, or long read information.  ... 
doi:10.1371/journal.pcbi.1007843 pmid:32469863 fatcat:n67u2cat5ncr5fj55a34fi5u7a

An automated iterative approach for protein structure refinement using pseudocontact shifts

Stefano Cucuzza, Peter Güntert, Andreas Plückthun, Oliver Zerbe
2021 Journal of Biomolecular NMR  
Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs.  ...  Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs.  ...  Michel for the initial biochemical setup and for developing the new N-terminal cap, and to M. Sitnik for the assignments of wild-type YM 4 A.  ... 
doi:10.1007/s10858-021-00376-8 pmid:34338940 pmcid:PMC8473369 fatcat:ezymopkw2faj7m4c6p4rwkjare

Predicting kinase inhibitors using bioactivity matrix derived informer sets

Huikun Zhang, Spencer S. Ericksen, Ching-pei Lee, Gene E. Ananiev, Nathan Wlodarchak, Peng Yu, Julie C. Mitchell, Anthony Gitter, Stephen J. Wright, F. Michael Hoffmann, Scott A. Wildman, Michael A. Newton (+1 others)
2019 PLoS Computational Biology  
We test the informer compounds on a target that is not part of the chemogenomic data, then predict the activity of the remaining compounds based on the experimental informer data and the chemogenomic data  ...  We compare different ways of using chemogenomic data to choose a small informer set of compounds based on previously measured bioactivity data.  ...  We also thank Yongna Xing and Vitali Stanevich for providing BGLF4 protein for assays and feedback on the manuscript.  ... 
doi:10.1371/journal.pcbi.1006813 pmid:31381559 pmcid:PMC6695194 fatcat:mmblevp77nbbzkqcn3sjxpghxy

Differentially Private Federated Learning on Heterogeneous Data [article]

Maxence Noble, Aurélien Bellet, Aymeric Dieuleveut
2022 arXiv   pre-print
Federated Learning (FL) is a paradigm for large-scale distributed learning which faces two key challenges: (i) efficient training from highly heterogeneous user data, and (ii) protecting the privacy of  ...  We focus on the challenging setting where users communicate with a "honest-but-curious" server without any trusted intermediary, which requires to ensure privacy not only towards a third-party with access  ...  Dieuleveut is partially supported by ANR-19-CHIA-0002-01 /chaire SCAI, and Hi! Paris.  ... 
arXiv:2111.09278v2 fatcat:6ur77f3gsjhlzid2di33hcik34
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