| 653 | -- | 659 | Ya Wang, Min Qian, Deliang Tang, Julie Herbstman, Frederica Perera, Shuang Wang. A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes |
| 660 | -- | 665 | Ren Hua Chung, Chen-Yu Kang. pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions |
| 666 | -- | 675 | Yaqiang Cao, Zhaoxiong Chen, Xingwei Chen, Daosheng Ai, Guoyu Chen, Joseph McDermott, Yi Huang, Xiaoxiao Guo, Jing-Dong J. Han. Accurate loop calling for 3D genomic data with cLoops |
| 676 | -- | 681 | Joshua Millstein, Francesca Battaglin, Malcolm Barrett, Shu Cao, Wu Zhang, Sebastian Stintzing, Volker Heinemann, Heinz-Josef Lenz. Partition: a surjective mapping approach for dimensionality reduction |
| 682 | -- | 689 | Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher. Fast and accurate correction of optical mapping data via spaced seeds |
| 690 | -- | 697 | Tianlei Xu, Peng Jin, Zhaohui S. Qin. Regulatory annotation of genomic intervals based on tissue-specific expression QTLs |
| 698 | -- | 703 | Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Víctor Barrera, Roderic Espín, Florian Thibord, Xavier Bofill-De Ros, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. Vlachos, Marc K. Halushka, Lorena Pantano. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API |
| 704 | -- | 712 | Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, ZongYuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song. PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins |
| 713 | -- | 720 | Mary A Wood, Austin Nguyen, Adam J. Struck, Kyle Ellrott, Abhinav Nellore, Reid F. Thompson. neoepiscope improves neoepitope prediction with multivariant phasing |
| 721 | -- | 727 | Robert S. Harris, Paul Medvedev. Improved representation of sequence bloom trees |
| 728 | -- | 734 | Timothy J. Hackmann. Accurate estimation of microbial sequence diversity with Distanced |
| 735 | -- | 741 | M. B. B. Gutierres, C. B. C. Bonorino, M. M. Rigo. ChaperISM: improved chaperone binding prediction using position-independent scoring matrices |
| 742 | -- | 750 | Yufeng Wu. Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach |
| 751 | -- | 757 | Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng. Integrating ab initio and template-based algorithms for protein-protein complex structure prediction |
| 758 | -- | 764 | Fergus Boyles, Charlotte M. Deane, Garrett M. Morris. Learning from the ligand: using ligand-based features to improve binding affinity prediction |
| 765 | -- | 772 | Erney Ramírez-Aportela, Jose Luis Vilas, Alisa Glukhova, Roberto Melero, Pablo Conesa, Marta Martínez, David Maluenda, Javier Mota, Amaya Jiménez, Javier Vargas, Roberto Marabini, Patrick M. Sexton, José María Carazo, Carlos Oscar Sánchez Sorzano. Automatic local resolution-based sharpening of cryo-EM maps |
| 773 | -- | 781 | Hannah De Los Santos, Emily J. Collins, Catherine Mann, April W. Sagan, Meaghan S. Jankowski, Kristin P. Bennett, Jennifer M. Hurley. ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output |
| 782 | -- | 788 | Jiebiao Wang, Bernie Devlin, Kathryn Roeder. Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression |
| 789 | -- | 797 | Pengchao Ye, Wenbin Ye 0002, Congting Ye, Shuchao Li, Lishan Ye, Guoli Ji, Xiaohui Wu. scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size |
| 798 | -- | 804 | Priyam Das, Christine B. Peterson, Kim-Anh Do, Rehan Akbani, Veerabhadran Baladandayuthapani. NExUS: Bayesian simultaneous network estimation across unequal sample sizes |
| 805 | -- | 812 | Wenjiang Deng, Tian Mou, Krishna R. Kalari, Nifang Niu, Liewei Wang, Yudi Pawitan, Trung-Nghia Vu. Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data |
| 813 | -- | 818 | Godwin Woo, Michael Fernandez, Michael Hsing, Nathan A. Lack, Ayse Derya Cavga, Artem Cherkasov. DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules |
| 819 | -- | 827 | Ziyi Chen, Chengyang Ji, Qin Shen, Wei Liu, F. Xiao-Feng Qin, Aiping Wu. Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes |
| 828 | -- | 841 | José Víctor Moreno-Mayar, Thorfinn Sand Korneliussen, Jyoti Dalal, Gabriel Renaud, Anders Albrechtsen, Rasmus Nielsen, Anna-Sapfo Malaspinas. A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data |
| 842 | -- | 850 | Cheng Peng, Jun Wang, Isaac Asante, Stan Louie, Ran Jin, Lida Chatzi, Graham Casey, Duncan C. Thomas, David V. Conti. A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits |
| 851 | -- | 858 | Yu-An Huang, Pengwei Hu, Keith C. C. Chan, Zhu-Hong You. Graph convolution for predicting associations between miRNA and drug resistance |
| 859 | -- | 864 | Hongyang Li, Yuanfang Guan. Machine learning empowers phosphoproteome prediction in cancers |
| 865 | -- | 871 | Noemi Di Nanni, Matteo Gnocchi, Marco Moscatelli, Luciano Milanesi, Ettore Mosca. Gene relevance based on multiple evidences in complex networks |
| 872 | -- | 879 | Rafsan Ahmed, Ilyes Baali, Cesim Erten, Evis Hoxha, Hilal Kazan. MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules |
| 880 | -- | 889 | Ashwani Kumar, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Sunyoung Kim, Khaled A Aly, Sandra Zilles, Mohan Babu. A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli |
| 890 | -- | 896 | Xavier Farré, Nino Spataro, Frédéric Haziza, Jordi Rambla, Arcadi Navarro. Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence |
| 897 | -- | 903 | Wei Zhang, Longlong Wang, Ke Liu, Xiaofeng Wei, Kai Yang, Wensi Du, Shiyu Wang, Nannan Guo, Chuanchuan Ma, Lihua Luo, Jinghua Wu, Liya Lin, Fan Yang, Fei Gao, Xie Wang, Tao Li, Ruifang Zhang, Nitin K. Saksena, Huanming Yang, Jian Wang, Lin Fang, Yong Hou, Xun Xu, Xiao Liu. PIRD: Pan Immune Repertoire Database |
| 904 | -- | 909 | Gen Li, Yu Su, Yu-Hang Yan, Jiayi Peng, Qing-Qing Dai, Xiang-Li Ning, Cheng-Long Zhu, Chen Fu, Michael A. McDonough, Christopher J. Schofield, Cheng Huang, Guo-Bo Li. MeLAD: an integrated resource for metalloenzyme-ligand associations |
| 910 | -- | 917 | Blair J. Rossetti, Steven A. Wilbert, Jessica L. Mark Welch, Gary G. Borisy, James G. Nagy. Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs |
| 918 | -- | 919 | Endre Bakken Stovner, Pål Sætrom. PyRanges: efficient comparison of genomic intervals in Python |
| 920 | -- | 921 | Tao Li, Shaokai Wang, Feng Luo, Fang-Xiang Wu, Jianxin Wang. MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries |
| 922 | -- | 924 | Oscar L. Rodriguez, Anna M. Ritz, Andrew J. Sharp, Ali Bashir. MsPAC: a tool for haplotype-phased structural variant detection |
| 925 | -- | 927 | Hrant Hovhannisyan, Ahmed Hafez, Carlos Lloréns, Toni Gabaldón. CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies |
| 928 | -- | 929 | Xin Guo, Bo Zhang, Wenqi Zeng, Shuting Zhao, Dongliang Ge. G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram |
| 930 | -- | 933 | Max Lam, Swapnil Awasthi, Hunna J. Watson, Jackie Goldstein, Georgia Panagiotaropoulou, Vassily Trubetskoy, Robert Karlsson, Oleksander Frei, Chun-Chieh Fan, Ward De Witte, Nina R. Mota, Niamh Mullins, Kim Brügger, S. Hong Lee, Naomi R. Wray, Nora Skarabis, Hailiang Huang, Benjamin M. Neale, Mark J. Daly, Manuel Mattheisen, Raymond Walters, Stephan Ripke. RICOPILI: Rapid Imputation for COnsortias PIpeLIne |
| 934 | -- | 935 | Tomasz J. Kurowski, Fady R. Mohareb. Tersect: a set theoretical utility for exploring sequence variant data |
| 936 | -- | 937 | Eric Hugoson, Wai Tin Lam, Lionel Guy. miComplete: weighted quality evaluation of assembled microbial genomes |
| 938 | -- | 939 | Harry J. Whitwell, Peter A. DiMaggio Jr.. HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs |
| 940 | -- | 941 | Riccardo Delli Ponti, Alexandros Armaos, Andrea Vandelli, Gian Gaetano Tartaglia. CROSSalive: a web server for predicting the in vivo structure of RNA molecules |
| 942 | -- | 944 | Tingyang Li, Ashootosh Tripathi, Fengan Yu, David H. Sherman, Arvind Rao. DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases |
| 945 | -- | 947 | Adriano de Bernardi Schneider, Colby T. Ford, Reilly Hostager, John Williams, Michael Cioce, Ümit V. Çatalyürek, Joel O. Wertheim, Daniel Janies. StrainHub: a phylogenetic tool to construct pathogen transmission networks |
| 948 | -- | 949 | Reshmi Ramakrishnan, Bert Houben, Lukasz Kreft, Alexander Botzki, Joost Schymkowitz, Frederic Rousseau. Protein Homeostasis Database: protein quality control in E.coli |
| 950 | -- | 952 | Jorge Roel-Touris, Alexandre M. J. J. Bonvin, Brian Jiménez-García. LightDock goes information-driven |
| 953 | -- | 955 | Aleksandra I. Jarmolinska, Anna Gambin, Joanna I. Sulkowska. Knot_pull - python package for biopolymer smoothing and knot detection |
| 956 | -- | 958 | Iñigo Marcos-Alcalde, Eduardo López-Viñas, Paulino Gómez-Puertas. MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces |
| 959 | -- | 960 | Aeri Lee, Dongsup Kim. CRDS: Consensus Reverse Docking System for target fishing |
| 961 | -- | 963 | Yoonji Lee, Jordan M. Baumhardt, Jimin Pei, Yuh Min Chook, Nick V. Grishin. pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes |
| 964 | -- | 965 | Krzysztof Polanski, Matthew D. Young, Zhichao Miao, Kerstin B. Meyer, Sarah A. Teichmann, Jong-Eun Park. BBKNN: fast batch alignment of single cell transcriptomes |
| 966 | -- | 969 | A Ozuna, D. Liberto, R. M. Joyce, K. B. Arnvig, Irene Nobeli. baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data |
| 970 | -- | 971 | Mickaël Canouil, Gerard A. Bouland, Amélie Bonnefond, Philippe Froguel, Leen M. 't Hart, Roderick C. Slieker. NACHO: an R package for quality control of NanoString nCounter data |
| 972 | -- | 973 | Vinícius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson, Luciana C. A. Regitano, Luiz Coutinho, Ralf Zimmer, Levi Waldron, Ludwig Geistlinger. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes |
| 974 | -- | 975 | Zheng Gao, Jonathan Terhorst, Cristopher V. Van Hout, Stilian Stoev. U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies |
| 976 | -- | 977 | Jordi Bartolome, Rui Alves, Francesc Solsona, Ivan Teixido. EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology |
| 978 | -- | 979 | Leonid Stolbov, Dmitry S. Druzhilovskiy, Anastasia V. Rudik, Dmitry Filimonov, Vladimir Poroikov, Marc C. Nicklaus. AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity |
| 980 | -- | 981 | Rafal Cylwa, Kornel Kielczewski, Marta Machnik, Urszula Oleksiewicz, Przemyslaw Biecek. KRAB ZNF explorer - the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas |
| 982 | -- | 983 | Thoba Lose, Peter van Heusden, Alan Christoffels. COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies |