default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBMC Bioinformatics, Volume 20
Volume 20, Number 1, December 2019
- Jun Ruan
, Zhen Liu, Ming Sun, Yue Wang, Junqiu Yue, Guoqiang Yu:
DBS: a fast and informative segmentation algorithm for DNA copy number analysis. 1:1-1:14 - Sarah Machado, Vincent Mercier, Nicolas Chiaruttini:
LimeSeg: a coarse-grained lipid membrane simulation for 3D image segmentation. 2:1-2:12 - Chia-Ying Chen, Trees-Juen Chuang:
NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors. 3:1-3:11 - Marco Seeland, Michael Rzanny, David Boho, Jana Wäldchen, Patrick Mäder:
Image-based classification of plant genus and family for trained and untrained plant species. 4:1-4:13 - Hezha Hassan, Siba Shanak:
GOTrapper: a tool to navigate through branches of gene ontology hierarchy. 20:1-20:6 - Harald Marx, Joshua J. Coon:
MS-Helios: a Circos wrapper to visualize multi-omic datasets. 21:1-21:4 - Toomas Haller, Tõnis Tasa, Andres Metspalu:
Manhattan Harvester and Cropper: a system for GWAS peak detection. 22:1-22:8 - Lixin Cheng, Pengfei Liu, Dong Wang, Kwong-Sak Leung:
Exploiting locational and topological overlap model to identify modules in protein interaction networks. 23:1-23:9 - Valentin Iglesias, Oscar Conchillo-Solé, Cristina Batlle, Salvador Ventura:
AMYCO: evaluation of mutational impact on prion-like proteins aggregation propensity. 24:1-24:5 - Robin Wellmann:
Optimum contribution selection for animal breeding and conservation: the R package optiSel. 25:1-25:13 - Apostolos Dimitromanolakis, Jingxiong Xu, Agnieszka Król, Laurent Briollais:
sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs. 26:1-26:9 - Ine Melckenbeeck, Pieter Audenaert, Thomas Van Parys, Yves Van de Peer, Didier Colle, Mario Pickavet:
Optimising orbit counting of arbitrary order by equation selection. 27:1-27:13 - Meng Wang, Lei Kong:
pblat: a multithread blat algorithm speeding up aligning sequences to genomes. 28:1-28:4 - Lech Nieroda, Lukas Maas, Scott Thiebes, Ulrich Lang, Ali Sunyaev, Viktor Achter, Martin Peifer:
iRODS metadata management for a cancer genome analysis workflow. 29:1-29:8 - Maarten W. Paul, H. Martijn de Gruiter, Zhanmin Lin, Willy M. Baarends, Wiggert A. van Cappellen, Adriaan B. Houtsmuller, Johan A. Slotman:
SMoLR: visualization and analysis of single-molecule localization microscopy data in R. 30:1-30:7 - Charlotte Debus, Ralf Floca, Michael Ingrisch, Ina Kompan, Klaus H. Maier-Hein, Amir Abdollahi, Marco Nolden:
MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging - design, implementation and application on the example of DCE-MRI. 31:1-31:18 - Akshay Tambe, Lior Pachter:
Barcode identification for single cell genomics. 32:1-32:9 - Mischa Schwendy, Ronald E. Unger, Mischa Bonn, Sapun H. Parekh:
Automated cell segmentation in FIJI® using the DRAQ5 nuclear dye. 39:1-39:9 - Tianyu Wang, Boyang Li, Craig E. Nelson, Sheida Nabavi:
Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data. 40:1-40:16 - Jingrong Zhang, Zihao Wang, Yu Chen, Renmin Han, Zhiyong Liu, Fei Sun, Fa Zhang:
PIXER: an automated particle-selection method based on segmentation using a deep neural network. 41:1-41:14 - Christine P'ng, Jeffrey Green, Lauren C. Chong, Daryl Waggott, Stephenie D. Prokopec, Mehrdad Shamsi, Francis Nguyen, Denise Y. F. Mak, Felix Lam, Marco A. Albuquerque, Ying Wu, Esther H. Jung, Maud H. W. Starmans, Michelle A. Chan-Seng-Yue, Cindy Q. Yao, Bianca Liang, Emilie Lalonde, Syed Haider, Nicole A. Simone, Dorota H. Sendorek, Kenneth C. Chu, Nathalie C. Moon, Natalie S. Fox, Michal R. Grzadkowski, Nicholas J. Harding, Clement Fung, Amanda R. Murdoch, Kathleen E. Houlahan, Jianxin Wang, David R. Garcia, Richard de Borja, Ren X. Sun, Xihui Lin, Gregory M. Chen, Aileen Lu, Yu-Jia Shiah, Amin Zia, Ryan Kearns, Paul C. Boutros:
BPG: Seamless, automated and interactive visualization of scientific data. 42:1-42:5 - Sunita Chandrasekaran, Eric Stahlberg:
Correction to: Computational approaches for cancer 2017 workshop overview. 43:1 - Dong Wei, Chuanying Liu, Xiaoqi Zheng, Yushuang Li:
Comprehensive anticancer drug response prediction based on a simple cell line-drug complex network model. 44:1-44:15 - Aleksandr Igorevich Zhernakov, Alexey Mikhailovich Afonin, Natalia Dmitrievna Gavriliuk, Olga Mikhailovna Moiseeva, Vladimir Aleksandrovich Zhukov:
s-dePooler: determination of polymorphism carriers from overlapping DNA pools. 45:1-45:6 - Xinyuan Zhang, Anna Okula Basile, Sarah A. Pendergrass, Marylyn D. Ritchie:
Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico. 46:1-46:10 - Qiangwei Zhou, Jing-Quan Lim, Wing-Kin Sung, Guoliang Li:
An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping. 47:1-47:11 - Qiu Xiao, Jiawei Luo, Cheng Liang, Jie Cai, Guanghui Li, Buwen Cao:
CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer. 67:1-67:13 - Tra-My Ngo, Yik-Ying Teo:
Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms. 68:1-68:9 - Jin Yao, Mark Hurle, Matthew R. Nelson, Pankaj Agarwal:
Predicting clinically promising therapeutic hypotheses using tensor factorization. 69:1-69:12 - Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz:
Analyzing a co-occurrence gene-interaction network to identify disease-gene association. 70:1-70:15 - Kamal Taha, Youssef Iraqi, Amira Al-Aamri:
Predicting protein functions by applying predicate logic to biomedical literature. 71:1-71:15 - Dat Quoc Nguyen, Karin Verspoor:
From POS tagging to dependency parsing for biomedical event extraction. 72:1-72:13 - Minoo Ashtiani, Payman Nickchi, Soheil Jahangiri-Tazehkand, Abdollah Safari, Mehdi Mirzaie, Mohieddin Jafari:
IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis. 73:1-73:4 - Sunjoo Bang, Sangjoon Son, Sooyoung Kim, Hyunjung Shin:
Disease Pathway Cut for Multi-Target drugs. 74:1-74:12 - Yongzhi Yang, Ying Li, Qiao Chen, Yongshuai Sun, Zhiqiang Lu:
WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations. 75:1-75:6 - Anghong Xiao, Zongze Wu, Shoubin Dong:
ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark. 76:1-76:13 - Hyrum D. Carroll, John L. Spouge, Mileidy Gonzalez:
MultiDomainBenchmark: a multi-domain query and subject database suite. 77:1-77:9 - Jimmy F. Zhang, Alex R. Paciorkowski, Paul A. Craig, Feng Cui:
BioVR: a platform for virtual reality assisted biological data integration and visualization. 78:1-78:10 - Giovanni Scala, Angela Serra, Veer Singh Marwah, Laura Aliisa Saarimäki, Dario Greco:
FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments. 79:1-79:7 - Kaisa Liimatainen, Lauri Kananen, Leena Latonen, Pekka Ruusuvuori:
Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks. 80:1-80:10 - Joshua Williams, Ruoting Yang, John L. Clifford, Daniel Watson, Ross Campbell, Derese Getnet, Raina Kumar, Rasha Hammamieh, Marti Jett:
Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays. 81:1-81:6 - Jake Alan Pitt, Julio R. Banga:
Parameter estimation in models of biological oscillators: an automated regularised estimation approach. 82:1-82:17 - Arnaud Amzallag, Sridhar Ramaswamy, Cyril H. Benes:
Statistical assessment and visualization of synergies for large-scale sparse drug combination datasets. 83:1-83:15 - Irina Kuznetsova, Artur Lugmayr, Stefan J. Siira, Oliver Rackham, Aleksandra Filipovska:
CirGO: an alternative circular way of visualising gene ontology terms. 84:1-84:7 - Xionghui Zhou, Xin-Yi Chu, Gang Xue, Jiang-Hui Xiong, Hong-Yu Zhang:
Identifying cancer prognostic modules by module network analysis. 85:1-85:11 - Hongli Fu, Yingxi Yang, Xiaobo Wang, Hui Wang, Yan Xu:
DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins. 86:1-86:10 - Xiao-Nan Fan, Shao-Wu Zhang, Song-Yao Zhang, Kunju Zhu, Songjian Lu:
Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information. 87:1-87:12 - Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski, Tristan Cordier:
SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data. 88:1-88:6 - Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein, Fredric E. Wondisford, Xiaoyang Su, Philip L. Lorenzi:
ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments. 89:1-89:9 - Taewoon Joo, Ji-Hye Choi, Ji-Hye Lee, So Eun Park, Youngsic Jeon, Sae Hoon Jung, Hyun Goo Woo:
SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package. 90:1-90:7 - Fatemeh Mansoori, Maseud Rahgozar, Kaveh Kavousi:
FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods. 92:1-92:21 - Yifeng Cui, Qiwen Dong, Daocheng Hong, Xikun Wang:
Predicting protein-ligand binding residues with deep convolutional neural networks. 93:1-93:12 - Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, Nengjun Yi:
Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information. 94:1-94:15 - Svetlana Vinogradova, Sachit D. Saksena, Henry N. Ward, Sébastien Vigneau, Alexander A. Gimelbrant:
MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin. 106:1-106:5 - Noemi Di Nanni, Marco Moscatelli, Matteo Gnocchi, Luciano Milanesi, Ettore Mosca:
isma: an R package for the integrative analysis of mutations detected by multiple pipelines. 107:1-107:9 - Arthur T. O. Melo, Iago Hale:
'apparent': a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information. 108:1-108:10 - Bing Zhang, Huihui Ren, Guoyan Huang, Yongqiang Cheng, Changzhen Hu:
Predicting blood pressure from physiological index data using the SVR algorithm. 109:1-109:15 - Adam Price, Adrian Caciula, Cheng Guo, Bohyun Lee, Juliet Morrison, Angela Rasmussen, W. Ian Lipkin, Komal Jain:
DEvis: an R package for aggregation and visualization of differential expression data. 110:1-110:7 - Leijie Li, Dongxue Che, Xiaodan Wang, Peng Zhang, Siddiq Ur Rahman, Jianbang Zhao, Jiantao Yu, Shiheng Tao, Hui Lu, Mingzhi Liao:
CellSim: a novel software to calculate cell similarity and identify their co-regulation networks. 111:1-111:9 - Fuyi Li, Yang Zhang, Anthony W. Purcell, Geoffrey I. Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li, Jiangning Song:
Positive-unlabelled learning of glycosylation sites in the human proteome. 112:1-112:17 - Artyom A. Egorov, Ekaterina A. Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev, Ivan V. Kulakovskiy:
svist4get: a simple visualization tool for genomic tracks from sequencing experiments. 113:1-113:6 - Pawel Blazej, Malgorzata Wnetrzak, Dorota Mackiewicz, Pawel Mackiewicz:
The influence of different types of translational inaccuracies on the genetic code structure. 114:1-114:14 - Karl Stamm, Aoy Tomita-Mitchell, Serdar Bozdag:
GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display. 115:1-115:6 - Héléna A. Gaspar, Gerome Breen:
Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics. 116:1-116:11 - Marco Di Salvo, Simone Puccio, Clelia Peano, Stephan Lacour, Pietro Alifano:
RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases. 117:1-117:11 - Burçak Otlu, Tolga Can:
JOA: Joint Overlap Analysis of multiple genomic interval sets. 121:1-121:14 - Brian B. Merritt, Lily S. Cheung:
GRIBCG: a software for selection of sgRNAs in the design of balancer chromosomes. 122:1-122:7 - Matt Ravenhall, Susana G. Campino, Taane G. Clark:
SV-Pop: population-based structural variant analysis and visualization. 136:1-136:4 - Qingchen Zhang, Lu Zhang, Chen Zhou, Yiyan Yang, Zuojing Yin, Dingfeng Wu, Kailin Tang, Zhiwei Cao:
DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination. 137:1-137:9 - Bastien Kovac, Jérôme Fehrenbach, Ludivine Guillaume, Pierre Weiss:
FitEllipsoid: a fast supervised ellipsoid segmentation plugin. 142:1-142:8 - Vu Viet Hoang Pham, Junpeng Zhang, Lin Liu, Buu Minh Thanh Truong, Taosheng Xu, Trung T. Nguyen, Jiuyong Li, Thuc Duy Le:
Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction. 143:1-143:12 - Christine Winter, Robin Kosch, Martin Ludlow, Albert Osterhaus, Klaus Jung:
Network meta-analysis correlates with analysis of merged independent transcriptome expression data. 144:1-144:10 - Khong-Loon Tiong, Chen-Hsiang Yeang:
MGSEA - a multivariate Gene set enrichment analysis. 145:1-145:22 - Pengfei Wang, Wensheng Zhu:
Replicability analysis in genome-wide association studies via Cartesian hidden Markov models. 146:1-146:12 - Daehong Kwon, Jongin Lee, Jaebum Kim:
GMASS: a novel measure for genome assembly structural similarity. 147:1-147:9 - Konrad Zych, Gerrit Gort, Chris A. Maliepaard, Ritsert C. Jansen, Roeland E. Voorrips:
FitTetra 2.0 - improved genotype calling for tetraploids with multiple population and parental data support. 148:1-148:8 - Ronald Smith, Taliesin J. Kinser, Gregory D. Conradi Smith, Joshua R. Puzey:
A likelihood ratio test for changes in homeolog expression bias. 149:1-149:11 - Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, Marko Dunjic, Peter F. Stadler, Katja Nowick:
SSS-test: a novel test for detecting positive selection on RNA secondary structure. 151:1-151:19 - Yu Xu, Zhe Lin, Chong Tang, Yujing Tang, Yue Cai, Hongbin Zhong, Xuebin Wang, Wenwei Zhang, Chongjun Xu, Jingjing Wang, Jian Wang, Huanming Yang, Linfeng Yang, Qiang Gao:
A new massively parallel nanoball sequencing platform for whole exome research. 153:1-153:9 - Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran, Dena Leshkowitz:
UTAP: User-friendly Transcriptome Analysis Pipeline. 154:1-154:7 - Meng Liu, Paul D. Thomas:
GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness. 155:1-155:15 - Ilknur Karadeniz, Arzucan Özgür:
Linking entities through an ontology using word embeddings and syntactic re-ranking. 156:1-156:12 - Tobias Zehnder, Philipp Benner, Martin Vingron:
Predicting enhancers in mammalian genomes using supervised hidden Markov models. 157:1-157:12 - Lei Cui, Jun Feng, Zizhao Zhang, Lin Yang:
High throughput automatic muscle image segmentation using parallel framework. 158:1-158:9 - Daniel Perez-Gil, Francisco J. Lopez, Joaquín Dopazo, Pablo Marín-García, Augusto Rendon, Ignacio Medina:
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources. 159:1-159:5 - Divy Kangeyan, Andrew J. Dunford, Sowmya Iyer, Chip Stewart, Megan Hanna, Gad Getz, Martin J. Aryee:
A (fire)cloud-based DNA methylation data preprocessing and quality control platform. 160:1-160:5 - Guangsheng Wu, Juan Liu, Xiang Yue:
Prediction of drug-disease associations based on ensemble meta paths and singular value decomposition. 134:1-134:13 - Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui Wang, Bingqing Lin, Jun Zhang:
A statistical normalization method and differential expression analysis for RNA-seq data between different species. 163:1-163:10 - Wei Gu, Reha Yildirimman, Emmanuel Van der Stuyft, Denny Verbeeck, Sascha Herzinger, Venkata P. Satagopam, Adriano Barbosa-Silva, Reinhard Schneider, Bodo M. H. Lange, Hans Lehrach, Yike Guo, David Henderson, Anthony Rowe:
Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium. 164:1-164:11 - Miriam Gjerdevik, Astanand Jugessur, Øystein A. Haaland, Julia Romanowska, Rolv T. Lie, Heather J. Cordell, Håkon K. Gjessing:
Haplin power analysis: a software module for power and sample size calculations in genetic association analyses of family triads and unrelated controls. 165:1-165:11 - Daphne Ezer, Joseph Keir:
NITPicker: selecting time points for follow-up experiments. 166:1-166:10 - Patrik Waldmann, Maja Ferencakovic, Gábor Mészáros, Negar Khayatzadeh, Ino Curik, Johann Sölkner:
AUTALASSO: an automatic adaptive LASSO for genome-wide prediction. 167:1-167:10 - Wei Li Wang, Zhou Yu, Luis R. Castillo-Menendez, Joseph Sodroski, Youdong Mao:
Robustness of signal detection in cryo-electron microscopy via a bi-objective-function approach. 169:1-169:17 - Yosef Masoudi-Sobhanzadeh, Habib Motieghader, Ali Masoudi-Nejad:
FeatureSelect: a software for feature selection based on machine learning approaches. 170:1-170:17 - Matthew McCoy, Vikram Shivakumar, Sridhar Nimmagadda, Mohsin Saleet Jafri, Subha Madhavan:
SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants. 171:1-171:8 - W. Garrett Jenkinson, Jordi Abante, Michael A. Koldobskiy, Andrew P. Feinberg, John Goutsias:
Ranking genomic features using an information-theoretic measure of epigenetic discordance. 175:1-175:17 - Jianfeng Cao, Ming-Kin Wong, Zhongying Zhao, Hong Yan:
3DMMS: robust 3D Membrane Morphological Segmentation of C. elegans embryo. 176:1-176:13 - Suyan Tian:
Identification of monotonically differentially expressed genes for non-small cell lung cancer. 177:1-177:9 - Kathrin Blagec, Hong Xu, Asan Agibetov, Matthias Samwald:
Neural sentence embedding models for semantic similarity estimation in the biomedical domain. 178:1-178:10 - Ousmane H. Cissé, Jason E. Stajich:
FGMP: assessing fungal genome completeness. 184:1-184:9 - Yun Zhang, Gautam Bandyopadhyay, David J. Topham, Ann R. Falsey, Xing Qiu:
Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure. 185:1-185:14 - Ana M. Untaroiu, Maureen A. Carey, Jennifer L. Guler, Jason A. Papin:
Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies. 186:1-186:9 - Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa, Ivan Viola:
Metabopolis: scalable network layout for biological pathway diagrams in urban map style. 187:1-187:20 - Nhan Thi Ho, Fan Li, Shuang Wang, Louise Kuhn:
metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models. 188:1-188:15 - Julián Candia, John S. Tsang:
eNetXplorer: an R package for the quantitative exploration of elastic net families for generalized linear models. 189:1-189:11 - Thomas Gatter, Peter F. Stadler:
Ryūtō: network-flow based transcriptome reconstruction. 190:1-190:14 - Lubna Pinky, Gilberto C. González-Parra, Hana M. Dobrovolny:
Effect of stochasticity on coinfection dynamics of respiratory viruses. 191:1-191:12 - Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost:
Detailed prediction of protein sub-nuclear localization. 205:1-205:15 - Jolanda H. M. van Bilsen, Lars Verschuren, Laura Wagenaar, Marlotte M. Vonk, Betty C. A. M. van Esch, Léon M. J. Knippels, Johan Garssen, Joost J. Smit, Raymond H. H. Pieters, Tim J. van den Broek:
A network-based approach for identifying suitable biomarkers for oral immunotherapy of food allergy. 206:1-206:11 - Bastian Pfeifer, Durrell D. Kapan:
Estimates of introgression as a function of pairwise distances. 207:1-207:11 - Marek Palkowski, Wlodzimierz Bielecki:
Tiling Nussinov's RNA folding loop nest with a space-time approach. 208:1-208:11 - Stefan Hammer, Wei Wang, Sebastian Will, Yann Ponty:
Fixed-parameter tractable sampling for RNA design with multiple target structures. 209:1-209:13 - Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna:
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. 210:1-210:13 - Ahmed Bin Zaman, Amarda Shehu:
Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction. 211:1-211:17 - Sara Rahiminejad, Mano Ram Maurya, Shankar Subramaniam:
Topological and functional comparison of community detection algorithms in biological networks. 212:1-212:25 - Alfredo Iacoangeli, Ahmad Al Khleifat, William Sproviero, Aleksey Shatunov, A. R. Jones, S. L. Morgan, Alan Pittman, Richard J. B. Dobson, S. J. Newhouse, Ammar Al-Chalabi:
DNAscan: personal computer compatible NGS analysis, annotation and visualisation. 213:1-213:10 - Thomas Hiscock:
Adapting machine-learning algorithms to design gene circuits. 214:1-214:13 - Lang Yang, Xia Zhang, Yuqi Liu, Hao Li, Shaofu Qiu, Peng Li, Hongbin Song:
CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR. 215:1-215:6 - Mohamed Reda Bouadjenek, Justin Zobel, Karin Verspoor:
Automated assessment of biological database assertions using the scientific literature. 216:1-216:22 - Jeremy P. Koelmel, Jason A. Cochran, Candice Z. Ulmer, Allison J. Levy, Rainey E. Patterson, Berkley C. Olsen, Richard A. Yost, John A. Bowden, Timothy J. Garrett:
Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values. 217:1-217:13 - Stefan Graw, Rosalyn Henn, Jeffrey A. Thompson, Devin C. Koestler:
pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS). 218:1-218:11 - Xin Li, Dongya Wu, Yue Cui, Bing Liu, Henrik Walter, Gunter Schumann, Chong Li, Tianzi Jiang:
Reliable heritability estimation using sparse regularization in ultrahigh dimensional genome-wide association studies. 219:1-219:11 - Arnaud Bonnaffoux, Ulysse Herbach, Angélique Richard, Anissa Guillemin, Sandrine Gonin-Giraud, Pierre-Alexis Gros, Olivier Gandrillon:
WASABI: a dynamic iterative framework for gene regulatory network inference. 220:1-220:19 - Lea M. Urpa, Simon Anders:
Focused multidimensional scaling: interactive visualization for exploration of high-dimensional data. 221:1-221:8 - Zhe Wang, Junming Hu, W. Evan Johnson, Joshua D. Campbell:
scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data. 222:1-222:9 - Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang, Jia Meng:
m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network. 223:1-223:12 - Chen Wang, Feng Gao, Georgios B. Giannakis, Gennaro D'Urso, Xiaodong Cai:
Efficient proximal gradient algorithm for inference of differential gene networks. 224:1-224:15 - Lifan Liang, Vicky Chen, Kunju Zhu, Xiaonan Fan, Xinghua Lu, Songjian Lu:
Integrating data and knowledge to identify functional modules of genes: a multilayer approach. 225:1-225:15 - Paula Pérez-Rubio, Claudio Lottaz, Julia C. Engelmann:
FastqPuri: high-performance preprocessing of RNA-seq data. 226:1-226:11 - Qiang Yan, Seth B. Roberts, J. Paul Brooks, Stephen S. Fong:
Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model. 227:1-227:13 - Davide Heller, Damian Szklarczyk, Christian von Mering:
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. 228:1-228:12 - Sahil D. Shah, Rosemary Braun:
GeneSurrounder: network-based identification of disease genes in expression data. 229:1-229:12 - Debangana Chakravorty, Krishnendu Banerjee, Tarunendu Mapder, Sudipto Saha:
In silico modeling of phosphorylation dependent and independent c-Myc degradation. 230:1-230:11 - Nathan Ungerleider, Erik K. Flemington:
SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation. 231:1-231:7 - Philipp Bongartz:
Resolving repeat families with long reads. 232:1-232:11 - Ali Navid, Yongqin Jiao, Sergio Ernesto Wong, Jennifer Pett-Ridge:
System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris. 233:1-233:16 - Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José Luis Roda García, Carlos J. Pérez-González, Marcos Colebrook, Carlos Flores:
NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly. 234:1-234:4 - Junpeng Zhang, Lin Liu, Taosheng Xu, Yong Xie, Chunwen Zhao, Jiuyong Li, Thuc Duy Le:
miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules. 235:1-235:12 - Xiaolong Zhang, Yanyan Shao, Jichao Tian, Yuwei Liao, Peiying Li, Yu Zhang, Jun Chen, Zhiguang Li:
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data. 236:1-236:6 - Najaf A. Shah, Casim A. Sarkar:
Variable cellular decision-making behavior in a constant synthetic network topology. 237:1-237:12 - Junrong Song, Wei Peng, Feng Wang:
A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph. 238:1-238:17 - Ti-Tai Wang, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang:
anamiR: integrated analysis of MicroRNA and gene expression profiling. 239:1-239:7 - Jaume Bonet, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck, Bruno E. Correia:
rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics. 240:1-240:13 - Neerja Thakkar, Chris Bailey-Kellogg:
Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity. 241:1-241:14 - Alokendra Ghosh, Ravi Radhakrishnan:
Time-dependent antagonist-agonist switching in receptor tyrosine kinase-mediated signaling. 242:1-242:14 - Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius:
PathMe: merging and exploring mechanistic pathway knowledge. 243:1-243:12 - Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong:
Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38. 252:1 - Akanksha Srivastava, Yuliya V. Karpievitch, Steven R. Eichten, Justin O. Borevitz, Ryan Lister:
HOME: a histogram based machine learning approach for effective identification of differentially methylated regions. 253:1-253:15 - Enrico Mossotto, J. J. Ashton, L. O'Gorman, Reuben J. Pengelly, R. M. Beattie, Ben D. MacArthur, Sarah Ennis:
GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data. 254:1-254:15 - Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres, Philipp Rescheneder:
Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. 258:1-258:16 - Juhyeon Kim, Insung Ahn:
Weekly ILI patient ratio change prediction using news articles with support vector machine. 259:1-259:16 - Huiwei Zhou, Chengkun Lang, Zhuang Liu, Shixian Ning, Yingyu Lin, Lei Du:
Knowledge-guided convolutional networks for chemical-disease relation extraction. 260:1-260:13 - Arash Bayat, Bruno Gaëta, Aleksandar Ignjatovic, Sri Parameswaran:
Pairwise alignment of nucleotide sequences using maximal exact matches. 261:1-261:15 - Andreas Hofmann, Sarah Preston, Megan Cross, H. M. P. Dilrukshi Herath, Anne Simon, Robin B. Gasser:
DRfit: a Java tool for the analysis of discrete data from multi-well plate assays. 262:1-262:6 - Vivekanand Sharma, Maria Isabel Restrepo, Indra Neil Sarkar:
Solr-Plant: efficient extraction of plant names from text. 263:1-263:4 - Ryan O. Schenck, Eszter Lakatos, Chandler Gatenbee, Trevor A. Graham, Alexander R. A. Anderson:
NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline. 264:1-264:6 - Alexandra R. Buckley, Trey Ideker, Hannah Carter, Nicholas J. Schork:
Rare variant phasing using paired tumor: normal sequence data. 265:1-265:11 - Wiktor Kusmirek, Agnieszka Szmurlo, Marek S. Wiewiórka, Robert M. Nowak, Tomasz Gambin:
Comparison of kNN and k-means optimization methods of reference set selection for improved CNV callers performance. 266:1-266:10 - Hiroki Konishi, Daisuke Komura, Hiroto Katoh, Shinichiro Atsumi, Hirotomo Koda, Asami Yamamoto, Yasuyuki Seto, Masashi Fukayama, Rui Yamaguchi, Seiya Imoto, Shumpei Ishikawa:
Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. 267:1-267:11 - Judith Somekh, Shai S. Shen-Orr, Isaac S. Kohane:
Batch correction evaluation framework using a-priori gene-gene associations: applied to the GTEx dataset. 268:1-268:10 - Zhiguo Li, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice M. McCarthy, Deanna L. Kroetz, Andrew S. Allen, Kouros Owzar:
Efficient estimation of grouped survival models. 269:1-269:11 - Poomarin Phloyphisut, Natapol Pornputtapong, Sira Sriswasdi, Ekapol Chuangsuwanich:
MHCSeqNet: a deep neural network model for universal MHC binding prediction. 270:1-270:10 - Wei Zheng, Dingjie Wang, Xiufen Zou:
Control of multilayer biological networks and applied to target identification of complex diseases. 271:1-271:12 - Lars Feuerbach, Lina Sieverling, Katharina I. Deeg, Philip Ginsbach, Barbara Hutter, Ivo Buchhalter, Paul A. Northcott, Sadaf S. Mughal, Priya Chudasama, Hanno Glimm, Claudia Scholl, Peter Lichter, Stefan Fröhling, Stefan M. Pfister, David T. W. Jones, Karsten Rippe, Benedikt Brors:
TelomereHunter - in silico estimation of telomere content and composition from cancer genomes. 272:1-272:11 - Heinrich Roder, Carlos Oliveira, Lelia Net, Benjamin Linstid, Maxim Tsypin, Joanna Roder:
Robust identification of molecular phenotypes using semi-supervised learning. 273:1-273:25 - Bruno M. S. Wanderley, Daniel S. A. de Araujo, María V. Quiroga, André M. Amado, Adrião D. D. Neto, Hugo Sarmento, Sebastián D. Metz, Fernando Unrein:
flowDiv: a new pipeline for analyzing flow cytometric diversity. 274:1-274:10 - Denise Thiel, Natasa Djurdjevac Conrad, Evgenia Ntini, Ria X. Peschutter, Heike Siebert, Annalisa Marsico:
Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis. 292:1-292:16 - Serge Léger, Maria Beatriz Walter Costa, Dan Tulpan:
Pairwise visual comparison of small RNA secondary structures with base pair probabilities. 293:1-293:12 - Maryam Masnadi-Shirazi, Mano Ram Maurya, Gerald M. Pao, Eugene Ke, Inder M. Verma, Shankar Subramaniam:
Time varying causal network reconstruction of a mouse cell cycle. 294:1-294:22 - Yulia Panina, Arno Germond, Brit G. David, Tomonobu M. Watanabe:
Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay. 295:1-295:12 - Dace Ruklisa, Alvis Brazma, Karlis Cerans, Thomas Schlitt, Juris Viksna:
Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ. 296:1-296:14 - Emily E. Ackerman, John F. Alcorn, Takeshi Hase, Jason E. Shoemaker:
A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery. 297:1-297:13 - Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier:
Illumina error correction near highly repetitive DNA regions improves de novo genome assembly. 298:1-298:13 - Zhongwang Yu, Yuangen Yao, Haiyou Deng, Ming Yi:
ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment. 299:1-299:11 - Thorsten Will, Volkhard Helms:
Differential analysis of combinatorial protein complexes with CompleXChange. 300:1-300:14 - Pascal Costanza, Charlotte Herzeel, Wilfried Verachtert:
A comparison of three programming languages for a full-fledged next-generation sequencing tool. 301:1-301:10 - Karsten Wüllems, Jan Kölling, Hanna Bednarz, Karsten Niehaus, Volkmar H. Hans, Tim W. Nattkemper:
Detection and visualization of communities in mass spectrometry imaging data. 303:1-303:12 - Efthymia Chantzi, Malin Jarvius, Mia Niklasson, Anna Segerman, Mats G. Gustafsson:
COMBImage2: a parallel computational framework for higher-order drug combination analysis that includes automated plate design, matched filter based object counting and temporal data mining. 304:1-304:20 - Jiao Chen, Jiating Huang, Yanni Sun:
TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data. 305:1-305:14 - Zheng Gao, Gang Fu, Chunping Ouyang, Satoshi Tsutsui, Xiaozhong Liu, Jeremy J. Yang, Christopher Gessner, Brian Foote, David J. Wild, Ying Ding, Qi Yu:
edge2vec: Representation learning using edge semantics for biomedical knowledge discovery. 306:1-306:15 - Beatriz Peñalver Bernabé, Ines Thiele, Eugene Galdones, Anaar Siletz, Sriram Chandrasekaran, Teresa K. Woodruff, Linda J. Broadbelt, Lonnie D. Shea:
Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. 307:1-307:16 - Kuan-Hsi Chen, Tsai-Feng Wang, Yuh-Jyh Hu:
Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme. 308:1-308:17 - Yannick Martin, Michel Page, Christophe Blanchet, Hidde de Jong:
WellInverter: a web application for the analysis of fluorescent reporter gene data. 309:1-309:18 - Chung-Yen Chen, Sen-Lin Tang, Seng-Cho Timothy Chou:
Taxonomy based performance metrics for evaluating taxonomic assignment methods. 310:1-310:11 - Mohammed AlQuraishi:
ProteinNet: a standardized data set for machine learning of protein structure. 311:1-311:10 - Bui Thi Mai Anh, Nick Papoulias, Serge Stinckwich, Mikal Ziane, Benjamin Roche:
The Kendrick modelling platform: language abstractions and tools for epidemiology. 312:1-312:13 - Ángela Casado, César Domínguez, Manuel García-Dominguez, Jónathan Heras, Adrián Inés, Eloy J. Mata, Vico Pascual:
CLoDSA: a tool for augmentation in classification, localization, detection, semantic segmentation and instance segmentation tasks. 323:1-323:14 - N. Ozlem Ozcan, Arzucan Özgür, Fikret Gürgen:
Statistical representation models for mutation information within genomic data. 324:1-324:13 - Joanna Roder, Carlos Oliveira, Lelia Net, Maxim Tsypin, Benjamin Linstid, Heinrich Roder:
A dropout-regularized classifier development approach optimized for precision medicine test discovery from omics data. 325:1-325:14 - Adil Al-Azzawi, Anes Ouadou, John J. Tanner, Jianlin Cheng:
AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images. 326:1-326:26 - Asif Zubair, I. Gary Rosen, Sergey V. Nuzhdin, Paul Marjoram:
Bayesian model selection for the Drosophila gap gene network. 327:1-327:12 - Eun-Youn Kim, Daniel A. Ashlock, Sung Ho Yoon:
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks. 328:1-328:13 - Hokuto Hirano, Kazuhiro Takemoto:
Difficulty in inferring microbial community structure based on co-occurrence network approaches. 329:1-329:14 - Ying Shen, Yaliang Li, Hai-Tao Zheng, Buzhou Tang, Min Yang:
Enhancing ontology-driven diagnostic reasoning with a symptom-dependency-aware Naïve Bayes classifier. 330:1-330:14 - Federico Marini, Harald Binder:
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components. 331:1-331:8 - Jiesi Luo, Wei Chen, Li Xue, Bin Tang:
Prediction of activity and specificity of CRISPR-Cpf1 using convolutional deep learning neural networks. 332:1-332:10 - Jiaxing Lin, Alexander B. Sibley, Ivo D. Shterev, Andrew Nixon, Federico Innocenti, Cliburn Chan, Kouros Owzar:
fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies. 333:1-333:11 - Courtney Schiffman, Lauren Petrick, Kelsi Perttula, Yukiko Yano, Henrik Carlsson, Todd Whitehead, Catherine Metayer, Josie Hayes, Stephen M. Rappaport, Sandrine Dudoit:
Filtering procedures for untargeted LC-MS metabolomics data. 334:1-334:10 - Daniel G. Piqué, Grasiella A. Andriani, Elaine Maggi, Samuel E. Zimmerman, John M. Greally, Cristina Montagna, Jessica Cara Mar:
Aneuvis: web-based exploration of numerical chromosomal variation in single cells. 336:1-336:10 - Stefano Teso, Luca Masera, Michelangelo Diligenti, Andrea Passerini:
Combining learning and constraints for genome-wide protein annotation. 338:1-338:14 - Michael C. Rendleman, John M. Buatti, Terry A. Braun, Brian J. Smith, Chibuzo Nwakama, Reinhard R. Beichel, Bartley Brown, Thomas L. Casavant:
Machine learning with the TCGA-HNSC dataset: improving usability by addressing inconsistency, sparsity, and high-dimensionality. 339:1-339:9 - Tongle Ma, Yongzhen Pei, Changguo Li, Meixia Zhu:
Periodicity and dosage optimization of an RNAi model in eukaryotes cells. 340:1-340:10 - Yanbu Guo, Weihua Li, Bingyi Wang, Huiqing Liu, Dongming Zhou:
DeepACLSTM: deep asymmetric convolutional long short-term memory neural models for protein secondary structure prediction. 341:1-341:12 - Manojkumar Kumaran, Umadevi Subramanian, Bharanidharan Devarajan:
Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data. 342:1-342:11 - Mi-Youn K. Brusniak, Hector Ramos, Bernard Lee, James M. Olson:
Laboratory information management software for engineered mini-protein therapeutic workflow. 343:1-343:10 - Xiaoshuang Liu, Zhenhe Yan, Chao Wu, Yang Yang, Xiaomin Li, Guangxin Zhang:
FastProNGS: fast preprocessing of next-generation sequencing reads. 345:1-345:6 - Qiao Ning, Miao Yu, Jinchao Ji, Zhiqiang Ma, Xiaowei Zhao:
Analysis and prediction of human acetylation using a cascade classifier based on support vector machine. 346:1-346:15 - Licheng Wang, Jingwen Suo, Yun Pan, Lixiang Li:
DDmap: a MATLAB package for the double digest problem using multiple genetic operators. 348:1-348:12 - Wei Chen, Toby Kenney, Joseph P. Bielawski, Hong Gu:
Testing adequacy for DNA substitution models. 349:1-349:16 - Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha:
Comparison of pathway analysis and constraint-based methods for cell factory design. 350:1-350:15 - Zengchao Mu, Ting Yu, Enfeng Qi, Juntao Liu, Guojun Li:
DCGR: feature extractions from protein sequences based on CGR via remodeling multiple information. 351:1-351:10 - Wenmin Zhang, Ben Jia, Chaochun Wei:
PaSS: a sequencing simulator for PacBio sequencing. 352:1-352:7 - Ying-Lian Gao, Zhen Cui, Jin-Xing Liu, Juan Wang, Chun-Hou Zheng:
NPCMF: Nearest Profile-based Collaborative Matrix Factorization method for predicting miRNA-disease associations. 353:1-353:10 - Kaining Hu, Kai Xu, Jing Wen, Bin Yi, Jinxiong Shen, Chaozhi Ma, Tingdong Fu, Yidan Ouyang, Jinxing Tu:
Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species. 354:1-354:20 - Bihai Zhao, Yulin Zhao, Xiaoxia Zhang, Zhihong Zhang, Fan Zhang, Lei Wang:
An iteration method for identifying yeast essential proteins from heterogeneous network. 355:1-355:13 - Marta B. Lopes, Sandra Casimiro, Susana Vinga:
Twiner: correlation-based regularization for identifying common cancer gene signatures. 356:1-356:15 - Marta B. Lopes, Sandra Casimiro, Susana Vinga:
Twiner: correlation-based regularization for identifying common cancer gene signatures. 356:1-356:15 - Rahul Shaw, C. Y. Maurice Cheung:
A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants. 357:1-357:11 - Roman Hornung, Marvin N. Wright:
Block Forests: random forests for blocks of clinical and omics covariate data. 358:1-358:17 - Matthew L. Hale, Ishwor Thapa, Dario Ghersi:
FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis. 359:1-359:8 - Tomás Vicar, Jan Balvan, Josef Jaros, Florian Jug, Radim Kolár, Michal Masarik, Jaromir Gumulec:
Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison. 360:1-360:25 - Leandro Gabriel Roser, Fernán Agüero, Daniel Oscar Sánchez:
FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files. 361:1-361:7 - Akio Miyao, Jianyu Song Kiyomiya, Keiko Iida, Koji Doi, Hiroshi Yasue:
Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data. 362:1-362:12 - Lennon Meléndez-Aranda, Ana Rebeca Jaloma-Cruz, Nina Pastor, Marina María de Jesús Romero-Prado:
In silico analysis of missense mutations in exons 1-5 of the F9 gene that cause hemophilia B. 363:1-363:13 - Ryan J. Eller, Sarath Chandra Janga, Susan Walsh:
Odyssey: a semi-automated pipeline for phasing, imputation, and analysis of genome-wide genetic data. 364:1-364:8 - Yi Li, Yanan Liu, Yiming Wu, Xudong Zhao:
JCD-DEA: a joint covariate detection tool for differential expression analysis on tumor expression profiles. 365:1-365:13 - Ruochen Yang, Xi Chen, Idoia Ochoa:
MassComp, a lossless compressor for mass spectrometry data. 368:1-368:10 - Sergii Domanskyi, Anthony Szedlak, Nathaniel T Hawkins, Jiayin Wang, Giovanni Paternostro, Carlo Piermarocchi:
Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters. 369:1-369:16 - Marina Esteban-Medina, María Peña-Chilet, Carlos Loucera, Joaquín Dopazo:
Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. 370:1-370:15 - Thomas W. McCarthy, Hsien-chao Chou, Volker P. Brendel:
SRAssembler: Selective Recursive local Assembly of homologous genomic regions. 371:1-371:13 - Ya-Chi Lin, Yueh-Chun Lee, Kai-Li Chang, Kuei-Yang Hsiao:
Analysis of common targets for circular RNAs. 372:1-372:6 - Congzhe Su, Jeffery D. Weir, Fei Zhang, Hao Yan, Teresa Wu:
ENTRNA: a framework to predict RNA foldability. 373:1-373:11 - Teresia M. Buza, Triza Tonui, Francesca Stomeo, Christian Tiambo, Robab Katani, Megan Schilling, Beatus Lyimo, Paul Gwakisa, Isabella M. Cattadori, Joram Buza, Vivek Kapur:
iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis. 374:1-374:18 - Aditya Sai, Nan Kong:
Exploring the information transmission properties of noise-induced dynamics: application to glioma differentiation. 375:1-375:11 - Christoph Ruttkies, Steffen Neumann, Stefan Posch:
Improving MetFrag with statistical learning of fragment annotations. 376:1-376:14 - Nguyen-Quoc-Khanh Le, Edward Kien Yee Yapp, Hui-Yuan Yeh:
ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins. 377:1-377:12 - Bie M. P. Verbist, Eva Adriaensen, Vikki Keersmaekers, Dea Putri, Marjolein Crabbe, Maarten Derks, Rytis Bagdziunas, Griet Laenen, Hans De Wolf:
Analyzing magnetic bead QuantiGene® Plex 2.0 gene expression data in high throughput mode using QGprofiler. 378:1-378:10 - Savvas Kinalis, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger:
Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data. 379:1-379:9 - Ryohei Eguchi, Naoaki Ono, Aki Hirai, Tetsuo Katsuragi, Satoshi Nakamura, Ming Huang, Md. Altaf-Ul-Amin, Shigehiko Kanaya:
Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks. 380:1-380:13 - Fortunato Bianconi, Chiara Antonini, Lorenzo Tomassoni, Paolo Valigi:
CRA toolbox: software package for conditional robustness analysis of cancer systems biology models in MATLAB. 385:1-385:19 - Han Yu, Rachael Hageman Blair:
Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer's disease. 386:1-386:12 - Vincent Demolombe, Alexandre G. de Brevern, Liza Figueredo Felicori, Christophe Nguyen, Ricardo Andrez Machado de Avila, Lionel Valera, Bénédicte Jardin-Watelet, Géraldine Lavigne, Aurélien Lebreton, Franck Molina, Violaine Moreau:
PEPOP 2.0: new approaches to mimic non-continuous epitopes. 387:1-387:14 - Sam Tracy, Guo-Cheng Yuan, Ruben Dries:
RESCUE: imputing dropout events in single-cell RNA-sequencing data. 388:1-388:11 - Eric T. Dawson, Sarah Wagner, David Roberson, Meredith Yeager, Joseph Boland, Erik Garrison, Stephen J. Chanock, Mark Schiffman, Tina Raine-Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello, Richard Durbin:
Viral coinfection analysis using a MinHash toolkit. 389:1-389:10 - Ruijie Song, Murat Acar:
Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness. 391:1-391:14 - Bruno Thiago de Lima Nichio, Aryel Marlus Repula de Oliveira, Camilla Reginatto de Pierri, Leticia Graziela Costa Santos, Alexandre Quadros Lejambre, Ricardo Assunção Vialle, Nilson Antônio da Rocha Coimbra, Dieval Guizelini, Jeroniza Nunes Marchaukoski, Fábio de Oliveira Pedrosa, Roberto Tadeu Raittz:
RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets. 392:1-392:7 - Emmy Borgmästars, Hendrik A. de Weerd, Zelmina Lubovac-Pilav, Malin Sund:
miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer. 393:1-393:17 - Anjali Silva, Steven J. Rothstein, Paul D. McNicholas, Sanjeena Subedi:
A multivariate Poisson-log normal mixture model for clustering transcriptome sequencing data. 394:1-394:11 - Pascal Dolejsch, Helge Hass, Jens Timmer:
Extensions of ℓ 1 regularization increase detection specificity for cell-type specific parameters in dynamic models. 395:1-395:13 - Jingwen Yu, Zhanwei Xuan, Xiang Feng, Quan Zou, Lei Wang:
A novel collaborative filtering model for LncRNA-disease association prediction based on the Naïve Bayesian classifier. 396:1-396:13 - Chuang Li, Kenli Li, Keqin Li, Feng Lin:
MCtandem: an efficient tool for large-scale peptide identification on many integrated core (MIC) architecture. 397:1-397:13 - Éva Csosz, Ferenc Tóth, Mohamed Mahdi, George Tsaprailis, Miklós Emri, József Tozsér:
Analysis of networks of host proteins in the early time points following HIV transduction. 398:1-398:18 - Suzanne M. Paley, Peter D. Karp:
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database. 399:1-399:13 - Linus Scheibenreif, Maria Littmann, Christine A. Orengo, Burkhard Rost:
FunFam protein families improve residue level molecular function prediction. 400:1-400:9 - Ge Liu, Haoyang Zeng, David K. Gifford:
Visualizing complex feature interactions and feature sharing in genomic deep neural networks. 401:1-401:14 - Ben C. Stöver, Sarah Wiechers, Kai F. Müller:
JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface. 402:1-402:15 - Jinghang Gu, Fuqing Sun, Longhua Qian, Guodong Zhou:
Chemical-induced disease relation extraction via attention-based distant supervision. 403:1-403:14 - Hailin Chen, Zuping Zhang, Dayi Feng:
Prediction and interpretation of miRNA-disease associations based on miRNA target genes using canonical correlation analysis. 404:1-404:8 - Grzegorz M. Boratyn, Jean Thierry-Mieg, Danielle Thierry-Mieg, Ben Busby, Thomas L. Madden:
Magic-BLAST, an accurate RNA-seq aligner for long and short reads. 405:1-405:19 - Rebecca C. Jackson, James P. Balhoff, Eric Douglass, Nomi L. Harris, Christopher J. Mungall, James A. Overton:
ROBOT: A Tool for Automating Ontology Workflows. 407:1-407:10 - Pengfei Liu, Hongjian Li, Shuai Li, Kwong-Sak Leung:
Improving prediction of phenotypic drug response on cancer cell lines using deep convolutional network. 408:1-408:14 - Junhui Wang, Michael Gribskov:
IRESpy: an XGBoost model for prediction of internal ribosome entry sites. 409:1-409:15 - Elies Ramon, Lluís A. Belanche Muñoz, Miguel Pérez-Enciso:
HIV drug resistance prediction with weighted categorical kernel functions. 410:1-410:13 - Richard Border, Stephen Becker:
Stochastic Lanczos estimation of genomic variance components for linear mixed-effects models. 411:1-411:16 - Wei Zhou, Xiaojuan He, Ziyi Chen, Danping Fan, Yonghua Wang, Hui Feng, Ge Zhang, Aiping Lu, Lianbo Xiao:
LncRNA HOTAIR-mediated Wnt/β-catenin network modeling to predict and validate therapeutic targets for cartilage damage. 412:1-412:13 - Marco Russo, Bruno De Lucca, Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi, Giovanni Capranico:
DROPA: DRIP-seq optimized peak annotator. 414:1-414:7 - Geonhee Lee, Chihyun Park, Jaegyoon Ahn:
Novel deep learning model for more accurate prediction of drug-drug interaction effects. 415:1-415:8 - T. J. M. Kuijpers, J. E. J. Wolters, Jos C. S. Kleinjans, Danyel G. J. Jennen:
DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks. 417:1-417:10 - Shintaro Katayama, Tiina Skoog, Cilla Söderhäll, Elisabet Einarsdottir, Kaarel Krjutskov, Juha Kere:
Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods. 418:1-418:9 - Mindaugas Margelevicius:
Estimating statistical significance of local protein profile-profile alignments. 419:1-419:13 - Carlos J. Rivera-Rivera, Juan I. Montoya-Burgos:
LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference. 420:1-420:4 - Mohamed K. Gunady, Stephen M. Mount, Héctor Corrada Bravo:
Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis. 421:1-421:19 - Paolo Perlasca, Marco Frasca, Cheick Tidiane Ba, Marco Notaro, Alessandro Petrini, Elena Casiraghi, Giuliano Grossi, Jessica Gliozzo, Giorgio Valentini, Marco Mesiti:
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction. 422:1-422:19 - Xinxing Yang, Ibrahim Zamit, Yu Liu, Jieyue He:
Additional Neural Matrix Factorization model for computational drug repositioning. 423:1-423:11 - Sree K. Chanumolu, Mustafa Albahrani, Hasan H. Otu:
FQStat: a parallel architecture for very high-speed assessment of sequencing quality metrics. 424:1-424:10 - Sam Henry, Bridget T. McInnes:
Indirect association and ranking hypotheses for literature based discovery. 425:1-425:19 - Christopher M. Wilson, Kaiqiao Li, Xiaoqing Yu, Pei Fen Kuan, Xuefeng Wang:
Multiple-kernel learning for genomic data mining and prediction. 426:1-426:7 - Xi Wang, Jiagao Lyu, Li Dong, Ke Xu:
Multitask learning for biomedical named entity recognition with cross-sharing structure. 427:1-427:13 - Pascal David Johann, Natalie Jäger, Stefan M. Pfister, Martin Sill:
RF_Purify: a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression. 428:1-428:9 - Jurica Seva, David Luis Wiegandt, Julian Goetze, Mario Lamping, Damian Rieke, Reinhold Schaefer, Patrick Jähnichen, Madeleine Kittner, Steffen Pallarz, Johannes Starlinger, Ulrich Keilholz, Ulf Leser:
VIST - a Variant-Information Search Tool for precision oncology. 429:1-429:11 - Yipei Wang, Xingyu Fan, Luoxin Chen, Eric I-Chao Chang, Sophia Ananiadou, Junichi Tsujii, Yan Xu:
Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries. 430:1-430:11 - Blythe S. Moreland, Kenji M. Oman, Ralf Bundschuh:
A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction. 431:1-431:15 - Janet C. Siebert, Charles Preston Neff, Jennifer M. Schneider, Emilie H. Regner, Neha Ohri, Kristine A. Kuhn, Brent E. Palmer, Catherine A. Lozupone, Carsten Görg:
VOLARE: visual analysis of disease-associated microbiome-immune system interplay. 432:1-432:13 - Arezo Torang, Paraag Gupta, David J. Klinke II:
An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets. 433:1-433:15 - Claus Weinholdt, Henri Wichmann, Johanna Kotrba, David H. Ardell, Matthias Kappler, Alexander W. Eckert, Dirk Vordermark, Ivo Grosse:
Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line. 434:1-434:14 - Joëlle Barido-Sottani, Samuel D. Chapman, Evsey Kosman, Arcady R. Mushegian:
Measuring similarity between gene interaction profiles. 435:1-435:13 - Hamid Bagheri, Usha Muppirala, Rick E. Masonbrink, Andrew J. Severin, Hridesh Rajan:
Shared data science infrastructure for genomics data. 436:1-436:13 - Wei Zhou, Karel K. M. Koudijs, Stefan Böhringer:
Influence of batch effect correction methods on drug induced differential gene expression profiles. 437:1-437:14 - Hyunwoo Kim, Sangjeong Lee, Heejin Park:
Target-small decoy search strategy for false discovery rate estimation. 438:1-438:6 - Bui Thi Mai Anh, Nick Papoulias, Serge Stinckwich, Mikal Ziane, Benjamin Roche:
Correction to: The Kendrick modelling platform: language abstractions and tools for epidemiology. 439:1-439:2 - Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun S. Seetharam, Eve Syrkin Wurtele:
fagin: synteny-based phylostratigraphy and finer classification of young genes. 440:1-440:14 - Alex Sánchez-Pla, Miquel Salicru, Jordi Ocana:
An equivalence approach to the integrative analysis of feature lists. 441:1-441:13 - Markos Antonopoulos, Dimitra D. Dionysiou, Georgios S. Stamatakos, Nikolaos K. Uzunoglu:
Three-dimensional tumor growth in time-varying chemical fields: a modeling framework and theoretical study. 442:1-442:36 - Yongchun Lü, Xiangrui Zeng, Xiaofang Zhao, Shirui Li, Hua Li, Xin Gao, Min Xu:
Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization. 443:1-443:13 - Yang Guo, Zhiman Zhong, Chen Yang, Jiangfeng Hu, Yaling Jiang, Zizhen Liang, Hui Gao, Jianxiao Liu:
Epi-GTBN: an approach of epistasis mining based on genetic Tabu algorithm and Bayesian network. 444:1-444:18 - Yuexiang Li, Xinpeng Xie, Linlin Shen, Shaoxiong Liu:
Reverse active learning based atrous DenseNet for pathological image classification. 445:1-445:15 - Lyuba V. Bozhilova, Alan Whitmore, Jonny Wray, Gesine Reinert, Charlotte M. Deane:
Measuring rank robustness in scored protein interaction networks. 446:1-446:14 - Tobias B. Alter, Birgitta E. Ebert:
Determination of growth-coupling strategies and their underlying principles. 447:1-447:17 - Eric Czech, Bülent Arman Aksoy, Pinar Aksoy, Jeff Hammerbacher:
Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging. 448:1-448:13 - Huimin Lei, Wenxu Liu, Jiarui Si, Ju Wang, Tao Zhang:
Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma. 449:1-449:13 - Franziska Schumann, Eric Blanc, Clemens Messerschmidt, Thomas Blankenstein, Antonia Busse, Dieter Beule:
SigsPack, a package for cancer mutational signatures. 450:1-450:9 - Christian Carsten Sachs, Joachim Koepff, Wolfgang Wiechert, Alexander Grünberger, Katharina Nöh:
mycelyso - high-throughput analysis of Streptomyces mycelium live cell imaging data. 452:1-452:7 - Emiliano Pereira-Flores, Frank Oliver Glöckner, Antonio Fernandez-Guerra:
Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. 453:1-453:13 - Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Días:
SamPler - a novel method for selecting parameters for gene functional annotation routines. 454:1-454:11 - Ngaam J. Cheung, Wookyung Yu:
Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico. 455:1-455:11 - Chuanyan Wu, Rui Gao, Yusen Zhang, Yang De Marinis:
PTPD: predicting therapeutic peptides by deep learning and word2vec. 456:1-456:8 - Dewan M. Sarwar, Reza Kalbasi, John H. Gennari, Brian E. Carlson, Maxwell Lewis Neal, Bernard de Bono, Koray Atalag, Peter J. Hunter, David P. Nickerson:
Model annotation and discovery with the Physiome Model Repository. 457:1-457:10 - Lindsay Rutter, Adrienne N. Moran Lauter, Michelle A. Graham, Dianne Cook:
Visualization methods for differential expression analysis. 458:1-458:31 - Yifei Chen:
Multiple-level biomedical event trigger recognition with transfer learning. 459:1-459:15 - Yuexi Gu, Jian Zu, Yu Li:
A novel evolutionary model for constructing gene coexpression networks with comprehensive features. 460:1-460:20 - Leanne S. Whitmore, Bernard Nguyen, Ali Pinar, Anthe George, Corey M. Hudson:
RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms. 461:1-461:14 - Mohan Timilsina, Haixuan Yang, Ratnesh Sahay, Dietrich Rebholz-Schuhmann:
Predicting links between tumor samples and genes using 2-Layered graph based diffusion approach. 462:1-462:20 - Anh Nhat Tran, Alex M. Dussaq, Timothy Kennell Jr., Christopher D. Willey, Anita B. Hjelmeland:
HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data. 463:1-463:11 - Aljaz Gaber, Gregor Guncar, Miha Pavsic:
Proper evaluation of chemical cross-linking-based spatial restraints improves the precision of modeling homo-oligomeric protein complexes. 464:1-464:12 - Paul Müller, Shada Abuhattum, Stephanie Möllmert, Elke Ulbricht, Anna V. Taubenberger, Jochen R. Guck:
nanite: using machine learning to assess the quality of atomic force microscopy-enabled nano-indentation data. 465:1-465:9 - Patrick M. Staunton, Aleksandra A. Miranda-CasoLuengo, Brendan J. Loftus, Isobel Claire Gormley:
BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus. 466:1-466:21 - Janet Wang, Thomas LaFramboise:
CytoConverter: a web-based tool to convert karyotypes to genomic coordinates. 467:1-467:6 - Yuchong Gong, Yanqing Niu, Wen Zhang, Xiaohong Li:
A network embedding-based multiple information integration method for the MiRNA-disease association prediction. 468:1-468:13 - Jianghui Wen, Yeshu Liu, Yu Shi, Haoran Huang, Bing Deng, Xinping Xiao:
A classification model for lncRNA and mRNA based on k-mers and a convolutional neural network. 469:1-469:14 - Marie Postel, Alice Karam, Guillaume Pézeron, Sylvie Schneider-Maunoury, Frédérique Clément:
A multiscale mathematical model of cell dynamics during neurogenesis in the mouse cerebral cortex. 470:1-470:24 - Rongquan Wang, Guixia Liu, Caixia Wang:
Identifying protein complexes based on an edge weight algorithm and core-attachment structure. 471:1-471:20 - Fuyong Xing, Yuanpu Xie, Xiaoshuang Shi, Pingjun Chen, Zizhao Zhang, Lin Yang:
Towards pixel-to-pixel deep nucleus detection in microscopy images. 472:1-472:16 - Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding:
HH-suite3 for fast remote homology detection and deep protein annotation. 473:1-473:15 - Andrea Degl'Innocenti, Gabriella Meloni, Barbara Mazzolai, Gianni Ciofani:
A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers. 474:1-474:16 - Mingjian Jiang, Zhen Li, Yujie Bian, Zhiqiang Wei:
A novel protein descriptor for the prediction of drug binding sites. 478:1-478:13 - Tongxuan Zhang, Hongfei Lin, Yuqi Ren, Liang Yang, Bo Xu, Zhihao Yang, Jian Wang, Yijia Zhang:
Adverse drug reaction detection via a multihop self-attention mechanism. 479:1-479:11 - Alejandro Lopez Rincon, Marlet Martínez-Archundia, Gustavo U. Martinez-Ruiz, Alexander Schönhuth, Alberto Paolo Tonda:
Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection. 480:1-480:17 - Felipe Kenji Nakano, Mathias Lietaert, Celine Vens:
Machine learning for discovering missing or wrong protein function annotations - A comparison using updated benchmark datasets. 485:1-485:32 - Bruce D. Parrello, Rory Butler, Philippe Chlenski, Robert Olson, Jamie C. Overbeek, Gordon D. Pusch, Veronika Vonstein, Ross A. Overbeek:
A machine learning-based service for estimating quality of genomes using PATRIC. 486:1-486:9 - Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin:
CAGEfightR: analysis of 5′-end data using R/Bioconductor. 487:1-487:13 - Chih-Hao Fang, Nawanol Theera-Ampornpunt, Michael A. Roth, Ananth Grama, Somali Chaterji:
AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU. 488:1-488:17 - Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette, Bjoern Peters:
Benchmark datasets of immune receptor-epitope structural complexes. 490:1-490:7 - Josefa Díaz Álvarez, Jordi A. Matias-Guiu, María Nieves Cabrera-Martín, José L. Risco-Martín, José L. Ayala:
An application of machine learning with feature selection to improve diagnosis and classification of neurodegenerative disorders. 491:1-491:12 - Marietta Kokla, Jyrki Virtanen, Marjukka Kolehmainen, Jussi Paananen, Kati Hanhineva:
Random forest-based imputation outperforms other methods for imputing LC-MS metabolomics data: a comparative study. 492:1-492:11 - Michael D. Linderman, Davin Chia, Forrest Wallace, Frank A. Nothaft:
DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark. 493:1-493:8 - Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt, Martin Hofmann-Apitius:
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm. 494:1-494:8 - James M. Holt, Brandon M. Wilk, Camille L. Birch, Donna M. Brown, Manavalan Gajapathy, Alexander C. Moss, Nadiya Sosonkina, Melissa A. Wilk, Julie A. Anderson, Jeremy M. Harris, Jacob M. Kelly, Fariba Shaterferdosian, Angelina E. Uno-Antonison, Arthur Weborg, Elizabeth A. Worthey:
VarSight: prioritizing clinically reported variants with binary classification algorithms. 496:1-496:10 - Yiren Jian, Xiaonan Wang, Jaidi Qiu, Huiwen Wang, Zhichao Liu, Yunjie Zhao, Chen Zeng:
DIRECT: RNA contact predictions by integrating structural patterns. 497:1-497:12 - Daniel Svensson, Rickard Sjögren, David Sundell, Andreas Sjödin, Johan Trygg:
doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows. 498:1-498:13 - Adèle Weber Zendrera, Nataliya Sokolovska, Hédi Soula:
Robust structure measures of metabolic networks that predict prokaryotic optimal growth temperature. 499:1-499:13 - Markos Antonopoulos, Dimitra D. Dionysiou, Georgios S. Stamatakos, Nikolaos K. Uzunoglu:
Publisher Correction to: Three-dimensional tumor growth in time-varying chemical fields: a modeling framework and theoretical study. 500:1-500:2 - Yuntong Li, Teresa W.-M. Fan, Andrew N. Lane, Woo-Young Kang, Susanne M. Arnold, Arnold J. Stromberg, Chi Wang, Li Chen:
SDA: a semi-parametric differential abundance analysis method for metabolomics and proteomics data. 501:1-501:10 - Fuyong Xing, Yuanpu Xie, Xiaoshuang Shi, Pingjun Chen, Zizhao Zhang, Lin Yang:
Correction to: Towards pixel-to-pixel deep nucleus detection in microscopy images. 509:1 - Kipoong Kim, Hokeun Sun:
Incorporating genetic networks into case-control association studies with high-dimensional DNA methylation data. 510:1-510:15 - Asma Ben Abacha, Dina Demner-Fushman:
A question-entailment approach to question answering. 511:1-511:23 - Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki:
RNA 3D structure prediction guided by independent folding of homologous sequences. 512:1-512:15 - Thomas Lemmin, Cinque S. Soto:
Glycosylator: a Python framework for the rapid modeling of glycans. 513:1-513:7 - David F. Nettleton, Dimitrios Katsantonis, Argyris Kalaitzidis, Natasa Sarafijanovic-Djukic, Pau Puigdollers, Roberto Confalonieri:
Predicting rice blast disease: machine learning versus process-based models. 514:1-514:16 - Lei Wang, Juhua Zhang:
Prediction of sgRNA on-target activity in bacteria by deep learning. 517:1-517:14 - Jon Mitchell Ambler, Shandukani Mulaudzi, Nicola J. Mulder:
GenGraph: a python module for the simple generation and manipulation of genome graphs. 519:1-519:8 - Nauman Ahmed, Jonathan Levy, Shanshan Ren, Hamid Mushtaq, Koen Bertels, Zaid Al-Ars:
GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data. 520:1-520:20 - Sunyoung Kwon, Ho Bae, Jeonghee Jo, Sungroh Yoon:
Comprehensive ensemble in QSAR prediction for drug discovery. 521:1-521:12 - Fan Yang, Yang Liu, Yanbin Wang, Zhijian Yin, Zhen Yang:
MIC_Locator: a novel image-based protein subcellular location multi-label prediction model based on multi-scale monogenic signal representation and intensity encoding strategy. 522:1-522:21 - Emma Persson, Mateusz Kaduk, Sofia K. Forslund, Erik L. L. Sonnhammer:
Domainoid: domain-oriented orthology inference. 523:1-523:12 - Huan Jin, Hunter N. B. Moseley:
Moiety modeling framework for deriving moiety abundances from mass spectrometry measured isotopologues. 524:1-524:12 - Konstantinos Pliakos, Celine Vens:
Network inference with ensembles of bi-clustering trees. 525:1-525:12 - Alan R. Rogers:
Legofit: estimating population history from genetic data. 526:1-526:10 - Jing Xu, Peng Wu, Yuehui Chen, Qingfang Meng, Hussain Dawood, Hassan Dawood:
A hierarchical integration deep flexible neural forest framework for cancer subtype classification by integrating multi-omics data. 527:1-527:11 - Rodolfo S. Allendes Osorio, Lokesh P. Tripathi, Kenji Mizuguchi:
CLINE: a web-tool for the comparison of biological dendrogram structures. 528:1-528:12 - Hao He, Jiaxiang Zhao, Guiling Sun:
Computational prediction of MoRFs based on protein sequences and minimax probability machine. 529:1-529:11 - Jing Xie, Tieming Ji, Marco A. R. Ferreira, Yahan Li, Bhaumik N. Patel, Rocio M. Rivera:
Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model. 530:1-530:13 - Alejandro Saettone, Marcelo Ponce, Syed Nabeel-Shah, Jeffrey Fillingham:
RACS: rapid analysis of ChIP-Seq data for contig based genomes. 533:1-533:17 - Andre Lamurias, Pedro Ruas, Francisco M. Couto:
PPR-SSM: personalized PageRank and semantic similarity measures for entity linking. 534:1-534:12 - Gregory M. Parkes, Mahesan Niranjan:
Uncovering extensive post-translation regulation during human cell cycle progression by integrative multi-'omics analysis. 536:1-536:13 - Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. 537:1-537:11 - Junwei Luo, Mengna Lyu, Ranran Chen, Xiaohong Zhang, Huimin Luo, Chaokun Yan:
SLR: a scaffolding algorithm based on long reads and contig classification. 539:1-539:11 - Ziad Al Bkhetan, Justin Zobel, Adam Kowalczyk, Karin Verspoor, Benjamin Goudey:
Exploring effective approaches for haplotype block phasing. 540:1-540:14 - Yahui Long, Jiawei Luo:
WMGHMDA: a novel weighted meta-graph-based model for predicting human microbe-disease association on heterogeneous information network. 541:1-541:18 - Elmar Bucher, Cheryl J. Claunch, Derrick Hee, Rebecca L. Smith, Kaylyn Devlin, Wallace Thompson, James E. Korkola, Laura M. Heiser:
Annot: a Django-based sample, reagent, and experiment metadata tracking system. 542:1-542:6 - Marcelo P. Segura-Lepe, Hector C. Keun, Timothy M. D. Ebbels:
Predictive modelling using pathway scores: robustness and significance of pathway collections. 543:1-543:11 - Jiao Chen, Jiayu Shang, Jianrong Wang, Yanni Sun:
A binning tool to reconstruct viral haplotypes from assembled contigs. 544:1-544:13 - Valerio Licursi, Federica Conte, Giulia Fiscon, Paola Paci:
MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis. 545:1-545:10 - Jing Ma, Ali Shojaie, George Michailidis:
A comparative study of topology-based pathway enrichment analysis methods. 546:1-546:14 - Toshiyuki T. Yokoyama, Yoshitaka Sakamoto, Masahide Seki, Yutaka Suzuki, Masahiro Kasahara:
MoMI-G: modular multi-scale integrated genome graph browser. 548:1-548:14 - Tianjun Li, Long Chen, Min Gan:
Quality control of imbalanced mass spectra from isotopic labeling experiments. 549:1-549:12 - Maryam Nazarieh, Hema Sekhar Reddy Rajula, Volkhard Helms:
Topology Consistency of Disease-specific Differential Co-regulatory Networks. 550:1-550:10 - Simonas Marcisauskas, Boyang Ji, Jens Nielsen:
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. 551:1-551:9 - Nathan LaPierre, Rob Egan, Wei Wang, Zhong Wang:
De novo Nanopore read quality improvement using deep learning. 552:1-552:9 - Fang-Dong Li, Wei Tong, En-Hua Xia, Chao-Ling Wei:
Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species. 553:1-553:11 - Danze Chen, Fan Zhang, Qianqian Zhao, Jianzhen Xu:
OmicsARules: a R package for integration of multi-omics datasets via association rules mining. 554:1-554:8 - Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya, Colin B. Begg:
An EM algorithm to improve the estimation of the probability of clonal relatedness of pairs of tumors in cancer patients. 555:1-555:8 - Yifan Jiang, Yao Jiang, Sheng Wang, Qin Zhang, Xiangdong Ding:
Optimal sequencing depth design for whole genome re-sequencing in pigs. 556:1-556:12 - Jacob R Heldenbrand, Saurabh Baheti, Matthew A. Bockol, Travis M. Drucker, Steven N. Hart, Matthew E. Hudson, Ravishankar K. Iyer, Michael Kalmbach, Katherine Irene Kendig, Eric W. Klee, Nathan R Mattson, Eric D. Wieben, Mathieu Wiepert, Derek E. Wildman, Liudmila S. Mainzer:
Recommendations for performance optimizations when using GATK3.8 and GATK4. 557:1-557:9 - Mario Stanke, Willy Bruhn, Felix Becker, Katharina Jasmin Hoff:
VARUS: sampling complementary RNA reads from the sequence read archive. 558:1-558:7 - Mengmeng Zhu, Michael Gribskov:
MiPepid: MicroPeptide identification tool using machine learning. 559:1-559:11 - Luca Nanni, Pietro Pinoli, Arif Canakoglu, Stefano Ceri:
PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets. 560:1-560:11 - Tobias Paczian, William L. Trimble, Wolfgang Gerlach, Travis Harrison, Andreas Wilke, Folker Meyer:
The MG-RAST API explorer: an on-ramp for RESTful query composition. 561:1-561:8 - Matús Medo, Daniel M. Aebersold, Michaela Medová:
ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data. 563:1-563:12 - Simon Dirmeier, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel:
PyBDA: a command line tool for automated analysis of big biological data sets. 564:1-564:6 - Milagros Marín, Francisco José Esteban, Hilario Ramírez-Rodrigo, Eduardo Ros, María José Saéz-Lara:
An integrative methodology based on protein-protein interaction networks for identification and functional annotation of disease-relevant genes applied to channelopathies. 565:1-565:13 - Alexander Davis, Ruli Gao, Nicholas E. Navin:
SCOPIT: sample size calculations for single-cell sequencing experiments. 566:1-566:6 - Yonghyun Nam, Dong-Gi Lee, Sunjoo Bang, Ju Han Kim, Jae-Hoon Kim, Hyunjung Shin:
The translational network for metabolic disease - from protein interaction to disease co-occurrence. 576:1-576:12 - Mahroo Moridi, Marzieh Ghadirinia, Ali Sharifi-Zarchi, Fatemeh Zare-Mirakabad:
The assessment of efficient representation of drug features using deep learning for drug repositioning. 577:1-577:11 - Yunyun Dong, Wenkai Yang, Jiawen Wang, Juanjuan Zhao, Yan Qiang, Zijuan Zhao, Ntikurako Guy-Fernand Kazihise, Yanfen Cui, Xiaotong Yang, Siyuan Liu:
MLW-gcForest: a multi-weighted gcForest model towards the staging of lung adenocarcinoma based on multi-modal genetic data. 578:1-578:14 - Daniel J. Giguere, Jean M. Macklaim, Brandon Y. Lieng, Gregory B. Gloor:
omicplotR: visualizing omic datasets as compositions. 580:1-580:5 - Attayeb Mohsen, Jonguk Park, Yi-An Chen, Hitoshi Kawashima, Kenji Mizuguchi:
Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks. 581:1-581:10 - Stanislav Listopad, Trina M. Norden-Krichmar:
A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons. 595:1-595:10 - Nauman Ahmed, Jonathan Levy, Shanshan Ren, Hamid Mushtaq, Koen Bertels, Zaid Al-Ars:
Correction to: GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data. 597:1-597:4 - Hong Qin:
Estimating network changes from lifespan measurements using a parsimonious gene network model of cellular aging. 599:1-599:10 - Bhusan K. Kuntal, Anirban Dutta, Sharmila S. Mande:
Correction to: CompNet: a GUI based tool for comparison of multiple biological interaction networks. 600:1 - Ling Zhang, Ishwor Thapa, Christian Haas, Dhundy Bastola:
Multiplatform biomarker identification using a data-driven approach enables single-sample classification. 601:1-601:13 - Xiaochuan Wang, Chen Li, Fuyi Li, Varun S. Sharma, Jiangning Song, Geoffrey I. Webb:
SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. 602:1-602:12 - Siddharth Subramaniyam, Michael A. DeJesus, Anisha Zaveri, Clare M. Smith, Richard Baker, Sabine Ehrt, Dirk Schnappinger, Christopher M. Sassetti, Thomas R. Ioerger:
Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. 603:1-603:15 - Mehdi Mirzaie:
Identification of native protein structures captured by principal interactions. 604:1-604:10 - Till Köster, Philipp Henning, Adelinde M. Uhrmacher:
Potential based, spatial simulation of dynamically nested particles. 607:1-607:16 - Russul Alanni, Jingyu Hou, Hasseeb Azzawi, Yong Xiang:
Deep gene selection method to select genes from microarray datasets for cancer classification. 608:1-608:15 - Jiale Liu, Xinqi Gong:
Attention mechanism enhanced LSTM with residual architecture and its application for protein-protein interaction residue pairs prediction. 609:1-609:11 - Christopher Grace, Martin Farrall, Hugh Watkins, Anuj Goel:
Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers. 610:1-610:5 - Yuanjie Liu, Jianhan Lin:
A general-purpose signal processing algorithm for biological profiles using only first-order derivative information. 611:1-611:17 - Ross Mawhorter, Ran Libeskind-Hadas:
Hierarchical clustering of maximum parsimony reconciliations. 612:1-612:12 - M. Shaffer, K. Thurimella, Kevin Quinn, K. Doenges, X. Zhang, S. Bokatzian, Nichole Reisdorph, Catherine A. Lozupone:
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data. 614:1-614:11 - Yaman Arkun:
Detection of biological switches using the method of Gröebner bases. 615:1-615:16 - Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. 616:1-616:5 - Huiwen Wang, Jiadi Qiu, Haoquan Liu, Ying Xu, Ya Jia, Yunjie Zhao:
HKPocket: human kinase pocket database for drug design. 617:1-617:11 - Olalekan Agbolade, Azree Nazri, Razali Yaakob, Abdul Azim Abdul Ghani, Yoke Kqueen Cheah:
3-Dimensional facial expression recognition in human using multi-points warping. 619 - Menghan Wang, Tianxin Yu, Jinpeng Liu, Li Chen, Arnold J. Stromberg, John L. Villano, Susanne M. Arnold, Chunming Liu, Chi Wang:
A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis. 620 - Hatice Akarsu, Lisandra Aguilar-Bultet, Laurent Falquet:
deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes. 621 - Dengju Yao, Xiaojuan Zhan, Chee-Keong Kwoh:
An improved random forest-based computational model for predicting novel miRNA-disease associations. 624 - Vincent Branders, Pierre Schaus, Pierre Dupont:
Identifying gene-specific subgroups: an alternative to biclustering. 625 - Jiechen Li, Xueyong Li, Xiang Feng, Bing Wang, Bihai Zhao, Lei Wang:
A novel target convergence set based random walk with restart for prediction of potential LncRNA-disease associations. 626 - Amarin Jettakul, Duangdao Wichadakul, Peerapon Vateekul:
Relation extraction between bacteria and biotopes from biomedical texts with attention mechanisms and domain-specific contextual representations. 627 - Alexander M. Sevy, Cinque S. Soto, Robin G. Bombardi, Jens Meiler, James E. Crowe Jr.:
Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures. 629 - Liyuan Guo, Wei Lin, Yidan Zhang, Wenhan Li, Jing Wang:
BEST: a web server for brain expression Spatio-temporal pattern analysis. 632 - Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler, Susann Müller:
flowEMMi: an automated model-based clustering tool for microbial cytometric data. 643 - Hui Liu, Wenhao Zhang, Lixia Nie, Xiancheng Ding, Judong Luo, Ling Zou:
Predicting effective drug combinations using gradient tree boosting based on features extracted from drug-protein heterogeneous network. 645 - Benjamin Ulfenborg:
Vertical and horizontal integration of multi-omics data with miodin. 649 - Elham Khodayari Moez, Morteza Hajihosseini, Jeffrey L. Andrews, Irina Dinu:
Longitudinal linear combination test for gene set analysis. 650 - Michael Mayers, Tong Shu Li, Núria Queralt-Rosinach, Andrew I. Su:
Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network. 653 - Louis Ranjard, Thomas K. F. Wong, Allen G. Rodrigo:
Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage. 654 - Martin Palazzo, Pierre Beauseroy, Patricio Yankilevich:
A pan-cancer somatic mutation embedding using autoencoders. 655 - Iñigo Prada-Luengo, Anders Krogh, Lasse Maretty, Birgitte Regenberg:
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. 663 - Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor, Jörg Hackermüller:
uap: reproducible and robust HTS data analysis. 664 - Lei Cai, Yufeng Wu, Jingyang Gao:
DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network. 665 - Guangyao Zhou, Jackson Loper, Stuart Geman:
Base-pair ambiguity and the kinetics of RNA folding. 666 - Javier De Velasco Oriol, Edgar E. Vallejo-Clemente, Karol Estrada, José Gerardo Tamez-Peña, Alzheimer's Disease Neuroimaging Initiative:
Benchmarking machine learning models for late-onset alzheimer's disease prediction from genomic data. 709 - Chandler Gatenbee, Ryan O. Schenck, Rafael R. Bravo, Alexander R. A. Anderson:
EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data. 710 - Jiajin Chen, Ruyang Zhang, Xuesi Dong, Lijuan Lin, Ying Zhu, Jieyu He, David C. Christiani, Yongyue Wei, Feng Chen:
shinyBN: an online application for interactive Bayesian network inference and visualization. 711 - Jacob R Heldenbrand, Saurabh Baheti, Matthew A. Bockol, Travis M. Drucker, Steven N. Hart, Matthew E. Hudson, Ravishankar K. Iyer, Michael Kalmbach, Katherine Irene Kendig, Eric W. Klee, Nathan R Mattson, Eric D. Wieben, Mathieu Wiepert, Derek E. Wildman, Liudmila S. Mainzer:
Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4. 722 - Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes, Burkhard Rost:
Modeling aspects of the language of life through transfer-learning protein sequences. 723 - Chunhui Liu, Xingyu Fan, Zhizhi Guo, Zhongjun Mo, Eric I-Chao Chang, Yan Xu:
Wound area measurement with 3D transformation and smartphone images. 724 - Ricardo Ramirez, Allen Michael Herrera, Joshua Ramirez, Chunjiang Qian, David W. Melton, Paula K. Shireman, Yu-Fang Jin:
Deriving a Boolean dynamics to reveal macrophage activation with in vitro temporal cytokine expression profiles. 725 - Remzi Celebi, Hüseyin Uyar, Erkan Yasar, Özgür Gümüs, Oguz Dikenelli, Michel Dumontier:
Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings. 726 - Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost:
Correction to: Detailed prediction of protein sub-nuclear localization. 727 - Kohei Amano, Tsubasa Matsumoto, Kenichi Tanaka, Kimito Funatsu, Masaaki Kotera:
Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. 728 - Charith B. Karunarathna, Jinko Graham:
perfectphyloR: An R package for reconstructing perfect phylogenies. 729 - Xin Su, Jing Xu, Yanbin Yin, Xiongwen Quan, Han Zhang:
Antimicrobial peptide identification using multi-scale convolutional network. 730 - Dan Jiang, Cong Xin, Jinhua Ye, Yingbo Yuan, Ming Fang:
ICGRM: integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset. 731 - Dvir Netanely, Neta Stern, Itay Laufer, Ron Shamir:
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. 732 - Barbara Rita Barricelli, Elena Casiraghi, Jessica Gliozzo, Veronica Huber, Biagio Eugenio Leone, Alessandro Rizzi, Barbara Vergani:
ki67 nuclei detection and ki67-index estimation: a novel automatic approach based on human vision modeling. 733 - A. B. M. Shamim Ul Hasan, Hiroyuki Kurata, Sebastian Pechmann:
Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation. 734 - Hyejin Cho, Hyunju Lee:
Biomedical named entity recognition using deep neural networks with contextual information. 735 - Ranjan Kumar Barman, Anirban Mukhopadhyay, Ujjwal Maulik, Santasabuj Das:
Identification of infectious disease-associated host genes using machine learning techniques. 736 - Alexandra Poos, Theresa Kordaß, Amol Kolte, Volker Ast, Marcus Oswald, Karsten Rippe, Rainer König:
Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. 737 - Vincent Demolombe, Alexandre G. de Brevern, Franck Molina, Géraldine Lavigne, Claude Granier, Violaine Moreau:
Benchmarking the PEPOP methods for mimicking discontinuous epitopes. 738 - Emanuel Maldonado, Agostinho Antunes:
LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. 739 - Rudi Alberts, Jinyu Chen, Louxin Zhang:
ZDOG: zooming in on dominating genes with mutations in cancer pathways. 740 - Judit Kumuthini, Lyndon Zass, Sumir Panji, Samson P. Salifu, Jonathan K. Kayondo, Victoria Nembaware, Mamana Mbiyavanga, Ajayi Olabode, Ali Kishk, Gordon Wells, Nicola J. Mulder:
The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research. 741 - Daniel Lichtblau:
Alignment-free genomic sequence comparison using FCGR and signal processing. 742 - Jérémy Amand, Tobias Fehlmann, Christina Backes, Andreas Keller:
DynaVenn: web-based computation of the most significant overlap between ordered sets. 743 - Zhen Cui, Ying-Lian Gao, Jin-Xing Liu, Juan Wang, Junliang Shang, Ling-Yun Dai:
The computational prediction of drug-disease interactions using the dual-network L2,1-CMF method. 5 - Oyetunji E. Ogundijo, Xiaodong Wang:
SeqClone: sequential Monte Carlo based inference of tumor subclones. 6 - Kevin Michael Boehm, Bhavneet Bhinder, Vijay Joseph Raja, Noah Dephoure, Olivier Elemento:
Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome. 7 - Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger G. Sutton, Derrick E. Fouts, Karen E. Nelson:
OMeta: an ontology-based, data-driven metadata tracking system. 8 - Ghanasyam Rallapalli, Pilar Corredor-Moreno, Edward Chalstrey, Martin Page, Daniel MacLean:
Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence. 9 - Andre Lamurias, Diana F. Sousa, Luka A. Clarke, Francisco M. Couto:
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. 10 - Peng Wang, Yu Zhang, Bei-Qi Wang, Jian-Long Li, Yi-Xin Wang, Dongdong Pan, Xian-Bo Wu, Wing Kam Fung, Ji-Yuan Zhou:
A statistical measure for the skewness of X chromosome inactivation based on case-control design. 11 - Minzhe Zhang, Qiwei Li, Donghyeon Yu, Bo Yao, Wei Guo, Yang Xie, Guanghua Xiao:
GeNeCK: a web server for gene network construction and visualization. 12 - Minzhe Zhang, Tao Wang, Rosa Sirianni, Philip W. Shaul, Yang Xie:
Identifying genes with tri-modal association with survival and tumor grade in cancer patients. 13 - Johny Ijaq, Girik Malik, Anuj Kumar, Partha Sarathi Das, Narendra Meena, Neeraja Bethi, Vijayaraghava Seshadri Sundararajan, Prashanth Suravajhala:
A model to predict the function of hypothetical proteins through a nine-point classification scoring schema. 14 - Takoua Jendoubi, Korbinian Strimmer:
A whitening approach to probabilistic canonical correlation analysis for omics data integration. 15 - Rong Zhu, Guangshun Li, Jin-Xing Liu, Ling-Yun Dai, Ying Guo:
ACCBN: ant-Colony-clustering-based bipartite network method for predicting long non-coding RNA-protein interactions. 16 - Morteza Chalabi Hajkarim, Vasileios Tsiamis, Lukas Käll, Fabio Vandin, Veit Schwämmle:
CoExpresso: assess the quantitative behavior of protein complexes in human cells. 17 - Umaporn Siangphoe, Kellie J. Archer, Nitai D. Mukhopadhyay:
Classical and Bayesian random-effects meta-analysis models with sample quality weights in gene expression studies. 18 - Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, Alain Denise:
CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts. 19 - Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin, Alexander L. Greninger:
VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank. 48 - Meiqi Wu, Yingxi Yang, Hui Wang, Yan Xu:
A deep learning method to more accurately recall known lysine acetylation sites. 49 - Patricia Maraver, Rubén Armañanzas, Todd A. Gillette, Giorgio A. Ascoli:
PaperBot: open-source web-based search and metadata organization of scientific literature. 50 - Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi, Seyed Abolfazl Motahari:
IMOS: improved Meta-aligner and Minimap2 On Spark. 51 - Leander Dony, Fei He, Michael P. H. Stumpf:
Parametric and non-parametric gradient matching for network inference: a comparison. 52 - Fang Zhang, Fengzhu Sun, Yihui Luan:
Statistical significance approximation for local similarity analysis of dependent time series data. 53 - Marco Moretto, Paolo Sonego, Ana B. Villaseñor-Altamirano, Kristof Engelen:
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_. 54 - Shadia Mikhael, Cyril R. Pernet:
A controlled comparison of thickness, volume and surface areas from multiple cortical parcellation packages. 55 - Nikolay Martyushenko, Eivind Almaas:
ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions. 56 - André Voigt, Eivind Almaas:
Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks. 58 - Ya-Wei Niu, Guanghui Wang, Gui-Ying Yan, Xing Chen:
Integrating random walk and binary regression to identify novel miRNA-disease association. 59 - Konstantin Okonechnikov, Serap Erkek, Jan O. Korbel, Stefan M. Pfister, Lukas Chavez:
InTAD: chromosome conformation guided analysis of enhancer target genes. 60 - Mohammad Zia, Paul Spurgeon, Adrian Levesque, Thomas R. Furlani, Jianxin Wang:
GenESysV: a fast, intuitive and scalable genome exploration open source tool for variants generated from high-throughput sequencing projects. 61 - Xiaozheng Li, Huazhen Wang, Huixin He, Jixiang Du, Jian Chen, Jinzhun Wu:
Intelligent diagnosis with Chinese electronic medical records based on convolutional neural networks. 62 - Yao Yao, Zheng Liu, Qi Wei, Stephen A. Ramsey:
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. 63 - Farzad Farnoud, Moshe Schwartz, Jehoshua Bruck:
Estimation of duplication history under a stochastic model for tandem repeats. 64 - Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
DeepPVP: phenotype-based prioritization of causative variants using deep learning. 65 - Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim I. Sorokin, Andrew Garazha, Andrey Pulin, Ilya I. Eremin, Anton Buzdin:
Shambhala: a platform-agnostic data harmonizer for gene expression data. 66 - Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach, Amjad Ali:
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. 123 - Hasiba Asma, Marc S. Halfon:
Computational enhancer prediction: evaluation and improvements. 174 - Joseph Brown, Aaron R. Phillips, David A. Lewis, Michael-Andres Mans, Yvonne Chang, Robert L. Tanguay, Elena S. Peterson, Katrina M. Waters, Susan C. Tilton:
Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration. 255 - Eva Gorrochategui, Joaquim Jaumot, Romà Tauler:
ROIMCR: a powerful analysis strategy for LC-MS metabolomic datasets. 256 - Joanna Roder, Benjamin Linstid, Carlos Oliveira:
Improving the power of gene set enrichment analyses. 257 - Florian Martin, Sylvain Gubian, Marja Talikka, Julia Hoeng, Manuel C. Peitsch:
NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks. 451 - Emile P. Chen, Roy S. Song, Xueer Chen:
Mathematical model of hypoxia and tumor signaling interplay reveals the importance of hypoxia and cell-to-cell variability in tumor growth inhibition. 507 - S. Ha, Elena S. Dimitrova, Stefan Hoops, Doaa Altarawy, Mitra Ansariola, D. Deb, Jane Glazebrook, R. Hillmer, Hossameldin Shahin, Fumiaki Katagiri, J. McDowell, Molly Megraw, João C. Setubal, B. M. Tyler, Reinhard C. Laubenbacher:
PlantSimLab - a modeling and simulation web tool for plant biologists. 508
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2024-12-23 19:19 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
