| 0 | -- | 0 | Renmin Han, Zhipeng Bao, Xiangrui Zeng, Tongxin Niu, Fa Zhang, Min Xu 0009, Xin Gao 0001. A joint method for marker-free alignment of tilt series in electron tomography |
| 0 | -- | 0 | Muhao Chen, Chelsea J.-T. Ju, Guangyu Zhou, Xuelu Chen, Tianran Zhang, Kai-Wei Chang, Carlo Zaniolo, Wei Wang. Multifaceted protein-protein interaction prediction based on Siamese residual RCNN |
| 0 | -- | 0 | Ali Ghaffaari, Tobias Marschall. Fully-sensitive seed finding in sequence graphs using a hybrid index |
| 0 | -- | 0 | Surag Nair, Daniel S. Kim, Jacob Perricone, Anshul Kundaje. Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts |
| 0 | -- | 0 | Lei Du, Kefei Liu 0001, Lei Zhu, Xiaohui Yao, Shannon L. Risacher, Lei Guo 0002, Andrew J. Saykin, Li Shen 0001. Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis: a longitudinal study of the ADNI cohort |
| 0 | -- | 0 | Martin Strazar, Lan Zagar, Jaka Kokosar, Vesna Tanko, Ales Erjavec, Pavlin G. Policar, Anze Staric, Janez Demsar, Gad Shaulsky, Vilas Menon, Andrew Lemire, Anup Parikh, Blaz Zupan. scOrange - a tool for hands-on training of concepts from single-cell data analytics |
| 0 | -- | 0 | Do-Hoon Lee, Sangseon Lee, Sun Kim. PRISM: methylation pattern-based, reference-free inference of subclonal makeup |
| 0 | -- | 0 | Vikas Bansal. Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes |
| 0 | -- | 0 | Jian Zhang, Lukasz A. Kurgan. SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences |
| 0 | -- | 0 | Markus Heinonen, Maria Osmala, Henrik Mannerström, Janne Wallenius, Samuel Kaski, Juho Rousu, Harri Lähdesmäki. Bayesian metabolic flux analysis reveals intracellular flux couplings |
| 0 | -- | 0 | Ruogu Lin, Xiangrui Zeng, Kris Kitani, Min Xu 0009. Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms |
| 0 | -- | 0 | Jakob Richter, Katrin Madjar, Jörg Rahnenführer. Model-based optimization of subgroup weights for survival analysis |
| 0 | -- | 0 | Camilo Valdes, Vitalii Stebliankin, Giri Narasimhan. Large scale microbiome profiling in the cloud |
| 0 | -- | 0 | Mengyun Yang, HuiMin Luo, Yaohang Li, Jianxin Wang. Drug repositioning based on bounded nuclear norm regularization |
| 0 | -- | 0 | Erin K. Molloy, Tandy J. Warnow. TreeMerge: a new method for improving the scalability of species tree estimation methods |
| 0 | -- | 0 | Mathias Cardner, Nathalie Meyer-Schaller, Gerhard Christofori, Niko Beerenwinkel. Inferring signalling dynamics by integrating interventional with observational data |
| 0 | -- | 0 | Jerzy Tiuryn, Ewa Szczurek. Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects |
| 0 | -- | 0 | Hao Yang, Hao Chi, Wen-Feng Zeng, Wen-Jing Zhou, Si-Min He 0001. pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework |
| 0 | -- | 0 | Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi. Selfish: discovery of differential chromatin interactions via a self-similarity measure |
| 0 | -- | 0 | . ISMB/ECCB 2019 PROCEEDINGS PAPERS COMMITTEE |
| 0 | -- | 0 | Anika Cheerla, Olivier Gevaert. Deep learning with multimodal representation for pancancer prognosis prediction |
| 0 | -- | 0 | Erfan Sayyari, Ban Kawas, Siavash Mirarab. TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification |
| 0 | -- | 0 | Hao Chen, Dipan Shaw, Jianyang Zeng, Dongbo Bu, Tao Jiang. DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning |
| 0 | -- | 0 | André Hennig, Kay Nieselt. Efficient merging of genome profile alignments |
| 0 | -- | 0 | Dai-Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka. ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra |
| 0 | -- | 0 | Martin D. Muggli, Bahar Alipanahi, Christina Boucher. Building large updatable colored de Bruijn graphs via merging |
| 0 | -- | 0 | Sumit Mukherjee, Thanneer M. Perumal, Kenneth Daily, Solveig K. Sieberts, Larsson Omberg, Christoph Preuss, Gregory W. Carter, Lara Mangravite, Benjamin A. Logsdon. Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation |
| 0 | -- | 0 | Sayed-Rzgar Hosseini, Ramón Díaz-Uriarte, Florian Markowetz, Niko Beerenwinkel. Estimating the predictability of cancer evolution |
| 0 | -- | 0 | Teppo Mikael Niinimäki, Mikko A. Heikkilä, Antti Honkela, Samuel Kaski. Representation transfer for differentially private drug sensitivity prediction |
| 0 | -- | 0 | Dan Guo, Kylie A. Bemis, Catherine Rawlins, Jeffrey Agar, Olga Vitek. Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues |
| 0 | -- | 0 | Krister M. Swenson, Mathieu Blanchette. Large-scale mammalian genome rearrangements coincide with chromatin interactions |
| 0 | -- | 0 | Song-Yao Zhang, Shao-Wu Zhang 0001, Xiao-Nan Fan 0001, Teng Zhang, Jia Meng, Yufei Huang. FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes |
| 0 | -- | 0 | Torsten Gross, Matthew Wongchenko, Yibing Yan, Nils Blüthgen. Robust network inference using response logic |
| 0 | -- | 0 | Wei Vivian Li, Jingyi Jessica Li. A statistical simulator scDesign for rational scRNA-seq experimental design |
| 0 | -- | 0 | Hirak Sarkar, Avi Srivastava, Robert Patro. Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level |
| 0 | -- | 0 | Hossein Sharifi Noghabi, Olga Zolotareva, Colin C. Collins, Martin Ester. MOLI: multi-omics late integration with deep neural networks for drug response prediction |
| 0 | -- | 0 | Dinithi Sumanaweera, Lloyd Allison, Arun Siddharth Konagurthu. Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors |
| 0 | -- | 0 | Caroline Labelle, Anne Marinier, Sébastien Lemieux. Enhancing the drug discovery process: Bayesian inference for the analysis and comparison of dose-response experiments |
| 0 | -- | 0 | Jiansheng Wu, Ben Liu, Wallace K. B. Chan, Weijian Wu, Tao Pang, Haifeng Hu 0004, Shancheng Yan, Xiaoyan Ke, Yang Zhang. Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors |
| 0 | -- | 0 | Héctor Climente-González, Chloé-Agathe Azencott, Samuel Kaski, Makoto Yamada. Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data |
| 0 | -- | 0 | Benjamin Chidester, Tianming Zhou, Minh N. Do, Jian Ma 0004. Rotation equivariant and invariant neural networks for microscopy image analysis |
| 0 | -- | 0 | Zichao Yan, Eric Lécuyer, Mathieu Blanchette. Prediction of mRNA subcellular localization using deep recurrent neural networks |
| 0 | -- | 0 | Michio Iwata, Longhao Yuan, Qibin Zhao, Yasuo Tabei, Francois Berenger, Ryusuke Sawada, Sayaka Akiyoshi, Momoko Hamano, Yoshihiro Yamanishi. Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm |
| 0 | -- | 0 | Azat M. Tagirdzhanov, Alexander Shlemov, Alexey Gurevich. NPS: scoring and evaluating the statistical significance of peptidic natural product-spectrum matches |
| 0 | -- | 0 | Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang. Efficient haplotype matching between a query and a panel for genealogical search |
| 0 | -- | 0 | Qiao Liu, Hairong Lv, Rui Jiang. hicGAN infers super resolution Hi-C data with generative adversarial networks |
| 0 | -- | 0 | Mitchell J. Wagner, Aditya Pratapa, T. M. Murali 0001. Reconstructing signaling pathways using regular language constrained paths |
| 0 | -- | 0 | Alexis Baudin, Soumya Paul, Cui Su, Jun Pang. Controlling large Boolean networks with single-step perturbations |
| 0 | -- | 0 | Lisa Handl, Adrin Jalali, Michael Scherer, Ralf Eggeling, Nico Pfeifer. Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data |
| 0 | -- | 0 | . Author Index |
| 0 | -- | 0 | Xiao Yang, Yasushi Saito, Arjun Rao, Hyunsung John Kim, Pranav Singh, Eric Scott, Matthew Larson, Wenying Pan, Mohini Desai, Earl Hubbell. Alignment-free filtering for cfNA fusion fragments |
| 0 | -- | 0 | Stefan Mautner, Soheila Montaseri, Milad Miladi, Martin Raden, Fabrizio Costa, Rolf Backofen. ShaKer: RNA SHAPE prediction using graph kernel |
| 0 | -- | 0 | Ameni Trabelsi, Mohamed Chaabane, Asa Ben-Hur. Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities |
| 0 | -- | 0 | Liang Huang 0001, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David A Hendrix, David H. Mathews. LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search |
| 0 | -- | 0 | Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf H. Fridman, Markus List, Tatsiana Aneichyk. Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology |
| 0 | -- | 0 | Bojian Yin, Marleen Balvert, Rick A. A. van der Spek, Bas E. Dutilh, Sander M. Bohté, Jan Veldink, Alexander Schönhuth. Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype |
| 0 | -- | 0 | Ivan Tolstoganov, Anton Bankevich, Zhoutao Chen, Pavel A. Pevzner. cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs |
| 0 | -- | 0 | Sahand Khakabimamaghani, Salem Malikic, Jeffrey Tang, Dujian Ding, Ryan Morin, Leonid Chindelevitch, Martin Ester. Collaborative intra-tumor heterogeneity detection |
| 0 | -- | 0 | Yana Bromberg, Nadia El-Mabrouk, Predrag Radivojac. ISMB/ECCB 2019 Proceedings |
| 0 | -- | 0 | Nuraini Aguse, Yuanyuan Qi, Mohammed El-Kebir. Summarizing the solution space in tumor phylogeny inference by multiple consensus trees |
| 0 | -- | 0 | Sahar Tavakoli, Shibu Yooseph. Learning a mixture of microbial networks using minorization-maximization |
| 0 | -- | 0 | Guillaume Marçais, Dan F. DeBlasio, Prashant Pandey, Carl Kingsford. Locality-sensitive hashing for the edit distance |
| 0 | -- | 0 | Welles Robinson, Roded Sharan, Mark D. M. Leiserson. Modeling clinical and molecular covariates of mutational process activity in cancer |
| 0 | -- | 0 | Jiafan Zhu, Xinhao Liu, Huw A. Ogilvie, Luay Nakhleh. A divide-and-conquer method for scalable phylogenetic network inference from multilocus data |
| 0 | -- | 0 | Aline Marguet, Marc Lavielle, Eugenio Cinquemani. Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data |
| 0 | -- | 0 | Reza Miraskarshahi, Hooman Zabeti, Tamon Stephen, Leonid Chindelevitch. MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks |
| 0 | -- | 0 | Soufiane Mourragui, Marco Loog, Mark A van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels. PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors |
| 0 | -- | 0 | Yan Gao, Bo Liu, Yadong Wang, Yi Xing. TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain |
| 0 | -- | 0 | Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz. Large-scale inference of competing endogenous RNA networks with sparse partial correlation |
| 0 | -- | 0 | Haoyang Zeng, David K. Gifford. DeepLigand: accurate prediction of MHC class I ligands using peptide embedding |
| 0 | -- | 0 | Avanti Shrikumar, Eva Prakash, Anshul Kundaje. GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs |
| 0 | -- | 0 | Pavel Skums, Viachaslau Tsyvina, Alex Zelikovsky. Inference of clonal selection in cancer populations using single-cell sequencing data |
| 2349 | -- | 2353 | Vikram Alva, Andrei N. Lupas. Histones predate the split between bacteria and archaea |
| 2354 | -- | 2361 | Alexander J. Nash, Boris Lenhard. A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates |
| 2362 | -- | 2370 | Catharina Lippmann, Alfred Ultsch, Jörn Lötsch. Computational functional genomics-based reduction of disease-related gene sets to their key components |
| 2371 | -- | 2379 | Zhihao Xia, Yu Li 0006, Bin Zhang, Zhongxiao Li, Yuhui Hu, Wei Chen, Xin Gao 0001. DeeReCT-PolyA: a robust and generic deep learning method for PAS identification |
| 2380 | -- | 2385 | Chang Sik Kim, Sumitra Mohan, Mahmood Ayub, Dominic G. Rothwell, Caroline Dive, Ged Brady, Crispin J. Miller. In silico error correction improves cfDNA mutation calling |
| 2386 | -- | 2394 | Duolin Wang, Yanchun Liang 0001, Dong Xu 0002. Capsule network for protein post-translational modification site prediction |
| 2395 | -- | 2402 | Xiaoying Wang, Bin Yu, Anjun Ma, Cheng Chen, Bingqiang Liu, Qin Ma 0003. Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique |
| 2403 | -- | 2410 | Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou. Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks |
| 2411 | -- | 2417 | Seung Hwan Hong, Keehyoung Joo, Jooyoung Lee. ConDo: protein domain boundary prediction using coevolutionary information |
| 2418 | -- | 2426 | David Simoncini, Kam Y. J. Zhang, Thomas Schiex, Sophie Barbe. A structural homology approach for computational protein design with flexible backbone |
| 2427 | -- | 2433 | Amaya Jiménez, Slavica Jonic, Tomás Majtner, Joaquín Otón, Jose Luis Vilas, David Maluenda, Javier Mota, Erney Ramírez-Aportela, Marta Martínez, Yaiza Rancel, Joan Segura, Rubén Sánchez García, Roberto Melero, Laura del Cano, Pablo Conesa, Lars Skjaerven, Roberto Marabini, José María Carazo, Carlos Oscar Sánchez Sorzano. Validation of electron microscopy initial models via small angle X-ray scattering curves |
| 2434 | -- | 2440 | Shinichiro Tsuchiya, Issaku Yamada, Kiyoko F. Aoki-Kinoshita. GlycanFormatConverter: a conversion tool for translating the complexities of glycans |
| 2441 | -- | 2448 | Yang Shi, Mengqiao Wang, Weiping Shi, Ji-Hyun Lee, Huining Kang, Hui Jiang. Accurate and efficient estimation of small P-values with the cross-entropy method: applications in genomic data analysis |
| 2449 | -- | 2457 | Andrew Parton, Victoria McGilligan, Melody Chemaly, Maurice O'Kane, Steven Watterson. New models of atherosclerosis and multi-drug therapeutic interventions |
| 2458 | -- | 2465 | Johanna Schwarz, Dominik Heider. GUESS: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making |
| 2466 | -- | 2474 | Jimmy Ka Ho Chiu, Rick Twee-Hee Ong. ARGDIT: a validation and integration toolkit for Antimicrobial Resistance Gene Databases |
| 2475 | -- | 2485 | Xiongtao Ruan, Robert F. Murphy. Evaluation of methods for generative modeling of cell and nuclear shape |
| 2486 | -- | 2488 | Hong-Dong Li, Tianjian Bai, Erin Sandford, Margit Burmeister, Yuanfang Guan. BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets |
| 2489 | -- | 2491 | Tobias Rausch, Markus Hsi-Yang Fritz, Jan O. Korbel, Vladimir Benes. Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing |
| 2492 | -- | 2494 | Tania Cuppens, Thomas E. Ludwig, Pascal Trouvé, Emmanuelle Génin. GEMPROT: visualization of the impact on the protein of the genetic variants found on each haplotype |
| 2495 | -- | 2497 | Gregory McInnes, Yosuke Tanigawa, Chris DeBoever, Adam Lavertu, Julia Eve Olivieri, Matthew Aguirre, Manuel A Rivas. Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics |
| 2498 | -- | 2500 | Ehsaneddin Asgari, Philipp C. Münch, Till R. Lesker, Alice C. McHardy, Mohammad R. K. Mofrad. DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection |
| 2501 | -- | 2503 | Jiamin Sun, Hao Liu, Jianxiao Liu, Shikun Cheng, Yong Peng, Qinghua Zhang, Jianbing Yan, Haijun Liu, Ling-Ling Chen. CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes |
| 2504 | -- | 2506 | Clément-Marie Train, Miguel Pignatelli, Adrian M. Altenhoff, Christophe Dessimoz. iHam and pyHam: visualizing and processing hierarchical orthologous groups |
| 2507 | -- | 2508 | Aleix Lafita, Pengfei Tian, Robert B. Best, Alex Bateman. TADOSS: computational estimation of tandem domain swap stability |
| 2509 | -- | 2511 | Thomas Sherman, Jack M. Fu, Robert B. Scharpf, Alexandre Bureau, Ingo Ruczinski. Detection of rare disease variants in extended pedigrees using RVS |
| 2512 | -- | 2514 | Bongsong Kim, Xinbin Dai, Wenchao Zhang, Zhaohong Zhuang, Darlene L. Sanchez, Thomas Lübberstedt, Yun Kang, Michael K. Udvardi, William D. Beavis, Shizhong Xu, Patrick X. Zhao. GWASpro: a high-performance genome-wide association analysis server |
| 2515 | -- | 2517 | Héléna A. Gaspar, Christopher Hübel, Gerome Breen. Drug Targetor: a web interface to investigate the human druggome for over 500 phenotypes |
| 2518 | -- | 2520 | Adrián Bazaga, Alfonso Valencia, María-José Rementeria. BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications |
| 2521 | -- | 2522 | Zheng Kuang, Ying Wang, Lei Li, Xiaozeng Yang. miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants |
| 2523 | -- | 2524 | S. Castillo-Lara, Josep F. Abril. PPaxe: easy extraction of protein occurrence and interactions from the scientific literature |
| 2525 | -- | 2527 | Ludovica Montanucci, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli. On the biases in predictions of protein stability changes upon variations: the INPS test case |
| 2528 | -- | 0 | Wei Zhang, Jianzhu Ma, Trey Ideker. Classifying tumors by supervised network propagation |