Content-Type: text/html; Oxford Academic
Oxford Academic
New issue alert
Biology Methods and Protocols is now included in the Emerging Sources Citation Index, making it the perfect home for your research.
Read our Instructions to Authors page and submit your research today
Volume 37 Issue 20
15 October 2021
Determining optical mapping errors by simulations 
Michal Va┼íinek; Marek B─Ťhálek; Petr Gajdo┼í; Regina Fillerová; Eva Kriegová
Comparison of structural variants detected by optical mapping with long-read next-generation sequencing 
Jakub Savara; Tomá┼í Novosád; Petr Gajdo┼í; Eva Kriegová
DeepEBV: a deep learning model to predict Epstein'Barr virus (EBV) integration sites 
Jiuxing Liang; Zifeng Cui; Canbiao Wu; Yao Yu ; Rui Tian ...
ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs 
Abhijit Chakraborty; Ferhat Ay; Ramana V Davuluri
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes border= 
Qingzhen Hou; Bas Stringer; Katharina Waury; Henriette Capel ; Reza Haydarlou ...
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction border= 
QHwan Kim; Joon-Hyuk Ko; Sunghoon Kim ; Nojun Park; Wonho Jhe
CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks 
Jianwei Hong; Ruitian Gao; Yang Yang
Rapid T-cell receptor interaction grouping with ting 
Felix Mölder; Ulrik Stervbo; Lucie Loyal; Petra Bacher ; Nina Babel ...
Clustering FunFams using sequence embeddings improves EC purity border= 
Maria Littmann; Nicola Bordin; Michael Heinzinger; Konstantin Schütze ; Christian Dallago ...
eCOMPASS: evaluative comparison of multiple protein alignments by statistical score border= 
Andrew F Neuwald; Bryan D Kolaczkowski; Stephen F Altschul
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning 
Jaspreet Singh; Thomas Litfin; Kuldip Paliwal; Jaswinder Singh ; Anil Kumar Hanumanthappa ...
In silico prediction of in vitro protein liquid'liquid phase separation experiments outcomes with multi-head neural attention 
Daniele Raimondi; Gabriele Orlando; Emiel Michiels; Donya Pakravan ; Anna Bratek-Skicki ...
Full-length de novo protein structure determination from cryo-EM maps using deep learning 
Jiahua He; Sheng-You Huang
ProteoMill: efficient network-based functional analysis portal for proteomics data border= 
Martin Rydén; Martin Englund; Neserin Ali
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis 
Tongchuan Zhang; Jaswinder Singh; Thomas Litfin; Jian Zhan ; Kuldip Paliwal ...
scConnect: a method for exploratory analysis of cell'cell communication based on single-cell RNA-sequencing data border= 
Jon E T Jakobsson; Ola Spjuth; Malin C Lagerström
VeTra: a tool for trajectory inference based on RNA velocity border= 
Guangzheng Weng; Junil Kim; Kyoung Jae Won
GEM: scalable and flexible gene'environment interaction analysis in millions of samples border= 
Kenneth E Westerman; Duy T Pham; Liang Hong ; Ye Chen; Magdalena Sevilla-González ...
Assessment of significance of conditionally independent GWAS signals 
Sahar Ghasemi; Alexander Teumer; Matthias Wuttke; Tim Becker
Capturing dynamic relevance in Boolean networks using graph theoretical measures border= 
Felix M Weidner; Julian D Schwab; Silke D Werle ; Nensi Ikonomi; Ludwig Lausser ...
Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery border= 
Huangqingbo Sun; Robert F Murphy
Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data 
Giuseppe Magazzù; Guido Zampieri; Claudio Angione
Inferring the experimental design for accurate gene regulatory network inference border= 
Deniz Seçilmi┼č; Thomas Hillerton; Sven Nelander ; Erik L L Sonnhammer
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate'product pairs border= 
Jasmin Hafner; Vassily Hatzimanikatis
MANIEA: a microbial association network inference method based on improved Eclat association rule mining algorithm 
Maidi Liu; Yanqing Ye; Jiang Jiang; Kewei Yang
Evaluating disease similarity based on gene network reconstruction and representation 
Yang Li; Wang Keqi; Guohua Wang
Omics community detection using multi-resolution clustering border= 
Ali Rahnavard; Suvo Chatterjee; Bahar Sayoldin; Keith A Crandall ; Fasil Tekola-Ayele ...
Target'Decoy MineR for determining the biological relevance of variables in noisy datasets 
Cesaré Ovando-Vázquez; Daniel Cázarez-García; Robert Winkler
TimiRGeN: R/Bioconductor package for time series microRNA'mRNA integration and analysis border= 
K Patel; S Chandrasegaran; I M Clark ; C J Proctor; D A Young ...
A combined recall and rank framework with online negative sampling for Chinese procedure terminology normalization 
Ming Liang; Kui Xue; Qi Ye; Tong Ruan
Autoencoder-based drug'target interaction prediction by preserving the consistency of chemical properties and functions of drugs 
Chang Sun; Yangkun Cao; Jin-Mao Wei; Jian Liu
Family Rank: a graphical domain knowledge informed feature ranking algorithm 
Michelle Saul; Valentin Dinu
Towards an automatic analysis of CHO-K1 suspension growth in microfluidic single-cell cultivation 
Dominik Stallmann; Jan P Göpfert; Julian Schmitz; Alexander Grünberger ; Barbara Hammer
Customized de novo mutation detection for any variant calling pipeline: SynthDNM 
Aojie Lian; James Guevara; Kun Xia; Jonathan Sebat
interacCircos: an R package based on JavaScript libraries for the generation of interactive circos plots 
Zhe Cui; Ya Cui; Tianyi Zang; Yadong Wang
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST border= 
Zhemin Zhou; Jane Charlesworth; Mark Achtman
SKSV: ultrafast structural variation detection from circular consensus sequencing reads 
Yadong Liu; Tao Jiang; Junhao Su; Bo Liu ; Tianyi Zang ...
TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets 
Ales Varabyou; Geo Pertea; Christopher Pockrandt; Mihaela Pertea
DamageProfiler: fast damage pattern calculation for ancient DNA 
Judith Neukamm; Alexander Peltzer; Kay Nieselt
tSFM 1.0: tRNA Structure'Function Mapper 
Travis J Lawrence; Fatemeh Hadi-Nezhad; Ivo Grosse; David H Ardell
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python border= 
She Zhang; James M Krieger; Yan Zhang ; Cihan Kaya; Burak Kaynak ...
RNAStructViz: graphical base pairing analysis 
Maxie Dion Schmidt; Anna Kirkpatrick; Christine Heitsch
VisuaLife: library for interactive visualization in rich web applications border= 
Justyna D Kry┼Ť; Dominik Gront
NeuroCirc: an integrative resource of circular RNA expression in the human brain 
Kieran Walsh; Akira Gokool; Hamid Alinejad-Rokny; Irina Voineagu
COBRAC: a fast implementation of convex biclustering with compression 
Haidong Yi; Le Huang; Gal Mishne; Eric C Chi
Quickomics: exploring omics data in an intuitive, interactive and informative manner 
Benbo Gao; Jing Zhu; Soumya Negi; Xinmin Zhang ; Stefka Gyoneva ...
GSpace: an exact coalescence simulator of recombining genomes under isolation by distance 
Thimothée Virgoulay; François Rousset; Camille Noûs; Raphaël Leblois
AMICI: high-performance sensitivity analysis for large ordinary differential equation models border= 
Fabian Fröhlich; Daniel Weindl; Yannik Schälte ; Dilan Pathirana; ┼ ukasz Paszkowski ...
mzRAPP: a tool for reliability assessment of data pre-processing in non-targeted metabolomics border= 
Yasin El Abiead; Maximilian Milford; Reza M Salek ; Gunda Koellensperger
TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures 
Mengyu Xie; Kyubum Lee; John H Lockhart; Scott D Cukras ; Rodrigo Carvajal ...
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis border= 
Eliot Ragueneau; Anjali Shrivastava; John H Morris ; Noemi del-Toro; Henning Hermjakob ...
SPDE: a multi-functional software for sequence processing and data extraction 
Dong Xu; Zhuchou Lu; Kangming Jin; Wenmin Qiu ; Guirong Qiao ...
MassExplorer: a computational tool for analyzing desorption electrospray ionization mass spectrometry data 
Vishnu Shankar; Robert Tibshirani; Richard N Zare
GEInter: an R package for robust gene'environment interaction analysis 
Mengyun Wu; Xing Qin; Shuangge Ma
A decoupled, modular and scriptable architecture for tools to curate data platforms border= 
Momo Langenstein; Henning Hermjakob; Manuel Bernal Llinares
FPM app: an open-source MATLAB application for simple and intuitive Fourier ptychographic reconstruction 
Miko┼éaj Rogalski; Piotr Zda┼"kowski; Maciej Trusiak
Unsubscribe       Manage email alerts
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

Our Privacy Policy sets out how Oxford University Press handles your personal information.

The content of this email is protected by copyright.
Oxford University Press

This email is intended for ------=_Part_971506078.1635542531431--