Volkhard Helms

38 papers Journal 35Unranked 2

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Inflow and outflow centrality: novel centrality metrics inspired by graph convolution. Appl. Netw. Sci. Aram Papazian, Volkhard Helms
2022	J	`jnl`	Optimized Data Set and Feature Construction for Substrate Prediction of Membrane Transporters. J. Chem. Inf. Model. Andreas Denger, Volkhard Helms
2021	J	`jnl`	Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data. Frontiers Bioinform. Markus Hollander, Trang Do, Thorsten Will, Volkhard Helms
2021	J	`jnl`	How does Sec63 affect the conformation of Sec61 in yeast? PLoS Comput. Biol. Pratiti Bhadra, Lalitha Yadhanapudi, Karin Römisch, Volkhard Helms
2021	J	`jnl`	Identification of Biomarkers Controlling Cell Fate In Blood Cell Development. Frontiers Bioinform. Maryam Nazarieh, Marc P. Hoeppner, Volkhard Helms
2021	J	`jnl`	ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures. J. Chem. Inf. Model. Markus Hollander, David J. N. P. Rasp, Moomal Aziz, Volkhard Helms
2020	J	`jnl`	Identification of Biomarkers Controlling Cell Fate In Blood Cell Development. CoRR Maryam Nazarieh, Volkhard Helms, Marc P. Hoeppner, Andre Franke
2020	J	`jnl`	TFmiR2: constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks. Bioinform. Maryam Nazarieh, Mohamed Hamed, Christian Spaniol, Thorsten Will, Volkhard Helms
2019	J	`jnl`	Differential analysis of combinatorial protein complexes with CompleXChange. BMC Bioinform. Thorsten Will, Volkhard Helms
2019	J	`jnl`	Topology Consistency of Disease-specific Differential Co-regulatory Networks. BMC Bioinform. Maryam Nazarieh, Hema Sekhar Reddy Rajula, Volkhard Helms
2018	J	`jnl`	MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks. Bioinform. Markus Hollander, Mohamed Hamed, Volkhard Helms, Kerstin Neininger
2017	J	`jnl`	Randomization Strategies Affect Motif Significance Analysis in TF-miRNA-Gene Regulatory Networks. J. Integr. Bioinform. Sepideh Sadegh, Maryam Nazarieh, Christian Spaniol, Volkhard Helms
2017	J	`jnl`	Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare. BMC Syst. Biol. Thorsten Will, Volkhard Helms
2016	J	`jnl`	Identification of key player genes in gene regulatory networks. BMC Syst. Biol. Maryam Nazarieh, Andreas Wiese, Thorsten Will, Mohamed Hamed, Volkhard Helms
2016	J	`jnl`	PPIXpress: construction of condition-specific protein interaction networks based on transcript expression. Bioinform. Thorsten Will, Volkhard Helms
2016	J	`jnl`	PreTIS: A Tool to Predict Non-canonical 5' UTR Translational Initiation Sites in Human and Mouse. PLoS Comput. Biol. Kerstin Reuter, Alexander Biehl, Laurena Koch, Volkhard Helms
2015	J	`jnl`	Graph-Based Clustering of Predicted Ligand-Binding Pockets on Protein Surfaces. J. Chem. Inf. Model. Jennifer Degac, Uwe Winter, Volkhard Helms
2015	J	`jnl`	TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. Nucleic Acids Res. Mohamed Hamed, Christian Spaniol, Maryam Nazarieh, Volkhard Helms
2014	J	`jnl`	AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing. J. Bioinform. Comput. Biol. Junfang Chen, Pavlo Lutsik, Ruslan Akulenko, Jörn Walter, Volkhard Helms
2014	J	`jnl`	Identifying transcription factor complexes and their roles. Bioinform. Thorsten Will, Volkhard Helms
2013	J	`jnl`	Batch tautomer generation with MolTPC. J. Comput. Chem. Thorsten Will, Michael C. Hutter, Johann Jauch, Volkhard Helms
2013	J	`jnl`	Rule-based regulatory and metabolic model for Quorum sensing in P. aeruginosa. BMC Syst. Biol. Nadine S. Schaadt, Anke Steinbach, Rolf W. Hartmann, Volkhard Helms
2013	J	`jnl`	Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. BMC Bioinform. Ahmad Barghash, Volkhard Helms
2011	J	`jnl`	Prediction of the Exposure Status of transmembrane beta Barrel residues from protein Sequence. J. Bioinform. Comput. Biol. Sikander Hayat, Peter Walter, Yungki Park, Volkhard Helms
2011	J	`jnl`	Statistical analysis and exposure status classification of transmembrane beta barrel residues. Comput. Biol. Chem. Sikander Hayat, Yungki Park, Volkhard Helms
2010	J	`jnl`	Classifying Substrate Specificities of Membrane Transporters from J. Chem. Inf. Model. Nadine S. Schaadt, Jan Christoph, Volkhard Helms
2010	J	`jnl`	Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction. J. Comput. Chem. Ling Wang, Boris Stumm, Volkhard Helms
2009	J	`jnl`	What induces pocket openings on protein surface patches involved in protein-protein interactions? J. Comput. Aided Mol. Des. Susanne Eyrisch, Volkhard Helms
2008	—	`conf`	Designing Binding Pockets on Protein Surfaces using the A* Algorithm. German Conference on Bioinformatics Susanne Eyrisch, Volkhard Helms
2008	J	`jnl`	MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon. Bioinform. Yungki Park, Volkhard Helms
2008	J	`jnl`	Prediction of the translocon-mediated membrane insertion free energies of protein sequences. Bioinform. Yungki Park, Volkhard Helms
2007	J	`jnl`	On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins. Bioinform. Yungki Park, Volkhard Helms
2007	J	`jnl`	Prediction of the burial status of transmembrane residues of helical membrane proteins. BMC Bioinform. Yungki Park, Sikander Hayat, Volkhard Helms
2007	—	`conf`	QVADIS - a Package to Compute Proton Transfer Pathways in Proteins. German Conference on Bioinformatics Kerstin Kunz, Volkhard Helms
2007	J	`jnl`	The ABC (Analysing Biomolecular Contacts)-database. J. Integr. Bioinform. Peter Walter, Sam Ansari, Volkhard Helms
2006	J	`jnl`	Energy barriers of proton transfer reactions between amino acid side chain analogs and water from ab initio calculations. J. Comput. Chem. Elena Herzog, Tomaso Frigato, Volkhard Helms, C. Roy D. Lancaster
1999	—	`ch.`	Conformational Transitions of Proteins from Atomistic Simulations. Computational Molecular Dynamics Volkhard Helms, James Andrew McCammon
1997	J	`jnl`	Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy. J. Comput. Chem. Volkhard Helms, Rebecca C. Wade