Publications

A compendium of next-generation patient-derived models for diverse cancers
The development of new therapeutics and the validation of pathogenetic cancer mechanisms require representative laboratory models1,2. …
Dina ElHarouni, Mushriq Al-Jazrawe, Seongmin Choi, Merve Dede, Toshinori Hinoue, Sean a Misek, Heeju Noh, Luca Zanella, Yuen-Yi Tseng, Hayley E Francies, Dennis Plenker, Cindy W Kyi, Julyann Perez-Mayoral, Megan J Stine, Eva Tonsing-Carter, Rachana Agarwal, Jean Claude Zenklusen, James M Clinton, Jennifer M Shelton, Timothy R Chu, William F Hooper, Xavi Loinaz, Paula Keskula, Jordan Tagle, Peyton C Kuhlers, Bahar Tercan, Sylvia F Boj, Alessandro Vasciaveo, Lorenzo Tomassoni, James M Crawford, Shawna Walsh, Claire Sinai, Sonam Bhatia, Priya Sridevi, Hardik Patel, Maria Antonietta Cerone, HCMI Network, Kyle Ellrott, Calvin J Kuo, Olivier Elemento, Semir Beyaz, Vincenzo Corbo, David L Spector, Rameen Beroukhim, Martin L Ferguson, Andrew D Cherniack, Peter W Laird, Nicolas Robine, Andrew McPherson, Katherine a Hoadley, Mathew J Garnett, David a Tuveson, Andrea Califano, Paul T Spellman, Keith L Ligon, Daniela S Gerhard, Louis M Staudt, Jesse S Boehm
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Eleven quick tips for Biomedical Federated Learning
Modern statistical and machine learning techniques are effective at describing, testing hypotheses and making predictions from complex …
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Towards a decentralized future for open-science databases
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Pooling multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal
AI-based embeddings offer the possibilities of encoding complex biological data into low-dimensional spaces, called embedding spaces, …
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A decentralized future for the open-science databases
The continuous and reliable open access to curated biological data repositories is indispensable for accelerating rigorous scientific …
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Robust software development practices improve citations of RNA-seq tools
RNA sequencing (RNA-seq) has emerged as an exemplary technology in biology and clinical applications, offering a crucial complement to …
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Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles
Traditional gene expression deconvolution methods assess a limited number of cell types, therefore do not capture the full complexity …
Bhavneet Bhinder, Verena Friedl, Sunantha Sethuraman, Davide Risso, Kami E Chiotti, R Jay Mashl, Kyle P Ellrott, Jordan a Lee, Christopher K Wong, Kofi Gyan, Aditya Deshpande, Marcin Imielinski, Rohan Bareja, Josh Stuart, Myron Peto, Katherine a Hoadley, Alexander J Lazar, Andrew D Cherniack, Jingchun Zhu, Shaolong Cao, Mark Rubin, Wenyi Wang, Oliver F Bathe, Nicolas Robine, Li Ding, Peter W Laird, Wanding Zhou, Hui Shen, Vésteinn Thorsson, Jen Jen Yeh, Matthew H Bailey, Daniel Cui Zhou, Xianlu L Peng, Mary Goldman, Yongsheng Li, Anil Korkut, Nidhi Sahni, D Neil Hayes, Michael K a Mensah, Ina Felau, Anab Kemal, Samantha Caesar-Johnson, John a Demchok, Liming Yang, Martin L Ferguson, Roy Tarnuzzer, Zhining Wang, Jean C Zenklusen, Cancer Genome Atlas Analysis Network, Paul Spellman, Olivier Elemento
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Protocol for obtaining cancer type and subtype predictions using subSCOPE
We present a protocol for obtaining cancer type and subtype predictions using a machine learning method (subSCOPE). We describe steps …
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Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods
As genes tend to be co-regulated as gene modules, feature selection in machine learning (ML) on gene expression data can be challenged …
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Aggregating multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal
AI based embeddings offer the possibilities of encoding complex biological data into low dimensional spaces, called embedding spaces, …
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Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction
Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment of …
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Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets
Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer’s underlying biology, bringing hope to …
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SyntheVAEiser: augmenting traditional machine learning methods with VAE-based gene expression sample generation for improved cancer subtype predictions
The accuracy of machine learning methods is often limited by the amount of training data that is available. We proposed to improve …
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The GA4GH Task Execution Application Programming Interface: Enabling Easy Multicloud Task Execution
The Global Alliance for Genomics and Health (GA4GH) Task Execution Service (TES) application programming interface (API) is a …
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recountmethylation enables flexible analysis of public blood DNA methylation array data
Thousands of DNA methylation (DNAm) array samples from human blood are publicly available on the Gene Expression Omnibus (GEO), but …
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Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space
The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to …
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GA4GH: International policies and standards for data sharing across genomic research and healthcare
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of …
Heidi L Rehm, Angela J H Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, Lawrence J Babb, Maxmillian P Barkley, Michael Baudis, Michael J S Beauvais, Tim Beck, Jacques S Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K Bonfield, Tiffany F Boughtwood, Guillaume Bourque, Sarion R Bowers, Anthony J Brookes, Michael Brudno, Matthew H Brush, David Bujold, Tony Burdett, Orion J Buske, Moran N Cabili, Daniel L Cameron, Robert J Carroll, Esmeralda Casas-Silva, Debyani Chakravarty, Bimal P Chaudhari, Shu Hui Chen, J Michael Cherry, Justina Chung, Melissa Cline, Hayley L Clissold, Robert M Cook-Deegan, Mélanie Courtot, Fiona Cunningham, Miro Cupak, Robert M Davies, Danielle Denisko, Megan J Doerr, Lena I Dolman, Edward S Dove, L Jonathan Dursi, Stephanie O M Dyke, James a Eddy, Karen Eilbeck, Kyle P Ellrott, Susan Fairley, Khalid a Fakhro, Helen v Firth, Michael S Fitzsimons, Marc Fiume, Paul Flicek, Ian M Fore, Mallory a Freeberg, Robert R Freimuth, Lauren a Fromont, Jonathan Fuerth, Clara L Gaff, Weiniu Gan, Elena M Ghanaim, David Glazer, Robert C Green, Malachi Griffith, Obi L Griffith, Robert L Grossman, Tudor Groza, Jaime M Guidry Auvil, Roderic Guigó, Dipayan Gupta, Melissa a Haendel, Ada Hamosh, David P Hansen, Reece K Hart, Dean Mitchell Hartley, David Haussler, Rachele M Hendricks-Sturrup, Calvin W L Ho, Ashley E Hobb, Michael M Hoffman, Oliver M Hofmann, Petr Holub, Jacob Shujui Hsu, Jean-Pierre Hubaux, Sarah E Hunt, Ammar Husami, Julius O Jacobsen, Saumya S Jamuar, Elizabeth L Janes, Francis Jeanson, Aina Jené, Amber L Johns, Yann Joly, Steven J M Jones, Alexander Kanitz, Kazuto Kato, Thomas M Keane, Kristina Kekesi-Lafrance, Jerome Kelleher, Giselle Kerry, Seik-Soon Khor, Bartha M Knoppers, Melissa a Konopko, Kenjiro Kosaki, Martin Kuba, Jonathan Lawson, Rasko Leinonen, Stephanie Li, Michael F Lin, Mikael Linden, Xianglin Liu, Isuru Udara Liyanage, Javier Lopez, Anneke M Lucassen, Michael Lukowski, Alice L Mann, John Marshall, Michele Mattioni, Alejandro Metke-Jimenez, Anna Middleton, Richard J Milne, Fruzsina Molnár-Gábor, Nicola Mulder, Monica C Munoz-Torres, Rishi Nag, Hidewaki Nakagawa, Jamal Nasir, Arcadi Navarro, Tristan H Nelson, Ania Niewielska, Amy Nisselle, Jeffrey Niu, Tommi H Nyrönen, Brian D O'Connor, Sabine Oesterle, Soichi Ogishima, Vivian Ota Wang, Laura a D Paglione, Emilio Palumbo, Helen E Parkinson, Anthony a Philippakis, Angel D Pizarro, Andreas Prlic, Jordi Rambla, Augusto Rendon, Renee a Rider, Peter N Robinson, Kurt W Rodarmer, Laura Lyman Rodriguez, Alan F Rubin, Manuel Rueda, Gregory a Rushton, Rosalyn S Ryan, Gary I Saunders, Helen Schuilenburg, Torsten Schwede, Serena Scollen, Alexander Senf, Nathan C Sheffield, Neerjah Skantharajah, Albert v Smith, Heidi J Sofia, Dylan Spalding, Amanda B Spurdle, Zornitza Stark, Lincoln D Stein, Makoto Suematsu, Patrick Tan, Jonathan a Tedds, Alastair a Thomson, Adrian Thorogood, Timothy L Tickle, Katsushi Tokunaga, Juha Törnroos, David Torrents, Sean Upchurch, Alfonso Valencia, Roman Valls Guimera, Jessica Vamathevan, Susheel Varma, Danya F Vears, Coby Viner, Craig Voisin, Alex H Wagner, Susan E Wallace, Brian P Walsh, Marc S Williams, Eva C Winkler, Barbara J Wold, Grant M Wood, J Patrick Woolley, Chisato Yamasaki, Andrew D Yates, Christina K Yung, Lyndon J Zass, Ksenia Zaytseva, Junjun Zhang, Peter Goodhand, Kathryn North, Ewan Birney
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A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery
The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the …
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Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20128-w.
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole …
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A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis …
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neoepiscope improves neoepitope prediction with multivariant phasing
The vast majority of tools for neoepitope prediction from DNA sequencing of complementary tumor and normal patient samples do not …
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Exploring Integrative Analysis Using the BioMedical Evidence Graph
The analysis of cancer biology data involves extremely heterogeneous data sets, including information from RNA sequencing, genome-wide …
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A community effort to create standards for evaluating tumor subclonal reconstruction
Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary …
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Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges
Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the …
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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
The phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance …
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Valection: design optimization for validation and verification studies
Platform-specific error profiles necessitate confirmatory studies where predictions made on data generated using one technology are …
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Population-level distribution and putative immunogenicity of cancer neoepitopes
Tumor neoantigens are drivers of cancer immunotherapy response; however, current prediction tools produce many candidates requiring …
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Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, …
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Germline contamination and leakage in whole genome somatic single nucleotide variant detection
The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient …
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C-Type Lectin Receptor (CLR)-Fc Fusion Proteins As Tools to Screen for Novel CLR/Bacteria Interactions: An Exemplary Study on Preselected Campylobacter jejuni Isolates
C-type lectin receptors (CLRs) are carbohydrate-binding receptors that recognize their ligands often in a Ca2+-dependent manner. Upon …
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A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
We report the results of a DREAM challenge designed to predict relative genetic essentialities based on a novel dataset testing 98,000 …
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TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within …
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Prophetic Granger Causality to infer gene regulatory networks
We introduce a novel method called Prophetic Granger Causality (PGC) for inferring gene regulatory networks (GRNs) from protein-level …
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Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, …
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Global optimization of somatic variant identification in cancer genomes with a global community challenge
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The Cancer Genome Atlas Pan-Cancer analysis project
The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular …
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Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
The Cancer Genome Atlas Pan-Cancer Analysis Working Group collaborated on the Synapse software platform to share and evolve data, …
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The UCSC Cancer Genomics Browser: update 2013
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse …
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TOPSAN: a dynamic web database for structural genomics
The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures …
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The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu
Sufu (Suppressor of Fused), a two-domain protein, plays a critical role in regulating Hedgehog signaling and is conserved from flies to …
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The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation
Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from …
Debanu Das, Nick v Grishin, Abhinav Kumar, Dennis Carlton, Constantina Bakolitsa, Mitchell D Miller, Polat Abdubek, Tamara Astakhova, Herbert L Axelrod, Prasad Burra, Connie Chen, Hsiu Ju Chiu, Michelle Chiu, Thomas Clayton, Marc C Deller, Lian Duan, Kyle Ellrott, Dustin Ernst, Carol L Farr, Julie Feuerhelm, Anna Grzechnik, Slawomir K Grzechnik, Joanna C Grant, Gye Won Han, Lukasz Jaroszewski, Kevin K Jin, Hope a Johnson, Heath E Klock, Mark W Knuth, Piotr Kozbial, S Sri Krishna, David Marciano, Daniel McMullan, Andrew T Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Silvya Oommachen, Jessica Paulsen, Christina Puckett, Ron Reyes, Christopher L Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, Henry Van Den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O Hodgson, John Wooley, Marc-André Elsliger, Ashley M Deacon, Adam Godzik, Scott a Lesley, Ian a Wilson
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The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold
KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal …
Debanu Das, Piotr Kozbial, Gye Won Han, Dennis Carlton, Lukasz Jaroszewski, Polat Abdubek, Tamara Astakhova, Herbert L Axelrod, Constantina Bakolitsa, Connie Chen, Hsiu Ju Chiu, Michelle Chiu, Thomas Clayton, Marc C Deller, Lian Duan, Kyle Ellrott, Marc-André Elsliger, Dustin Ernst, Carol L Farr, Julie Feuerhelm, Anna Grzechnik, Joanna C Grant, Kevin K Jin, Hope a Johnson, Heath E Klock, Mark W Knuth, S Sri Krishna, Abhinav Kumar, David Marciano, Daniel McMullan, Mitchell D Miller, Andrew T Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Silvya Oommachen, Jessica Paulsen, Christina Puckett, Ron Reyes, Christopher L Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, Henry Van Den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O Hodgson, John Wooley, Ashley M Deacon, Adam Godzik, Scott a Lesley, Ian a Wilson
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The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function
Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been …
Debanu Das, Robert D Finn, Dennis Carlton, Mitchell D Miller, Polat Abdubek, Tamara Astakhova, Herbert L Axelrod, Constantina Bakolitsa, Connie Chen, Hsiu Ju Chiu, Michelle Chiu, Thomas Clayton, Marc C Deller, Lian Duan, Kyle Ellrott, Dustin Ernst, Carol L Farr, Julie Feuerhelm, Joanna C Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K Jin, Heath E Klock, Mark W Knuth, Piotr Kozbial, S Sri Krishna, Abhinav Kumar, David Marciano, Daniel McMullan, Andrew T Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Christopher L Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, Henry Van Den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O Hodgson, John Wooley, Marc-André Elsliger, Ashley M Deacon, Adam Godzik, Scott a Lesley, Ian a Wilson
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Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger
Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the …
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Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism
The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion …
Constantina Bakolitsa, Abhinav Kumar, Kevin K Jin, Daniel McMullan, S Sri Krishna, Mitchell D Miller, Polat Abdubek, Claire Acosta, Tamara Astakhova, Herbert L Axelrod, Prasad Burra, Dennis Carlton, Connie Chen, Hsiu Ju Chiu, Thomas Clayton, Debanu Das, Marc C Deller, Lian Duan, Ylva Elias, Kyle Ellrott, Dustin Ernst, Carol L Farr, Julie Feuerhelm, Joanna C Grant, Anna Grzechnik, Slawomir K Grzechnik, Gye Won Han, Lukasz Jaroszewski, Hope a Johnson, Heath E Klock, Mark W Knuth, Piotr Kozbial, David Marciano, Andrew T Morse, Kevin D Murphy, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Jessica Paulsen, Christina Puckett, Ron Reyes, Christopher L Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, Christina v Trout, Henry Van Den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith O Hodgson, John Wooley, Marc Andre Elsliger, Ashley M Deacon, Adam Godzik, Scott a Lesley, Ian a Wilson
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Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases
Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly …
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Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules
The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first …
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Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism
BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over …
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Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron
Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and …
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A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution
BT1062 from Bacteroides thetaiotaomicron is a homolog of Mfa2 (PGN0288 or PG0179), which is a component of the minor fimbriae in …
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Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families
The microbes that inhabit particular environments must be able to perform molecular functions that provide them with a competitive …
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Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain
Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for …
Qingping Xu, Alex Bateman, Robert D Finn, Polat Abdubek, Tamara Astakhova, Herbert L Axelrod, Constantina Bakolitsa, Dennis Carlton, Connie Chen, Hsiu Ju Chiu, Michelle Chiu, Thomas Clayton, Debanu Das, Marc C Deller, Lian Duan, Kyle Ellrott, Dustin Ernst, Carol L Farr, Julie Feuerhelm, Joanna C Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K Jin, Heath E Klock, Mark W Knuth, Piotr Kozbial, S Sri Krishna, Abhinav Kumar, David Marciano, Daniel McMullan, Mitchell D Miller, Andrew T Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Christopher L Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, Henry Van Den Bedem, Dana Weekes, Tiffany Wooten, Keith O Hodgson, John Wooley, Marc-André Elsliger, Ashley M Deacon, Adam Godzik, Scott a Lesley, Ian a Wilson
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Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes
SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur exclusively in morphologically complex …
Qingping Xu, Bjørn a Traag, Joost Willemse, Daniel McMullan, Mitchell D Miller, Marc-André Elsliger, Polat Abdubek, Tamara Astakhova, Herbert L Axelrod, Constantina Bakolitsa, Dennis Carlton, Connie Chen, Hsiu Ju Chiu, Maksymilian Chruszcz, Thomas Clayton, Debanu Das, Marc C Deller, Lian Duan, Kyle Ellrott, Dustin Ernst, Carol L Farr, Julie Feuerhelm, Joanna C Grant, Anna Grzechnik, Slawomir K Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K Jin, Heath E Klock, Mark W Knuth, Piotr Kozbial, S Sri Krishna, Abhinav Kumar, David Marciano, Wladek Minor, A Mieke Mommaas, Andrew T Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Silvya Oommachen, Jessica Paulsen, Christina Puckett, Ron Reyes, Christopher L Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, Henry Van Den Bedem, Shuren Wang, Dana Weekes, Keith O Hodgson, John Wooley, Ashley M Deacon, Adam Godzik, Scott a Lesley, Ian a Wilson, Gilles P Van Wezel
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Improving the performance of protein threading using insertion/deletion frequency arrays
As a protein evolves, not every part of the amino acid sequence has an equal probability of being deleted or for allowing insertions, …
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A historical perspective of template-based protein structure prediction
This chapter presents a broad and a historical overview of the problem of protein structure prediction. Different structure prediction …
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Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays
As a protein evolves, not every part of the amino acid sequence has an equal probability of being deleted or for allowing insertions, …
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A generalized threading model using integer programming that allows for secondary structure element deletion
Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek …
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PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction
Knowledge of the detailed structure of a protein is crucial to our understanding of the biological functions of that protein. The gap …
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A computational pipeline for protein structure prediction and analysis at genome scale
Experimental techniques alone cannot keep up with the production rate of protein sequences, while computational techniques for protein …
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PROSPECT II: protein structure prediction program for genome-scale applications
A new method for fold recognition is developed and added to the general protein structure prediction package PROSPECT ( …
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Restriction enzyme recognition sequence search program
A critical and difficult part of characterizing restriction enzymes and methylases is the identification of recognition sequences. To …
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Identifying transcription factor binding sites through Markov chain optimization
Even though every cell in an organism contains the same genetic material, each cell does not express the same cohort of genes. …
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