Submissions from 2019
Framing technology challenges associated with improving cancer immunotherapies., James R Heath
Average Fitness Differences on NK Landscapes., Wim Hordijk, Stuart A Kauffman, and Peter F Stadler
Molecular Diversity Required for the Formation of Autocatalytic Sets., Wim Hordijk, Mike Steel, and Stuart A Kauffman
A Blueprint for Systems Biology., Trey Ideker and Leroy Hood
Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data., Vera Ignjatovic, Philipp E Geyer, Krishnan K Palaniappan, Jessica E Chaaban, Gilbert S Omenn, Mark S Baker, Eric W Deutsch, and Jochen M Schwenk
Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies., Jukka Intosalmi, Adrian C Scott, Michelle Hays, Nicholas Flann, Olli Yli-Harja, Harri Lähdesmäki, Aimée M Dudley, and Alexander Skupin
Six Month Abstinence Heterogeneity in the Best Quit Study., Harold S Javitz, Terry M Bush, Jennifer C Lovejoy, Alula J Torres, Tallie Wetzel, Ken P Wassum, Marcia M Tan, Nabil Alshurafa, and Bonnie Spring
Cancer cell population growth kinetics at low densities deviate from the exponential growth model and suggest an Allee effect., Kaitlyn E Johnson, Grant Howard, William Mo, Michael K Strasser, Ernesto A B F Lima, Sui Huang, and Amy Brock
Cancer cell population growth kinetics at low densities deviate from the exponential growth model and suggest an Allee effect., Kaitlyn E Johnson, Grant Howard, William Mo, Michael K Strasser, Ernesto A B F Lima, Sui Huang, and Amy Brock
Assessing protein sequence database suitability using de novo sequencing., Richard Johnson, Brian C Searle, Brook L Nunn, Jason M Gilmore, Molly Phillips, Chris T Amemiya, Michelle Heck, and Michael J MacCoss
An Inflammatory Landscape for Preoperative Neurologic Deficits in Glioblastoma., Amal Katrib, Hyun-Hwan Jeong, Nina L Fransen, Kristin S Henzel, and Jeremy A Miller
Genomic and molecular characterization of preterm birth., Theo A Knijnenburg, Joseph G Vockley, Nyasha Chambwe, David L Gibbs, Crystal Humphries, Kathi C Huddleston, Elisabeth Klein, Prachi Kothiyal, Ryan Tasseff, Varsha Dhankani, Dale L Bodian, Wendy S W Wong, Gustavo Glusman, Denise E Mauldin, Michael Miller, Joseph Slagel, Summer Elasady, Jared C Roach, Roger Kramer, Kalle Leinonen, Jasper Linthorst, Rajiv Baveja, Robin Baker, Benjamin D Solomon, Greg Eley, Ramaswamy K Iyer, George L Maxwell, Brady Bernard, Ilya Shmulevich, Leroy Hood, and John E Niederhuber
The Impact of Moyamoya Disease and, Ming-Jen Lee, Shannon Fallen, Yong Zhou, David Baxter, Kelsey Scherler, Meng-Fai Kuo, and Kai Wang
Distinct Profiles of Cell-Free MicroRNAs in Plasma of Veterans with Post-Traumatic Stress Disorder., Min Young Lee, David Baxter, Kelsey Scherler, Taek-Kyun Kim, Xiaogang Wu, Duna Abu-Amara, Janine Flory, Rachel Yehuda, Charles Marmar, Marti Jett, Inyoul Lee, Kai Wang, and Leroy Hood
A biological function based biomarker panel optimization process., Min Young Lee, Taek-Kyun Kim, Kathie-Anne Walters, and Kai Wang
Characterizing the cancer-associated microbiome with small RNA sequencing data., Wei-Hao Lee, Kai-Pu Chen, Kai Wang, Hsuan-Cheng Huang, and Hsueh-Fen Juan
Synthesis and preclinical validation of novel P2Y1 receptor ligands as a potent anti-prostate cancer agent., Hien Thi Thu Le, Tatu Rimpilainen, Saravanan Konda Mani, Akshaya Murugesan, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu
Inhibition of heme sequestration of histidine-rich protein 2 using multiple epitope-targeted peptides., JingXin Liang, David N Bunck, Anvita Mishra, Sunga Hong, Matthew N Idso, and James R Heath
Inhibition of heme sequestration of histidine-rich protein 2 using multiple epitope-targeted peptides., JingXin Liang, David N Bunck, Anvita Mishra, Sunga Hong, Matthew N Idso, and James R Heath
Time-dependent saddle-node bifurcation: Breaking time and the point of no return in a non-autonomous model of critical transitions., Jeremiah H Li, Felix X-F Ye, Hong Qian, and Sui Huang
Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites., Scott E Lindner, Kristian E Swearingen, Melanie J Shears, Michael P Walker, Erin N Vrana, Kevin J Hart, Allen M Minns, Photini Sinnis, Robert L Moritz, and Stefan H I Kappe
Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction., Xindong Liu, Yun Wang, Huiping Lu, Jing Li, Xiaowei Yan, Minglu Xiao, Jing Hao, Andrei Alekseev, Hiep Khong, Tenghui Chen, Rui Huang, Jin Wu, Qiwen Zhao, Qi Wu, Senlin Xu, Xiaohu Wang, Wei Jin, Shicang Yu, Yan Wang, Lai Wei, Aibo Wang, Bo Zhong, Ling Ni, Xiaolong Liu, Roza Nurieva, Lilin Ye, Qiang Tian, Xiu-Wu Bian, and Chen Dong
Liquid biopsy-based single-cell metabolic phenotyping of lung cancer patients for informative diagnostics., Ziming Li, Zhuo Wang, Yin Tang, Xiang Lu, Jie Chen, Yu Dong, Baojun Wu, Chunying Wang, Liu Yang, Zhili Guo, Min Xue, Shun Lu, Wei Wei, and Qihui Shi
Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop., Mark E Lowe, Dana K Andersen, Richard M Caprioli, Jyoti Choudhary, Zobeida Cruz-Monserrate, Anil K Dasyam, Christopher E Forsmark, Fred S Gorelick, Joe W Gray, Mark Haupt, Kimberly A Kelly, Kenneth P Olive, Sylvia K Plevritis, Noa Rappaport, Holger R Roth, Hanno Steen, S Joshua Swamidass, Temel Tirkes, Aliye Uc, Kirill Veselkov, David C Whitcomb, and Aida Habtezion
Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop., Mark E Lowe, Dana K Andersen, Richard M Caprioli, Jyoti Choudhary, Zobeida Cruz-Monserrate, Anil K Dasyam, Christopher E Forsmark, Fred S Gorelick, Joe W Gray, Mark Haupt, Kimberly A Kelly, Kenneth P Olive, Sylvia K Plevritis, Noa Rappaport, Holger R Roth, Hanno Steen, S Joshua Swamidass, Temel Tirkes, Aliye Uc, Kirill Veselkov, David C Whitcomb, and Aida Habtezion
Identification of Cross-linked Peptides Using Isotopomeric Cross-linkers., Jie Luo, Jacob Bassett, and Jeff Ranish
4D electron microscopy of T cell activation., Yue Lu, Byung-Kuk Yoo, Alphonsus H C Ng, Jungwoo Kim, Sinchul Yeom, Jau Tang, Milo M Lin, Ahmed H Zewail, and James R Heath
4D electron microscopy of T cell activation., Yue Lu, Byung-Kuk Yoo, Alphonsus H C Ng, Jungwoo Kim, Sinchul Yeom, Jau Tang, Milo M Lin, Ahmed H Zewail, and James R Heath
Reproducible big data science: A case study in continuous FAIRness., Ravi Madduri, Kyle Chard, Mike D'Arcy, Segun C Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W Deutsch, Cory C Funk, Ben Heavner, Matthew A Richards, Paul Shannon, Gustavo Glusman, Nathan D Price, Carl Kesselman, and Ian Foster
Influenza A Reinfection in Sequential Human Challenge: Implications for Protective Immunity and "Universal" Vaccine Development., Matthew J Memoli, Alison Han, Kathie-Anne Walters, Lindsay Czajkowski, Susan Reed, Rani Athota, Luz Angela Rosas, Adriana Cervantes-Medina, Jae-Keun Park, David M Morens, John C Kash, and Jeffery K Taubenberger
MITF has a central role in regulating starvation-induced autophagy in melanoma., Katrin Möller, Sara Sigurbjornsdottir, Asgeir O Arnthorsson, Vivian Pogenberg, Ramile Dilshat, Valerie Fock, Solveig H Brynjolfsdottir, Christian Bindesboll, Margret Bessadottir, Helga M Ogmundsdottir, Anne Simonsen, Lionel Larue, Matthias Wilmanns, Vesteinn Thorsson, Eirikur Steingrimsson, and Margret H Ogmundsdottir
Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks., Aliyu Musa, Shailesh Tripathi, Matthias Dehmer, Olli Yli-Harja, Stuart A Kauffman, and Frank Emmert-Streib
Publisher Correction: Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer., Huân M Ngô, Ying Zhou, Hernan Lorenzi, Kai Wang, Taek-Kyun Kim, Yong Zhou, Kamal El Bissati, Ernest Mui, Laura Fraczek, Seesandra V Rajagopala, Craig W Roberts, Fiona L Henriquez, Alexandre Montpetit, Jenefer M Blackwell, Sarra E Jamieson, Kelsey Wheeler, Ian J Begeman, Carlos Naranjo-Galvis, Ney Alliey-Rodriguez, Roderick G Davis, Liliana Soroceanu, Charles Cobbs, Dennis A Steindler, Kenneth Boyer, A Gwendolyn Noble, Charles N Swisher, Peter T Heydemann, Peter Rabiah, Shawn Withers, Patricia Soteropoulos, Leroy Hood, and Rima McLeod
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree., Charles J Norsigian, Neha Pusarla, John Luke McConn, James T Yurkovich, Andreas Dräger, Bernhard O Palsson, and Zachary King
Single-Cell Glia and Neuron Gene Expression in the Central Amygdala in Opioid Withdrawal Suggests Inflammation With Correlated Gut Dysbiosis., Sean J O'Sullivan, Evangelia Malahias, James Park, Ankita Srivastava, Beverly A S Reyes, Jon Gorky, Rajanikanth Vadigepalli, Elisabeth J Van Bockstaele, and James S Schwaber
Advances in Identifying and Characterizing the Human Proteome., Young-Ki Paik, Christopher M Overall, Fernando Corrales, Eric W Deutsch, Lydie Lane, and Gilbert S Omenn
Advances in Identifying and Characterizing the Human Proteome., Young-Ki Paik, Christopher M Overall, Fernando Corrales, Eric W Deutsch, Lydie Lane, and Gilbert S Omenn
Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate., Carmen G Palii, Qian Cheng, Mark A Gillespie, Paul Shannon, Michalina Mazurczyk, Giorgio Napolitani, Nathan D Price, Jeffrey A Ranish, Edward Morrissey, Douglas R Higgs, and Marjorie Brand
Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases., Dipak Panigrahy, Allison Gartung, Jun Yang, Haixia Yang, Molly M Gilligan, Megan L Sulciner, Swati S Bhasin, Diane R Bielenberg, Jaimie Chang, Birgitta A Schmidt, Julia Piwowarski, Anna Fishbein, Dulce Soler-Ferran, Matthew A Sparks, Steven J Staffa, Vidula Sukhatme, Bruce D Hammock, Mark W Kieran, Sui Huang, Manoj Bhasin, Charles N Serhan, and Vikas P Sukhatme
Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases., Dipak Panigrahy, Allison Gartung, Jun Yang, Haixia Yang, Molly M Gilligan, Megan L Sulciner, Swati S Bhasin, Diane R Bielenberg, Jaimie Chang, Birgitta A Schmidt, Julia Piwowarski, Anna Fishbein, Dulce Soler-Ferran, Matthew A Sparks, Steven J Staffa, Vidula Sukhatme, Bruce D Hammock, Mark W Kieran, Sui Huang, Manoj Bhasin, Charles N Serhan, and Vikas P Sukhatme
MicroRNA-transcriptome networks in whole blood and monocytes of women undergoing preterm labour., Alison G Paquette, Oksana Shynlova, Xiaogang Wu, Mark Kibschull, Kai Wang, Nathan D Price, and Stephen J Lye
Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement., Avinash B Patel, Camille M Moore, Basil J Greber, Jie Luo, Stefan A Zukin, Jeff Ranish, and Eva Nogales
Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders., Jocelynn R Pearl, Carlo Colantuoni, Dani E Bergey, Cory C Funk, Paul Shannon, Bijoya Basu, Alex M Casella, Rediet T Oshone, Leroy Hood, Nathan D Price, and Seth A Ament
Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood., Songming Peng, Jesse M Zaretsky, Alphonsus H C Ng, William Chour, Michael T Bethune, Jongchan Choi, Alice Hsu, Elizabeth Holman, Xiaozhe Ding, Katherine Guo, Jungwoo Kim, Alexander M Xu, John E Heath, Won Jun Noh, Jing Zhou, Yapeng Su, Yue Lu, Jami McLaughlin, Donghui Cheng, Owen N Witte, David Baltimore, Antoni Ribas, and James R Heath
Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation., Eliza Jr Peterson, Rebeca Bailo, Alissa C Rothchild, Mario L Arrieta-Ortiz, Amardeep Kaur, Min Pan, Dat Mai, Abrar A Abidi, Charlotte Cooper, Alan Aderem, Apoorva Bhatt, and Nitin S Baliga
Absence of full-length dystrophin impairs normal maturation and contraction of cardiomyocytes derived from human induced pluripotent stem cells., J Manuel Pioner, Xuan Guan, Jordan M Klaiman, Alice W Racca, Lil Pabon, Veronica Muskheli, Jesse Macadangdang, Cecilia Ferrantini, Michael R Hoopmann, Robert L Moritz, Deok-Ho Kim, Chiara Tesi, Corrado Poggesi, Charles E Murry, Martin K Childers, David L Mack, and Michael Regnier
A Pan-Cancer Approach to Predict Responsiveness to Immune Checkpoint Inhibitors by Machine Learning., Maurizio Polano, Marco Chierici, Michele Dal Bo, Davide Gentilini, Federica Di Cintio, Lorena Baboci, David L Gibbs, Cesare Furlanello, and Giuseppe Toffoli
A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research., M Poyet, M Groussin, S M Gibbons, J Avila-Pacheco, X Jiang, S M Kearney, A R Perrotta, B Berdy, S Zhao, T D Lieberman, P K Swanson, M Smith, S Roesemann, J E Alexander, S A Rich, J Livny, H Vlamakis, C Clish, K Bullock, A Deik, J Scott, K A Pierce, R J Xavier, and E J Alm
Gene annotation errors are common in the mammalian mitochondrial genomes database., Carlos F Prada and Jeffrey L Boore
Spatial presentation of biological molecules to cells by localized diffusive transfer., Mary C Regier, Emily Olszewski, Christoph C Carter, John D Aitchison, Alexis Kaushansky, Jennifer Davis, Erwin Berthier, David J Beebe, and Kelly R Stevens
Opportunities and Challenges in Interpreting and Sharing Personal Genomes., Irit R Rubin and Gustavo Glusman
In vivo proteomics identifies the competence regulon and AliB oligopeptide transporter as pathogenic factors in pneumococcal meningitis., Frank Schmidt, Niamatullah Kakar, Tanja C Meyer, Maren Depke, Ilias Masouris, Gerhard Burchhardt, Alejandro Gómez-Mejia, Vishnu Dhople, Leiv S Håvarstein, Zhi Sun, Robert L Moritz, Uwe Völker, Uwe Koedel, and Sven Hammerschmidt
Incorporating In-Source Fragments Improves Metabolite Identification Accuracy in Untargeted LCMS and LCMS/MS Datasets., Brian C Searle, Jacob C Lippincott, and Phillip M Seitzer
An efficient solution for resolving iTRAQ and TMT channel crosstalk., Brian C Searle and Alfred L Yergey
Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism., Muhammad Shahid, Minhyung Kim, Min Young Lee, Austin Yeon, Sungyong You, Hyung L Kim, and Jayoung Kim
Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism., Muhammad Shahid, Minhyung Kim, Min Young Lee, Austin Yeon, Sungyong You, Hyung L Kim, and Jayoung Kim
Proteomic Analysis of Plasmodium Merosomes: The Link between Liver and Blood Stages in Malaria., Melanie J Shears, Raja Sekhar Nirujogi, Kristian E Swearingen, Santosh Renuse, Satish Mishra, Panga Jaipal Reddy, Robert L Moritz, Akhilesh Pandey, and Photini Sinnis
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling., Fangzhou Shen, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D Price, Chenguang Liu, and Zhuo Wang
PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline., David Shteynberg, Eric W Deutsch, David S Campbell, Michael R Hoopmann, Ulrike Kusebauch, Dave Lee, Luis Mendoza, Mukul K Midha, Zhi Sun, Anthony D Whetton, and Robert L Moritz
Mechanistic inferences on metabolic dysfunction in PTSD from an integrated model and multi-omic analysis: Role of glucocorticoid receptor sensitivity., Pramod R Somvanshi, Synthia H Mellon, Janine D Flory, Duna Abu-Amara, Ptsd Systems Biology Consortium, Owen M Wolkowitz, Rachel Yehuda, Marti Jett, Leroy Hood, Charles Marmar, and Francis J Doyle
Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance., Yapeng Su, Marcus Bintz, Yezi Yang, Lidia Robert, Alphonsus H C Ng, Victoria Liu, Antoni Ribas, James R Heath, and Wei Wei
A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry., Kristian E Swearingen, Jimmy K Eng, David Shteynberg, Vladimir Vigdorovich, Timothy A Springer, Luis Mendoza, D Noah Sather, Eric W Deutsch, Stefan H I Kappe, and Robert L Moritz
Circulatory metastin/kisspeptin-1 in polycystic ovary syndrome: a systematic review and meta-analysis with diagnostic test accuracy., Seshadri Reddy Varikasuvu, V Satya Prasad, V C Vamshika, M V Satyanarayana, and Panga Jaipal Reddy
Circulating Angiopoietin-like 8 protein (ANGPTL8/Betatrophin) in patients with polycystic ovary syndrome: a systematic review and multi effect size meta-analysis., Seshadri Reddy Varikasuvu, Panga Jaipal Reddy, and M V Satyanarayana
Plasmodium Secretion Induces Hepatocyte Lysosome Exocytosis and Promotes Parasite Entry., Kamalakannan Vijayan, Igor Cestari, Fred D Mast, Elizabeth K K Glennon, Suzanne M McDermott, Heather S Kain, Alyssa M Brokaw, John D Aitchison, Kenneth Stuart, and Alexis Kaushansky
2-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)benzonitrile as novel inhibitor of receptor tyrosine kinase and PI3K/AKT/mTOR signaling pathway in glioblastoma., Anisha Viswanathan, Dinesh Kute, Aliyu Musa, Saravanan Konda Mani, Vili Sipilä, Frank Emmert-Streib, Fedor I Zubkov, Atash V Gurbanov, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
Battling Glioblastoma: A Novel Tyrosine Kinase Inhibitor with Multi-Dimensional Anti-Tumor Effect (Running Title: Cancer Cells Death Signalling Activation)., Anisha Viswanathan, Aliyu Musa, Akshaya Murugesan, João R Vale, Carlos A M Afonso, Saravanan Konda Mani, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu
The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases., Juan Antonio Vizcaíno, Peter Kubiniok, Kevin Kovalchik, Qing Ma, Jérôme Despault Duquette, Ian Mongrain, Eric W Deutsch, Bjoern Peters, Alessandro Sette, Isabelle Sirois, and Etienne Caron
Differential Effects of Influenza Virus NA, HA Head, and HA Stalk Antibodies on Peripheral Blood Leukocyte Gene Expression during Human Infection., Kathie-Anne Walters, Ruoqing Zhu, Michael Welge, Kelsey Scherler, Jae-Keun Park, Zainab Rahil, Hao Wang, Loretta Auvil, Colleen Bushell, Min Young Lee, David Baxter, Tyler Bristol, Luz Angela Rosas, Adriana Cervantes-Medina, Lindsay Czajkowski, Alison Han, Matthew J Memoli, Jeffery K Taubenberger, and John C Kash
Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science., Susan T Weintraub, Michael R Hoopmann, and Magnus Palmblad
Special Issue on Single-Cell Multiomics for Immuno-Oncology and Cancer Systems Biology., Wei Wei and Rong Fan
Buparlisib in Patients With Recurrent Glioblastoma Harboring Phosphatidylinositol 3-Kinase Pathway Activation: An Open-Label, Multicenter, Multi-Arm, Phase II Trial., Patrick Y Wen, Mehdi Touat, Brian M Alexander, Ingo K Mellinghoff, Shakti Ramkissoon, Christine S McCluskey, Kristine Pelton, Sam Haidar, Sankha S Basu, Sarah C Gaffey, Loreal E Brown, Juan Emmanuel Martinez-Ledesma, Shaofang Wu, Jungwoo Kim, Wei Wei, Mi-Ae Park, Jason T Huse, John G Kuhn, Mikael L Rinne, Howard Colman, Nathalie Y R Agar, Antonio M Omuro, Lisa M DeAngelis, Mark R Gilbert, John F de Groot, Timothy F Cloughesy, Andrew S Chi, Thomas M Roberts, Jean J Zhao, Eudocia Q Lee, Lakshmi Nayak, James R Heath, Laura L Horky, Tracy T Batchelor, Rameen Beroukhim, Susan M Chang, Azra H Ligon, Ian F Dunn, Dimpy Koul, Geoffrey S Young, Michael D Prados, David A Reardon, W K Alfred Yung, and Keith L Ligon
Buparlisib in Patients With Recurrent Glioblastoma Harboring Phosphatidylinositol 3-Kinase Pathway Activation: An Open-Label, Multicenter, Multi-Arm, Phase II Trial., Patrick Y Wen, Mehdi Touat, Brian M Alexander, Ingo K Mellinghoff, Shakti Ramkissoon, Christine S McCluskey, Kristine Pelton, Sam Haidar, Sankha S Basu, Sarah C Gaffey, Loreal E Brown, Juan Emmanuel Martinez-Ledesma, Shaofang Wu, Jungwoo Kim, Wei Wei, Mi-Ae Park, Jason T Huse, John G Kuhn, Mikael L Rinne, Howard Colman, Nathalie Y R Agar, Antonio M Omuro, Lisa M DeAngelis, Mark R Gilbert, John F de Groot, Timothy F Cloughesy, Andrew S Chi, Thomas M Roberts, Jean J Zhao, Eudocia Q Lee, Lakshmi Nayak, James R Heath, Laura L Horky, Tracy T Batchelor, Rameen Beroukhim, Susan M Chang, Azra H Ligon, Ian F Dunn, Dimpy Koul, Geoffrey S Young, Michael D Prados, David A Reardon, W K Alfred Yung, and Keith L Ligon
Blood metabolome predicts gut microbiome α-diversity in humans., Tomasz Wilmanski, Noa Rappaport, John C Earls, Andrew T Magis, Ohad Manor, Jennifer Lovejoy, Gilbert S Omenn, Leroy Hood, Sean M Gibbons, and Nathan D Price
Proximate grassland and shrub-encroached sites show dramatic restructuring of soil bacterial communities., Xingjia Xiang, Sean M Gibbons, He Li, Haihua Shen, and Haiyan Chu
Small Molecule KRAS Agonist for Mutant KRAS Cancer Therapy., Ke Xu, Dongkyoo Park, Andrew T Magis, Jun Zhang, Wei Zhou, Gabriel L Sica, Suresh S Ramalingam, Walter J Curran, and Xingming Deng
Blood Is a Window into Health and Disease., James T Yurkovich and Leroy Hood
A systems approach to clinical oncology uses deep phenotyping to deliver personalized care., James T Yurkovich, Qiang Tian, Nathan D Price, and Leroy Hood
EcoFABs: advancing microbiome science through standardized fabricated ecosystems., Karsten Zengler, Kirsten Hofmockel, Nitin Baliga, Scott W Behie, Hans C Bernstein, James B Brown, José R Dinneny, Sheri A Floge, Samuel P Forry, Matthias Hess, Scott A Jackson, Christer Jansson, Stephen R Lindemann, Jennifer Pett-Ridge, Costas Maranas, Ophelia S Venturelli, Matthew D Wallenstein, Elizabeth A Shank, and Trent R Northen
Survivin is a prognostic marker and therapeutic target for extranodal, nasal-type natural killer/T cell lymphoma., Li Zhang, Yi Wei, Xiaowei Yan, Na Li, Haolan Song, Li Yang, Yang Wu, Yu-Feng Xi, Hua-Wei Weng, Jian-Hua Li, Edward H Lin, and Li-Qun Zou
Adaptive Evolution within Gut Microbiomes of Healthy People., Shijie Zhao, Tami D Lieberman, Mathilde Poyet, Kathryn M Kauffman, Sean M Gibbons, Mathieu Groussin, Ramnik J Xavier, and Eric J Alm
Development of Hematopoietic Stem Cell-Engineered Invariant Natural Killer T Cell Therapy for Cancer., Yanni Zhu, Drake J Smith, Yang Zhou, Yan-Ruide Li, Jiaji Yu, Derek Lee, Yu-Chen Wang, Stefano Di Biase, Xi Wang, Christian Hardoy, Josh Ku, Tasha Tsao, Levina J Lin, Alexander T Pham, Heesung Moon, Jami McLaughlin, Donghui Cheng, Roger P Hollis, Beatriz Campo-Fernandez, Fabrizia Urbinati, Liu Wei, Larry Pang, Valerie Rezek, Beata Berent-Maoz, Mignonette H Macabali, David Gjertson, Xiaoyan Wang, Zoran Galic, Scott G Kitchen, Dong Sung An, Siwen Hu-Lieskovan, Paula J Kaplan-Lefko, Satiro N De Oliveira, Christopher S Seet, Sarah M Larson, Stephen J Forman, James R Heath, Jerome A Zack, Gay M Crooks, Caius G Radu, Antoni Ribas, Donald B Kohn, Owen N Witte, and Lili Yang
Genetic Predisposition Impacts Clinical Changes in a Lifestyle Coaching Program., Niha Zubair, Matthew P Conomos, Leroy Hood, Gilbert S Omenn, Nathan D Price, Bonnie J Spring, Andrew T Magis, and Jennifer C Lovejoy
Submissions from 2018
Cell death as a trigger for morphogenesis., Boris Aguilar, Ahmadreza Ghaffarizadeh, Christopher D Johnson, Gregory J Podgorski, Ilya Shmulevich, and Nicholas S Flann
Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy., Mariet Allen, Xue Wang, Daniel J Serie, Samantha L Strickland, Jeremy D Burgess, Shunsuke Koga, Curtis S Younkin, Thuy T Nguyen, Kimberly G Malphrus, Sarah J Lincoln, Melissa Alamprese, Kuixi Zhu, Rui Chang, Minerva M Carrasquillo, Naomi Kouri, Melissa E Murray, Joseph S Reddy, Cory Funk, Nathan D Price, Todd E Golde, Steven G Younkin, Yan W Asmann, Julia E Crook, Dennis W Dickson, and Nilüfer Ertekin-Taner
Transcriptional regulatory networks underlying gene expression changes in Huntington's disease., Seth A Ament, Jocelynn R Pearl, Jeffrey P Cantle, Robert M Bragg, Peter J Skene, Sydney R Coffey, Dani E Bergey, Vanessa C Wheeler, Marcy E MacDonald, Nitin S Baliga, Jim Rosinski, Leroy E Hood, Jeffrey B Carroll, and Nathan D Price
The Micronemal, Silvia A Arredondo, Kristian E Swearingen, Thomas Martinson, Ryan Steel, Dorender A Dankwa, Anke Harupa, Nelly Camargo, William Betz, Vladimir Vigdorovich, Brian G Oliver, Niwat Kangwanrangsan, Tomoko Ishino, Noah Sather, Sebastian Mikolajczak, Ashley M Vaughan, Motomi Torii, Robert L Moritz, and Stefan H I Kappe
Efficient region-based test strategy uncovers genetic risk factors for functional outcome in bipolar disorder., Monika Budde, Stefanie Friedrichs, Ney Alliey-Rodriguez, Seth Ament, Judith A Badner, Wade H Berrettini, Cinnamon S Bloss, William Byerley, Sven Cichon, Ashley L Comes, William Coryell, David W Craig, Franziska Degenhardt, Howard J Edenberg, Tatiana Foroud, Andreas J Forstner, Josef Frank, Elliot S Gershon, Fernando S Goes, Tiffany A Greenwood, Yiran Guo, Maria Hipolito, Leroy Hood, Brendan J Keating, Daniel L Koller, William B Lawson, Chunyu Liu, Pamela B Mahon, Melvin G McInnis, Francis J McMahon, Sandra M Meier, Thomas W Mühleisen, Sarah S Murray, Caroline M Nievergelt, John I Nurnberger, Evaristus A Nwulia, James B Potash, Danjuma Quarless, John Rice, Jared C Roach, William A Scheftner, Nicholas J Schork, Tatyana Shekhtman, Paul D Shilling, Erin N Smith, Fabian Streit, Jana Strohmaier, Szabolcs Szelinger, Jens Treutlein, Stephanie H Witt, Peter P Zandi, Peng Zhang, Sebastian Zöllner, Heike Bickeböller, Peter G Falkai, John R Kelsoe, Markus M Nöthen, Marcella Rietschel, Thomas G Schulze, and Dörthe Malzahn
Simultaneous vs. sequential treatment for smoking and weight management in tobacco quitlines: 6 and 12 month outcomes from a randomized trial., Terry Bush, Jennifer Lovejoy, Harold Javitz, Alula Jimenez Torres, Ken Wassum, Marcia M Tan, and Bonnie Spring
Niche emergence as an autocatalytic process in the evolution of ecosystems., Roberto Cazzolla Gatti, Brian Fath, Wim Hordijk, Stuart Kauffman, and Robert Ulanowicz
TLR5 decoy receptor as a novel anti-amyloid therapeutic for Alzheimer's disease., Paramita Chakrabarty, Andrew Li, Thomas B Ladd, Michael R Strickland, Emily J Koller, Jeremy D Burgess, Cory C Funk, Pedro E Cruz, Mariet Allen, Mariya Yaroshenko, Xue Wang, Curtis Younkin, Joseph Reddy, Benjamin Lohrer, Leonie Mehrke, Brenda D Moore, Xuefei Liu, Carolina Ceballos-Diaz, Awilda M Rosario, Christopher Medway, Christopher Janus, Hong-Dong Li, Dennis W Dickson, Benoit I Giasson, Nathan D Price, Steven G Younkin, Nilüfer Ertekin-Taner, and Todd E Golde
Chemotherapy-generated cell debris stimulates colon carcinoma tumor growth via osteopontin., Jaimie Chang, Swati S Bhasin, Diane R Bielenberg, Vikas P Sukhatme, Manoj Bhasin, Sui Huang, Mark W Kieran, and Dipak Panigrahy
Targeting Mcl-1 enhances DNA replication stress sensitivity to cancer therapy., Guo Chen, Andrew T Magis, Ke Xu, Dongkyoo Park, David S Yu, Taofeek K Owonikoko, Gabriel L Sica, Sarah W Satola, Suresh S Ramalingam, Walter J Curran, Paul W Doetsch, and Xingming Deng
Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer's disease., Jaeyoon Chung, Xiaoling Zhang, Mariet Allen, Xue Wang, Yiyi Ma, Gary Beecham, Thomas J Montine, Steven G Younkin, Dennis W Dickson, Todd E Golde, Nathan D Price, Nilüfer Ertekin-Taner, Kathryn L Lunetta, Jesse Mez, Richard Mayeux, Jonathan L Haines, Margaret A Pericak-Vance, Gerard Schellenberg, Gyungah R Jun, and Lindsay A Farrer
Criticality Distinguishes the Ensemble of Biological Regulatory Networks., Bryan C Daniels, Hyunju Kim, Douglas Moore, Siyu Zhou, Harrison B Smith, Bradley Karas, Stuart A Kauffman, and Sara I Walker
The Cytoscape Automation app article collection., Barry Demchak, David Otasek, Alexander R Pico, Gary D Bader, Keiichiro Ono, Brett Settle, Eric Sage, John H Morris, William Longabaugh, Christian Lopes, Michael Kucera, Adam Treister, Benno Schwikowski, Piet Molenaar, and Trey Ideker
Expanding the Use of Spectral Libraries in Proteomics., Eric W Deutsch, Yasset Perez-Riverol, Robert J Chalkley, Mathias Wilhelm, Stephen Tate, Timo Sachsenberg, Mathias Walzer, Lukas Käll, Bernard Delanghe, Sebastian Böcker, Emma L Schymanski, Paul Wilmes, Viktoria Dorfer, Bernhard Kuster, Pieter-Jan Volders, Nico Jehmlich, Johannes P C Vissers, Dennis W Wolan, Ana Y Wang, Luis Mendoza, Jim Shofstahl, Andrew W Dowsey, Johannes Griss, Reza M Salek, Steffen Neumann, Pierre-Alain Binz, Henry Lam, Juan Antonio Vizcaíno, Nuno Bandeira, and Hannes Röst
Digitizing omics profiles by divergence from a baseline., Wikum Dinalankara, Qian Ke, Yiran Xu, Lanlan Ji, Nicole Pagane, Anching Lien, Tejasvi Matam, Elana J Fertig, Nathan D Price, Laurent Younes, Luigi Marchionni, and Donald Geman
In vitro characterization of alkylaminophenols-induced cell death., Phuong Doan, Olga Anufrieva, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
