cran: APIS | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0118708

The Sound and the Fury—Bees Hiss when Expecting Danger
Cited by: 12
Author(s): Henja-Niniane Wehmann, David Gustav, Nicholas H. Kirkerud, C. Giovanni Galizia
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0004207

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum
Cited by: 97
Author(s): Dongying Wu, Jason Raymond, Martin Wu, Sourav Chatterji, Qinghu Ren, Joel E. Graham, Donald A. Bryant, Frank T. Robb, Albert S. Colman, Luke J. Tallon, Jonathan H. Badger, Ramana Madupu, Naomi Ward, Jonathan A. Eisen
Software Mentions: 3
Published: almost 16 years ago

10.1186/s12864-020-06894-3

PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome
Cited by: 13
Author(s): Hua Zhang, Hanzhi Xu, Huiru Liu, Xiaolan Pan, Meng Xu, Gege Zhang, Maoxian He
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-32511-1

Enhanced Prediction of Hot Spots at Protein-Protein Interfaces Using Extreme Gradient Boosting
Cited by: 62
Author(s): Hao Wang, Chuyao Liu, Lei Deng
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.49816

Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment
Cited by: 16
Author(s): Jordan G. Okie, Amisha T. Poret-Peterson, Zarraz M.-P. Lee, Alexander Richter, Luis David Alcaraz, Luis E. Eguiarte, Janet L. Siefert, Valeria Souza, Chris L. Dupont, James J. Elser
Software Mentions: 3
Published: almost 5 years ago

10.3390/molecules23102535

Machine Learning Approaches for Protein–Protein Interaction Hot Spot Prediction: Progress and Comparative Assessment
Cited by: 61
Author(s): Siyu Liu, Chuyao Liu, Lei Deng
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0020388

Going Deeper: Metagenome of a Hadopelagic Microbial Community
Cited by: 86
Author(s): Emiley A. Eloe, Douglas Fadrosh, M. A. Novotny, Lisa Zeigler Allen, Maria Kim, Mary‐Jane Lombardo, Joyclyn Yee-Greenbaum, Shibu Yooseph, Eric E. Allen, Roger S. Lasken, Shannon J. Williamson, Douglas H. Bartlett
Software Mentions: 2
Published: over 13 years ago

10.3389/fnbeh.2013.00029

APIS—a novel approach for conditioning honey bees
Cited by: 22
Author(s): Nicholas H. Kirkerud, Henja-Niniane Wehmann, C. Giovanni Galizia, David Gustav
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0173107

Postoperative pain treatment after total knee arthroplasty: A systematic review
Cited by: 117
Author(s): Anders Peder Højer Karlsen, Mik Wetterslev, Signe Elisa Hansen, Morten Sejer Hansen, Ole Mathiesen, Jørgen B. Dahl
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2013.00084

Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages
Cited by: 67
Author(s): Cristina Takacs-Vesbach, William P. Inskeep, Zackary J. Jay, Markus J. Herrgård, Douglas B. Rusch, Susannah G. Tringe, Mark A. Kozubal, Natsuko Hamamura, Richard E. Macur, Bruce W. Fouke, Anna‐Louise Reysenbach, Timothy R. McDermott, Ryan deM. Jennings, Nicolas W. Hengartner, Gary Xie
Software Mentions: 2
Published: almost 12 years ago

10.3389/fmicb.2013.00095

Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry
Cited by: 60
Author(s): William P. Inskeep, Zackary J. Jay, Markus J. Herrgård, Mark A. Kozubal, Douglas B. Rusch, Susannah G. Tringe, Richard E. Macur, Ryan deM. Jennings, Eric S. Boyd, John R. Spear, Francisco Roberto
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2011-12-10-r100

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
Cited by: 103
Author(s): Robert S. Coyne, Linda I. Hannick, Dhanasekaran Shanmugam, Jessica B. Hostetler, Daniel Brami, Vinita Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H. Badger, Ujjwal Kumar, Milton H. Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W. Mather, Akhil B. Vaidya, David E. Wilkes, Vidyalakshmi Rajagopalan, David J. Asai, Chad G. Pearson, R. C. Findly, Harry W. Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S. Roos, Donna Cassidy-Hanley, Theodore G. Clark
Software Mentions: 2
Published: almost 14 years ago

10.3389/fnbeh.2017.00098

Different Roles for Honey Bee Mushroom Bodies and Central Complex in Visual Learning of Colored Lights in an Aversive Conditioning Assay
Cited by: 33
Author(s): Jenny Aino Plath, Brian V. Entler, Nicholas H. Kirkerud, Ulrike Schlegel, C. Giovanni Galizia, Andrew B. Barron
Software Mentions: 1
Published: over 7 years ago

10.1089/heq.2018.0059

Differential Effects of Pregnancy-Specific Alcohol Policies on Drinking Among Pregnant Women by Race/Ethnicity
Cited by: 11
Author(s): Sarah C. M. Roberts, Amy A. Mericle, Meenakshi S. Subbaraman, Sue Thomas, Ryan Treffers, Kevin Delucchi, William C. Kerr
Software Mentions: 1
Published: almost 6 years ago

10.3390/insects10100340

Sub-Lethal Doses of Clothianidin Inhibit the Conditioning and Biosensory Abilities of the Western Honeybee Apis mellifera
Cited by: 8
Author(s): Merle T. Bartling, Andreas Vilcinskas, Kwang-Zin Lee
Software Mentions: 1
Published: about 5 years ago

10.1128/mSystems.00125-16

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
Cited by: 66
Author(s): Lisa Zeigler Allen, John P. McCrow, Karolina Ininbergs, Christopher L. Dupont, Jonathan H. Badger, Jeffery M. Hoffman, Martin Ekman, Andrew E. Allen, Birgitta Bergman, J. Craig Venter
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-018-2009-5

Protein-protein interface hot spots prediction based on a hybrid feature selection strategy
Cited by: 75
Author(s): Yu Qiao, Yi Xiong, Hongyun Gao, Xiaolei Zhu, Youzhi Zhang
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.7695

Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron-ion interaction pseudopotential features
Cited by: 21
Author(s): Junfeng Xia, Z.Q. Yue, Yunqiang Di, Xiaolei Zhu, Chun-Hou Zheng
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-11-174

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility
Cited by: 177
Author(s): Junfeng Xia, Xing Zhao, Jiangning Song, Dongqing Huang
Software Mentions: 1
Published: over 14 years ago

10.3390/biom4030827

The 26S Proteasome and Initiation of Gene Transcription
Cited by: 33
Author(s): Geetha Durairaj, Peter Kaiser
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pbio.0040286

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Cited by: 675
Author(s): Jonathan A. Eisen, Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer Wortman, Jonathan H. Badger, Qinghu Ren, Paolo Amedeo, Kristie M. Jones, Luke J. Tallon, Arthur L. Delcher, Steven L. Salzberg, Joana C. Silva, Brian J. Haas, William H. Majoros, Maryam Sharafi Farzad, Jane M. Carlton, Roger K. Smith, Jyoti Garg, Ronald E. Pearlman, Kathleen M. Karrer, Lei Sun, Gerard Manning, Nels C. Elde, Aaron P. Turkewitz, David J. Asai, David E. Wilkes, Yufeng Wang, Hong-Hong Cai, Kathleen Collins, Balint Stewart, Suzanne R. Lee, Katarzyna Wilamowska, Zasha Weinberg, Walter L. Ruzzo, Dorota Włoga, Jacek Gaertig, Joseph Frankel, Che-Chia Tsao, Martin A. Gorovsky, Patrick J. Keeling, Ross F. Waller, Nicola J. Patron, J. Michael Cherry, Nicholas A. Stover, Cynthia J. Krieger, Christina del Toro, Hilary F. Ryder, Sondra Williamson, Rebecca Barbeau, Eileen P. Hamilton, Eduardo Orias
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pgen.1000141

Complete Genome Sequence of the N2-Fixing Broad Host Range Endophyte Klebsiella pneumoniae 342 and Virulence Predictions Verified in Mice
Cited by: 237
Author(s): Derrick E. Fouts, Heather L. Tyler, Robert T. DeBoy, Sean C. Daugherty, Qinghu Ren, Jonathan H. Badger, A. Scott Durkin, Heather Huot, Susmita Shrivastava, Sagar Kothari, Robert J. Dodson, Yasmin Ali Mohamoud, Hoda Khouri, Luiz Fernando Würdig Roesch, Karen A. Krogfelt, Carsten Struve, Eric W. Triplett, Barbara A. Methé
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0009773

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function
Cited by: 173
Author(s): William P. Inskeep, Douglas B. Rusch, Zackary J. Jay, Markus J. Herrgård, Mark A. Kozubal, Toby H. Richardson, Richard E. Macur, Natsuko Hamamura, Ryan deM. Jennings, Bruce W. Fouke, Anna‐Louise Reysenbach, Francisco Roberto, Mark Young, Ariel Schwartz, Eric S. Boyd, Jonathan H. Badger, Eric J. Mathur, Alice C. Ortmann, Mary M. Bateson, Gill G. Geesey, M.E. Frazier
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0009605

The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon
Cited by: 227
Author(s): Amber Hartman, Cédric Norais, Jonathan H. Badger, Stéphane Delmas, Sam Haldenby, Ramana Madupu, Jeffrey M. Robinson, Hoda Khouri, Qinghu Ren, Todd M. Lowe, Julie A. Maupin-Furlow, Mecky Pohlschröder, Charles J. Daniels, Friedhelm Pfeiffer, Thorsten Allers, Jonathan A. Eisen
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0089549

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
Cited by: 165
Author(s): Chris L. Dupont, Jenny Larsson, Shibu Yooseph, Karolina Ininbergs, Johannes Goll, Johannes Asplund-Samuelsson, John P. McCrow, Narin Celepli, Lisa Zeigler Allen, Martin Ekman, Andrew J. Lucas, Åke Hagström, Mathangi Thiagarajan, Björn Brindefalk, Alexander Richter, Anders F. Andersson, Aaron Tenney, Daniel Lundin, Andrey Tovchigrechko, Johan A. A. Nylander, Daniel Brami, Jonathan H. Badger, Andrew E. Allen, Douglas B. Rusch, Jeff Hoffman, Erling Norrby, Robert M. Friedman, Jarone Pinhassi, J. Craig Venter, Birgitta Bergman
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0052542

Density Can Be Misleading for Low-Density Species: Benefits of Passive Acoustic Monitoring
Cited by: 96
Author(s): Tracey L. Rogers, Michaela B. Ciaglia, Holger Klinck, Colin Southwell
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0042047

Metagenomic Exploration of Viruses throughout the Indian Ocean
Cited by: 103
Author(s): Shannon J. Williamson, Lisa Zeigler Allen, Hernán Lorenzi, Douglas Fadrosh, Daniel Brami, Mathangi Thiagarajan, John P. McCrow, Andrey Tovchigrechko, Shibu Yooseph, J. Craig Venter
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0208509

The association between excise tax structures and the price variability of alcoholic beverages in the United States
Cited by: 3
Author(s): Ce Shang, Xuening Wang, Frank J. Chaloupka
Software Mentions: 1
Published: almost 6 years ago

10.3389/fnbeh.2017.00094

Aversive Learning of Colored Lights in Walking Honeybees
Cited by: 13
Author(s): Nicholas H. Kirkerud, Ulrike Schlegel, C. Giovanni Galizia
Software Mentions: 1
Published: over 7 years ago

Ecosyste.ms: Papers

Projects: cran: APIS

Papers Mentioning APIS 30