Ecosyste.ms: Papers

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: over 5 years ago

10.1111/mec.13636

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event
Cited by: 34
Author(s): Kevin Schneider, Philipp Resl, Toby Spribille
Software Mentions: 11
Published: over 8 years ago

10.15252/msb.20177697

Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations
Cited by: 153
Author(s): Julia Jabs, Franziska Maria Zickgraf, Jeongbin Park, Sven Wagner, Xiaoqi Jiang, Katharina Jechow, Kortine Kleinheinz, Umut Toprak, Marc A. Schneider, Michael Meister, Saskia Spaich, Marc Sütterlin, Matthias Schlesner, Andreas Trumpp, Martin R. Sprick, Roland Eils, Christian Conrad
Software Mentions: 11
Published: about 7 years ago

10.1186/1471-2164-14-892

RNA-Seq optimization with eQTL gold standards
Cited by: 24
Author(s): Shannon Ellis, Saloni Gupta, Foram N. Ashar, Joel S. Bader, Andrew B. West, Dan E. Arking
Software Mentions: 9
Published: about 11 years ago

10.3389/fmicb.2021.641643

Temporal Bacterial Community Diversity in the Nicotiana tabacum Rhizosphere Over Years of Continuous Monocropping
Cited by: 10
Author(s): Yan Ling, Wenyou Zhang, Wangjun Duan, Yizheng Zhang, Wen Zheng, Xianjun Lai
Software Mentions: 9
Published: over 3 years ago

10.3389/fphys.2018.01945

A Quantitative Comparison of Clinically Employed Parameters in the Assessment of Acute Cerebral Ischemia Using Dynamic Susceptibility Contrast Magnetic Resonance Imaging
Cited by: 1
Author(s): Christian Našel, Uros Klickovic, Heike-Marie Kührer, Kersten Villringer, Jochen B. Fiebach, Arno Villringer, Ewald Moser
Software Mentions: 9
Published: almost 6 years ago

10.3389/fmicb.2021.649517

Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST
Cited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: over 3 years ago

10.1534/g3.119.400185

ARMOR: An <u>A</u>utomated <u>R</u>eproducible <u>MO</u>dular Workflow for Preprocessing and Differential Analysis of <u>R</u>NA-seq Data
Cited by: 35
Author(s): Stephany Orjuela, Ronald Huang, Katharina Hembach, Mark D. Robinson, Charlotte Soneson
Software Mentions: 8
Published: over 5 years ago

10.1186/s40168-019-0748-9

Microbial communities of the house fly Musca domestica vary with geographical location and habitat
Cited by: 58
Author(s): Rahel Park, Maria C. Dzialo, Stijn Spaepen, Donat Nsabimana, Kim Gielens, Herman Devriese, Sam Crauwels, Raúl Y. Tito, Jeroen Raes, Bart Lievens, Kevin J. Verstrepen
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0023947

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction
Cited by: 19
Author(s): Christopher S. Poultney, Glenn L. Butterfoss, Michelle Gutwein, Kevin Drew, David Gresham, Kristin C. Gunsalus, Dennis Shasha, Richard Bonneau
Software Mentions: 8
Published: over 13 years ago

10.1111/pbi.12958

The developmental dynamics of the <i>Populus</i> stem transcriptome
Cited by: 92
Author(s): Qing Chao, Zili Gao, Dong Zhang, Biligen-Gaowa Zhao, Fengqin Dong, Chunxiang Fu, Lijun Liu, Bai-Chen Wang
Software Mentions: 8
Published: over 6 years ago

10.1002/elsc.202000053

Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard
Cited by: 3
Author(s): Marc Porr, F. Lange, Daniel Marquard, Laura Niemeyer, Patrick Lindner, Thomas Scheper, Sascha Beutel
Software Mentions: 8
Published: about 4 years ago

10.1186/s40246-016-0063-5

Human genome meeting 2016
Cited by: 10
Author(s): Arpita Srivastava, Y. Wang, Raymond Y. Huang, Chris J. Skinner, Tommy G. Thompson, Lucille Addison Pollard, Teresa L. Wood, Feng Luo, Robert B. Stevenson, Renato Polimanti, Joel Gelernter, Xin-Ying Lin, I. Y. Lim, Yi-Chieh Wu, Ai Ling Teh, L. Chen, I. M. Aris, Soo-Youn Soh, Mya Thway Tint, Julia L. MacIsaac, Fui W Yap, Kenneth Kwek, S. M. Saw, Michael S. Kobor, Michael J. Meaney, Keith M. Godfrey, Yap Seng Chong, Joanna D. Holbrook, Y. S. Lee, P. D. Gluckman, Neerja Karnani, Ashish Kapoor, D. Lee, Aravinda Chakravarti, Christian Maercker, Fritz Graf, Michael Boutros, Georgios Stamoulis, Fabio Santoni, Periklis Makrythanasis, Audrey Letourneau, Michel Guipponi, Nikolaos Panousis, Marco Garieri, Pascale Ribaux, Emilie Falconnet, Christelle Borel, Stylianos E. Antonarakis, Sonia Kumar, Joanne E. Curran, John Blangero, Samit Chatterjee, Jennifer A. Akiyama, Dallas R. Auer, Courtney Berrios, L Pennacchio, Tarak Donti, Gerarda Cappuccio, Marcus J. Miller, Paldeep S. Atwal, A. L. Kennedy, Aaron L. Cardon, Carlos A. Bacino, Lisa Emrick, Jozef Hertecant, F Bäumer, Brenda E. Porter, Matthew N. Bainbridge, Penelope E. Bonnen, Brett H. Graham, Reid Sutton, Qin Sun, Sarah H. Elsea, Zhi-Liang Hu, P. Wang, Yun Zhu, Jinying Zhao, Momiao Xiong, David A. Bennett, Alfredo Hidalgo‐Miranda, Sandra Romero-Córdoba, Sergio Rodrı́guez-Cuevas, Rosa Rebollar-Vega, Elena Tagliabue, Maria Iorio, Elvira D’Ippolito, Stefano Baroni, Bogumił Kaczkowski, Yoïchi Tanaka, Hideya Kawaji, Albin Sandelin, Robin Andersson, Masumi Itoh, Timo Lassmann, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Colin A. Semple, Elisabeth Rosenthal, Brian H. Shirts, Laura M. Amendola, Cecilia Gracia Gallego, Martha Horike‐Pyne, Amber Burt, Peggy D. Robertson, P. Beyers, Chris Nefcy, DL Veenstra, Fuki M. Hisama, Robin L. Bennett, Michael O. Dorschner, Deborah A. Nickerson, Joseph D. Smith, Karynne Patterson, David R. Crosslin, Rami Nassir, N. Zubair, Tom Harrison, Ulrike Peters, Gail P. Jarvik, Francesca Menghi, Koichiro Inaki, Xingyi Woo, Prerna Kumar, Krzysztof R. Grzęda, Ankit Malhotra, H. Kim, Duygu Ucar, Phung Trang Shreckengast, Krishna Karuturi, James Keck, James Chuang, E. T. Liu, Boyang Ji, Alioto Tyler, Guruprasad Ananda, G. Carter, Hamid Nikbakht, Martin Montagne, Michele Zeinieh, A. Harutyunyan, Melissa K. McConechy, Nada Jabado, Pierre Lavigne, Jacek Majewski, Jennifer B. Goldstein, Michael J. Overman, Gauri Varadhachary, Rachna T. Shroff, Robert A. Wolff, M. M. Javle, Andy Futreal, D. Fogelman, Leny Bravo, Williams Fajardo, Humberto Serna Gómez, Carlos Castañeda, Christian Rolfo, Joseph A. Pinto, Kadir C. Akdemir, Lynda Chin, Shanna Patterson, Cara Statz, Susan M. Mockus, S. N. Nikolaev, Ximena Bonilla, Laurent Parmentier, Bryan King, Fedor Bezrukov, Gulhan Kaya, Vincent Zoete, Vladimir B. Seplyarskiy, Heather Sharpe, Thomas W. McKee, Konstantin Popadin, Nicole Basset-Séguin, Rouaa Ben Chaabene, M. E. Andrianova, C Verdan, K. Grosdemange, Olga Sumara, Martin Eilers, Iannis Aifantis, Olivier Michielin, FJ de Sauvage, Stylianos E. Antonarakis, Somsak Likhitrattanapisal, Stephen E. Lincoln, Allison W. Kurian, Andrea Desmond, Shihui Yang, Yukio Kobayashi, James M. Ford, Leif W. Ellisen, Ted Peters, Karine Alvarez, Emporia Faith Hollingsworth, Dolores López‐Terrada, Alex Hastie, Željko Džakula, Andy Wing Chun Pang, Elaine T. Lam, Thomas Anantharaman, Michael Saghbini, Hua Cao, BioNano Genomics, Claudia Gonzaga‐Jauregui, Lijia Ma, Alejandra King, Erika B. Rosenzweig, U. B. Krishnan, Jeffrey G. Reid, J. D. Overton, Frederick E. Dewey, Woo-Keun Chung, Kathy M. Small, Adam P. DeLuca, Frans P.M. Cremers, Richard A. Lewis, V. Puech, Benjamin Bakall, R. Silva-Garcia, Klaus Rohrschneider, Marie Leys, Fadi Shaya, Edwin M Stone, Nara Sobreira, François Schiettecatte, Hong‐Qing Ling, Eric Pugh, David R. Witmer, Kyle M. Hetrick, P. Zhang, Kimberly F. Doheny, David Valle, Ada Hamosh, Shalini N. Jhangiani, Zeynep Coban Akdemir, Matthew N. Bainbridge, Wu‐Lin Charng, Wojciech Wiszniewski, Tomasz Gambin, Ender Karaca, Yavuz Bayram, Mohammad K. Eldomery, Jennifer E. Posey, Hv. Doddapaneni, Jingyuan Hu, V. Reid Sutton, Donna M. Muzny, Eric Boerwinkle, James R. Lupski, Richard A. Gibbs, Sandhya Shekar, William Salerno, Adam C. English, Adina Mangubat, Jeremy Bruestle, Adrian Thorogood, Bartha Maria Knoppers, Global Alliance for Genomics, Hazuki Takahashi, Kazuhiro R. Nitta, A. Kozhuharova, Ana Maria Suzuki, Hemant Sharma, Diego Cotella, Claudia Santoro, S. Zucchelli, Stefano Gustincich, J. J. Mulvihill, Gareth Baynam, W. A. Gahl, Stephen C. Groft, Kenjiro Kosaki, Paul Lasko, Béla Melegh, Domenica Taruscio, Rajarshi Ghosh, Sharon E. Plon, Steven E. Scherer, Xiang Qin, Rashesh Sanghvi, Kimberly Walker, Tsoyu Chiang, Donna M. Muzny, L. Wang, John L. Black, Eric Boerwinkle, Richard M. Weinshilboum, R.A. Gibbs, Tatiana V. Karpinets, Tiffany L. Calderone, Khalida Wani, Xiaoxing Yu, Caitlin Creasy, Cara L. Haymaker, Marie-Andrée Forget, Vashisht Gopal Yennu Nanda, Jason Roszik, Jennifer A. Wargo, Lauren E. Haydu, Xiaofei Song, Alexander J. Lazar, Jeffrey E. Gershenwald, M. A. Davies, Chantale Bernatchez, J. Zhang, Simon Woodman, Elissa J. Chesler, Todd B. Reynolds, Jason A Bubier, C M D Wendell Phillips, Michael A. Langston, Erich J. Baker, Nancy U. Lin, Christopher I. Amos, Vince D. Calhoun, Otto Dobretsberger, M. Egger, F. Leimgruber, Simon Sadedin, Alicia Oshlack, Victor Andrew A. Antonio, Noriaki Ono, Clark Kendrick Go, Zaheer Ahmed, Mohan Bolisetty, Saman Zeeshan, Esther Aguirre Anguiano, Abhishek Sarkar, Madhusudan R. Nandineni, Chao Zeng, Jie Shao, Tianzhu Liang, Kevin Pham, Y. Chee-Wei, Dongsheng Li, W. Lai-Ping, Duan Lian, Rick Ong Twee Hee, Yuzaimi Yunus, Farhang Aghakhanian, Siti Shuhada Mokhtar, C. V. Lok-Yung, Jong Bhak, Matthew Phipps, Xu Shuhua, T. Yik-Ying, Vinod Kumar, Hoh BoonPeng, Ian Campbell, Mary‐Anne Young, Pettengill James, Lifepool, Manjari Rain, Ghulam Mohammad, Ritushree Kukreti, Qadar Pasha, Ainur Akilzhanova, C. Guelly, Zhannur Abilova, Saule Rakhimova, Ainur Akhmetova, Ulykbek Kairov, Slave Trajanoski, Zhaxybay Zhumadilov, Makhabbat Bekbossynova, Cassie A. Schumacher, Sardul Singh Sandhu, Timothy T. Harkins, Vladimir Makarov, Robert Glenn, Zeineen Momin, B. Dilrukshi, Hsiao Tuan Chao, Qingchang Meng, Brent M. Gudenkauf, R. Kshitij, Joy C. Jayaseelan, Caitlin Nessner, S. Lee, K. Blankenberg, Lora Lewis, Yi Han, Huyen Dinh, S. Jireh, Christian Buhay, X. Liu, Q. Wang, Yao Ding, Narayanan Veeraraghavan, Ya Ping Yang, Arthur L. Beaudet, Christine M. Eng, Kim C. Worley, Y. Liu, Daniel Hughes, Shwetha C. Murali, R. Alan Harris, Adam C. English, Oliver A. Hampton, Peter A. Larsen, Christine R. Beck, M. Wang, Christie Kovar, William Salerno, Anne D. Yoder, Stephen M. Richards, Jeffrey Rogers, M. Raveenedran, Chenghai Xue, Mahmoud Dahdouli, Linda J. Cox, Guangyi Fan, Betsy Ferguson, J. Hovarth, Zachary P. Johnson, Sree Kanthaswamy, M. Kubisch, Martin Ward Platt, Daniel G. Smith, Eric J. Vallender, Roger W. Wiseman, Jennifer E. Below, Fuli Yu, Jaime Lin, Y. Zhang, Zhengqing Ouyang, Andrew Moore, Z. Wang, Johannes Hofmann, Purdue Mp, Rachael Z. Stolzenberg‐Solomon, Shelsey J. Weinstein, Demetrius Albanês, C. S. Liu, Wei‐Yi Cheng, Timothy Lin, Qiong Lan, Nathaniel Rothman, SI Berndt, E. S. Chen, Hoda Bahrami, A. Khoshzaban, S. Heidari Keshal, K. K. R. Alharbi, M. Zhalbinova, Ainur Akilzhanova, Mahabbat Bekbosynova, Ш.К. Мырзахметова, Maher Matar, N. Mili, Robert J. Molinari, Yussanne Ma, Stéphane Guerrier, Nasser A. Elhawary, Mohammed T. Tayeb, Neda M. Bogari, N. Qotb, Sarah A. McClymont, Paul W. Hook, Loyal A. Goff, Andrew S. McCallion, Yong Kong, Jacob Charette, Wanda L. Hicks, Jürgen Κ. Naggert, Lue Ping Zhao, Patsy M. Nishina, Burhan Edrees, Mohammad Athar, Faisal A. Al‐Allaf, Mohiuddin M. Taher, Wahab Khan, Abdellatif Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, Abeer Abdullah Al Anazi, N. Altayeb, Muhammad Ahmed, K. Alansary, Zainularifeen Abduljaleel, Anton Kratz, Pascal Béguin, Stéphane Poulain, Makoto Kaneko, C. Takahiko, Atsuko Matsunaga, Sachi Kato, Nicolas Bertin, Réjan Vigot, Charles Plessy, Thomas Lavstsen, Dan Graur, Jens Friis-Nielsen, Jose M. G. Izarzugaza, Søren Brunak, Anurupa Chakraborty, Jolly Basak, and Rajendrani Mukhopadhyay, Benjamin Soibam, Dhritishree Das, Nupur Biswas, Das S, Sinjini Sarkar, Anirban Maitra, Chandan Kumar Panda, Prasenjit Majumder, Heba Morsy, Ahmed Mohammed Gaballah, M Parikh Samir, M. Shamseya, Hisham Mahrous, Ayesha Ghazal, Waleed Arafat, M. Hashish, Joshua J. Gruber, Natalie Jaeger, Matthew Snyder, Kashyap Patel, Shannon Bowman, Trisha N. Davis, D Kraushaar, Amy B. Emerman, Salvatore Russello, Noa Henig, Cynthia L. Hendrickson, K. Zhang, Mauricio Rodríguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales, Natalie Jäger, J. Chen, Robert W. Haile, Megan P. Hitchins, Julia Brooks, Silvia Jiménez-Morales, Mónica Morales Ramírez, Javier Martín‐Núñez, Valerie Bekker, Yriana Rodrigues Leal, Esteban Jiménez, Aída Carolina Medina, Alfredo Hidalgo, Jorge Mejía, V. Halytskiy, Jürgen Κ. Naggert, Gayle B. Collin, K. DeMauro, R. Hanusek, K. Belhassa, Khadija Belhassan, Laila Bouguenouch, I. Samri, H. Sayel, Fz. moufid, I. El Bouchikhi, S. Trhanint, H. Hamdaoui, I. Elotmani, I. Khtiri, O. Kettani, L. Quibibo, M. Ahagoud, Mohammed Abdou Abbassi, Karim Ouldim, А. В. Марусин, А. Н. Корнетов, M. G. Swarovskaya, K. Vagaiceva, Vadim Stepanov, Eva Maria Cutiongco de la Paz, Rody G. Sy, Julián Nevado, Paul Ferdinand M. Reganit, L. C. S. dos Santos, Jose Donato A. Magno, Felix Eduardo R. Punzalan, Deborah Ignacia D. Ona, Erasmo Gonzalo D.V. Llanes, R. L. Santos-Cortes, Raphael Enrique Tiongco, Jaime Alfonso M. Aherrera, Lauro L. Abrahan, P. Pagauitan-Alan, Kathryn H. Morelli, J. S. Domire, Nibedita Pyne, Shirley F. Harper, Ralph Royal Burgess, Mamdooh Gari, Ashraf Dallol, Haneen Alsehli, Abdullah Gari, Mamdooh Gari, A. A. Abuzenadah, M. G. Thomas, Mahadeo A. Sukhai, Shruti Garg, Maksym Misyura, T. Zhang, Anna Schuh, Tracy Stockley, Suzanne Kamel‐Reid, Stephen T. Sherry, Chunlin Xiao, Douglas J. Slotta, Kurt Rodarmer, Michael Feolo, Michael Kimelman, Georgy Godynskiy, Christopher D. O’Sullivan, Eugene Yaschenko, Claudia Rangel‐Escareño, H. Rueda-Zarate, Iftikhar Aslam Tayubi, Reema R Mohammed, Iqbal Ike K. Ahmed, Tamar Ahmed, Sahil Seth, Samirkumar B. Amin, Xinjie Mao, Hui Sun, Roeland Verhaak, S. J. Whiite, Jesse Farek, Z. Kahn, Takeya Kasukawa, Marina Lizio, Jayson Harshbarger, S. Hisashi, Jessica Severin, A. Imad, Sedef Şahin, Thomas Charles Augustus Freeman, Katherine Unger Baillie, Sandhya Shekar, Abbes Salem, Mecheala Abbas Ali, Ahmed Ibrahim, M. Sofi Ibrahim, H Barrera, Lourdes Garza, Julian Torres, V. Barajas, Alfredo Ulloa‐Aguirre, David Kershenobich, Shahroj Mortaji, Pedro Guizar, Eliezer Loera, Karen Moreno, Adriana De León, Daniela Monsiváis, Jackeline Gómez, Raquel Cardiel, Jesús Carlos Fernández-López, V. Bonifaz-Peña, Andrew Contreras, Linda M. Polfus, X. Wang, Vivek Philip, A. A. Abuzenadah, Rola Turki, Asli Uyar, A. Kaygun, Sayed Zaman, E. García de Castro Márquez, Josna George, Cynthia L. Hendrickson, Dakota Starr, Mark E. Baird, Brian Kirkpatrick, Kent J. Sheets, Rainer Nitsche, L. Prieto-Lafuente, Melissa Landrum, J. Lee, Wendy S. Rubinstein, Donna Maglott, P. K. R. Thavanati, A. Escoto de Dios, Rolando Hernandez, M. E. Aguilar Aldrate, Mirna Mejia, K. R. R. Kanala, Neelum Shahzad, Elisabeth Huber, Alice J. Dan, Wolfgang Herr, G. Sprotte, Josef Köstler, Andreas Hiergeist, AE Gessner, Reinhard Andreesen, Elmar Holler, Faisal A. Al‐Allaf, Abdullah A. Al-Ashwal, Mohiuddin M. Taher, Halah Abalkhail, Ahmad F. Al-Allaf, R. Bamardadh, Olga Filiptsova, M. M. Kobets, Yu. M. Kobets, Ievgeniia Burlaka, I. Timoshyna, M. M. Kobets, Muhammad Mohiuddin, A. Zainularifeen, Alfaqih Samar Mohammed, Tarek Owaidah
Software Mentions: 7
Published: over 8 years ago

10.1111/1462-2920.15314

Metagenomic assessment of the global diversity and distribution of bacteria and fungi
Cited by: 39
Author(s): Mohammad Bahram, Tarquin Netherway, Clémence Frioux, Pamela Ferretti, Luís Pedro Coelho, Stefan Geisen, Peer Bork, Falk Hildebrand
Software Mentions: 7
Published: about 4 years ago

10.1126/scitranslmed.abe9599

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro
Cited by: 57
Author(s): Miguel Reyes, Michael R. Filbin, Roby P. Bhattacharyya, Abraham Sonny, Arnav Mehta, Kianna Billman, Kyle R. Kays, Mayra Pinilla-Vera, Maura Benson, Lisa A. Cosimi, Deborah T. Hung, Bruce D. Levy, Alexandra Chloé Villani, Moshe Sade-Feldman, Rebecca M. Baron, Marcia B. Goldberg, Paul C. Blainey, Nir Hacohen
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0204076

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Cited by: 62
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Jong S. Leong, Cameron M. Nugent, Roy G. Danzmann, Moira M. Ferguson, Agnieszka Stadnik, Robert H. Devlin, Robin Muzzerall, Michael G. Edwards, William S. Davidson, Ben F. Koop
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0218789

Jscatter, a program for evaluation and analysis of experimental data
Cited by: 23
Author(s): Ralf Biehl
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2105-12-452

eXframe: reusable framework for storage, analysis and visualization of genomics experiments
Cited by: 5
Author(s): Amit Sinha, Emily Merrill, Scott A. Armstrong, Tim W. Clark, Sudeshna Das
Software Mentions: 7
Published: about 13 years ago

10.1038/s41598-017-05377-y

Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes
Cited by: 33
Author(s): Zupeng Wang, Yifei Liu, Li Li, Dawei Li, Qiong Zhang, Yangtao Guo, Shuaibin Wang, Caihong Zhong, Hongwen Huang
Software Mentions: 7
Published: over 7 years ago

10.1186/s12864-021-07441-4

A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks
Cited by: 2
Author(s): Pedro Gabriel Nachtigall, Luiz Augusto Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13007-020-00611-7

DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models
Cited by: 22
Author(s): Ilana Lambert, Christine Paysant‐Le Roux, Stefano Colella, Marie-Laure Martin
Software Mentions: 6
Published: over 4 years ago

10.1111/pbi.12834

Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (<i>Triticum aestivum</i>)
Cited by: 21
Author(s): Amanda Burridge, Paul Wilkinson, Mark Winfield, Gary Barker, Alexandra M. Allen, Jane A. Coghill, Christy Waterfall, Keith J. Edwards
Software Mentions: 6
Published: about 7 years ago

10.1523/ENEURO.0085-20.2020

<i>neurotic</i>: Neuroscience Tool for Interactive Characterization
Cited by: 4
Author(s): Jeffrey P. Gill, Samuel Garcia, Lena H. Ting, Mengnan Wu, Hillel J. Chiel
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0053822

Efficient and Comprehensive Representation of Uniqueness for Next-Generation Sequencing by Minimum Unique Length Analyses
Cited by: 31
Author(s): Helena Storvall, Daniel Ramsköld, Rickard Sandberg
Software Mentions: 6
Published: almost 12 years ago

10.1002/stem.2521

Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells
Cited by: 37
Author(s): Agata Stryjewska, Ruben Dries, Tim Pieters, Griet Verstappen, Andrea Conidi, Kathleen Coddens, Annick Francis, Lieve Umans, Wilfred F. J. van IJcken, Geert Berx, Leo A. van Grunsven, Frank Grosveld, Steven Goossens, Jody J. Haigh, Danny Huylebroeck
Software Mentions: 6
Published: about 8 years ago

10.3390/ijms21093384

A Data-Driven Review of the Genetic Factors of Pregnancy Complications
Cited by: 14
Author(s): Yury A. Barbitoff, Alexander Tsarev, Elena S. Vashukova, Evgeniia M Maksiutenko, Л. В. Коваленко, Л. Д. Белоцерковцева, Andrey S. Glotov
Software Mentions: 6
Published: over 4 years ago

10.1186/s13073-016-0382-0

Non-coding single nucleotide variants affecting estrogen receptor binding and activity
Cited by: 5
Author(s): Amir Bahreini, Kevin M. Levine, Lucas Santana-Santos, Panayiotis V. Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich, Adrian V. Lee
Software Mentions: 6
Published: about 8 years ago

10.1186/s12864-019-6034-1

De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia
Cited by: 19
Author(s): Eugeni Belda, Ferdinand Nanfack-Minkeu, Karin Eiglmeier, Guillaume Carissimo, Inge Holm, Mawlouth Diallo, Diawo Diallo, Amélie Vantaux, Saorin Kim, Igor V. Sharakhov, Kenneth D. Vernick
Software Mentions: 6
Published: over 5 years ago

10.12688/wellcomeopenres.16661.2

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
Cited by: 120
Author(s): Áine O’Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Isaac I Bogoch, Kamran Khan, Jane P. Messina, Houriiyah Tegally, Richard Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse A. Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo I. Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita Desai, Vasanthapuram Ravi, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Antonio Parisi, Angelica Bianco, Darı́o Garcı́a de Viedma, Sergio Buenestado‐Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William D. Rawlinson, Ira W. Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward C. Holmes, Kirsten St. George, Erica Lasek‐Nesselquist, Reina S. Sikkema, Bas B. Oude Munnink, Marion Koopmans, Mia Brytting, Vannavada Sudha Rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin K. Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine V. F. Carrington, Nikita Sahadeo, Michael J. Carr, Gabo Gonzalez, Search Alliance San Diego, SeqCOVID-Spain, Túlio de Oliveira, Nuno Rodrigues Faria, Andrew Rambaut, Moritz U. G. Kraemer
Software Mentions: 5
Published: over 3 years ago

10.3389/fpls.2021.695439

Genome-Wide Identification and Characterization of Small Peptides in Maize
Cited by: 15
Author(s): Yan Liang, Wanchao Zhu, Sijia Chen, Qidong Jia, Li Lin
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-15-1103

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
Cited by: 75
Author(s): Romain Blanc-Mathieu, Bram Verhelst, Évelyne Derelle, Stéphane Rombauts, François‐Yves Bouget, Isabelle A. Carré, Annie Château, Adam Eyre‐Walker, Nigel Grimsley, Hervé Moreau, Benoît Piégu, Éric Rivals, Wendy Schackwitz, Yves Van de Peer, Gwenaël Piganeau
Software Mentions: 5
Published: about 10 years ago

10.3389/fmicb.2018.01035

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean
Cited by: 45
Author(s): Josephine Z. Rapp, Mar Fernández‐Méndez, Christina Bienhold, Antje Boetius
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2164-15-555

piRNAQuest: searching the piRNAome for silencers
Cited by: 49
Author(s): Arijita Sarkar, Ranjan Kumar Maji, Sudipto Saha, Zhumur Ghosh
Software Mentions: 5
Published: over 10 years ago

10.1002/ece3.6806

Consequences of multiple imputation of missing standard deviations and sample sizes in meta‐analysis
Cited by: 21
Author(s): Stephan Kambach, Helge Bruelheide, Katharina Gerstner, Jessica Gurevitch, Michael Beckmann, Ralf Seppelt
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.64932

Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci
Cited by: 41
Author(s): Victoria J Sugrue, Joseph A. Zoller, Pritika Narayan, Ake T. Lu, Oscar Ortega‐Recalde, Megan Grant, C. Simon Bawden, Skye R. Rudiger, Amin Haghani, Donna M. Bond, Reuben R Hore, Michael Garratt, Karen E. Sears, Nan Wang, Xiangdong Yang, Russell G. Snell, Timothy A Hore, Steve Horvath
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2016.00499

Azithromycin Attenuates Pseudomonas-Induced Lung Inflammation by Targeting Bacterial Proteins Secreted in the Cultured Medium
Cited by: 6
Author(s): Teresinha Leal, Gabriella Bergamini, François Huaux, Nadtha Panin, Sabrina Noël, Barbara Dhooghe, Jérémy Boris Haaf, Pierluigi Mauri, Sara Motta, Dario Di Silvestre, Paola Melotti, Claudio Sorio
Software Mentions: 5
Published: about 8 years ago

10.3390/ijms21197281

SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features
Cited by: 10
Author(s): António Preto, Irina S. Moreira
Software Mentions: 5
Published: about 4 years ago

10.15252/msb.20209844

Integrative characterization of the near‐minimal bacterium <i>Mesoplasma florum</i>
Cited by: 8
Author(s): Dominick Matteau, Jean-Christophe Lachance, Frédéric Grenier, Samuel Gauthier, James M. Daubenspeck, Kevin Dybvig, Daniel Garneau, Thomas F. Knight, Pierre-Étienne Jacques, Sébastien Rodrigue
Software Mentions: 5
Published: about 4 years ago

10.1038/sdata.2019.8

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining
Cited by: 33
Author(s): Markus Gastauer, Mabel Patricia Ortiz Vera, Kleber Padovani de Souza, Eder S. Pires, Ronnie Alves, Cecílio Fróis Caldeira, Sílvio Júnio Ramos, Guilherme Oliveira
Software Mentions: 5
Published: almost 6 years ago

10.1111/mec.12833

Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (<i>Lagopus lagopus scotica</i>)
Cited by: 52
Author(s): Marius Wenzel, Stuart B. Piertney
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0051292

Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes
Cited by: 9
Author(s): Francesco Lescai, Silvia Bonfiglio, Chiara Bacchelli, Estelle Chanudet, Aoife Waters, Sanjay M. Sisodiya, Dalia Kasperavičiūtė, Julie Williams, Denise Harold, John Hardy, Robert Kleta, Sebahattin Çırak, Richard Williams, John C. Achermann, John Anderson, David P. Kelsell, Tom Vulliamy, Henry Houlden, Nicholas W. Wood, Una Marie Sheerin, Gian Paolo Tonini, Donna S. Mackay, Khalid Hussain, Jane C. Sowden, Veronica A. Kinsler, Justyna Osinska, Tony Brooks, Mike Hubank, Philip L. Beales, Elia Stupka
Software Mentions: 5
Published: about 12 years ago

10.1186/s12862-021-01753-5

Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals
Cited by: 4
Author(s): Simin Chai, Ran Tian, Juanjuan Bi, Shixia Xu, Wenhua Ren
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41597-019-0341-x

The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies
Cited by: 50
Author(s): Christoph Rzymski, Tiago Tresoldi, Simon J. Greenhill, Mei-Shin Wu, Nathanael E. Schweikhard, Maria Koptjevskaja‐Tamm, Volker Gast, Timotheus Adrianus Bodt, Abbie Hantgan, Gereon A. Kaiping, S. Chang, Yunfan Lai, Natalia Morozova, Heini Arjava, Nataliia Hübler, Ezequiel Koile, Steve Pepper, Mariann Proos, Briana Van Epps, Ingrid Blanco, Carolin Hundt, Sergei Monakhov, Kristina Pianykh, Sallona Ramesh, Russell D. Gray, Robert Forkel, Johann‐Mattis List
Software Mentions: 5
Published: almost 5 years ago

10.1093/molbev/msab144

Population Structure Limits Parallel Evolution in Sticklebacks
Cited by: 30
Author(s): Bohao Fang, Petri Kemppainen, Paolo Momigliano, Juha Merilä
Software Mentions: 5
Published: over 3 years ago

10.1111/1751-7915.13519

Raman–deuterium isotope probing to study metabolic activities of single bacterial cells in human intestinal microbiota
Cited by: 44
Author(s): Yi Wang, Jiabao Xu, Lingchao Kong, Tang Liu, Lingbo Yi, Hongjuan Wang, Wei E. Huang, Kewei Chen
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0237066

Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways
Cited by: 12
Author(s): Juan R. Ureña‐Peralta, Raúl Pérez-Moraga, Francisco García‐García, Consuelo Guerri
Software Mentions: 5
Published: over 4 years ago

10.1523/JNEUROSCI.0827-19.2019

Mammillothalamic Disconnection Alters Hippocampocortical Oscillatory Activity and Microstructure: Implications for Diencephalic Amnesia
Cited by: 34
Author(s): Christopher M. Dillingham, Michal M. Milczarek, James C. Perry, Bethany E. Frost, Greg D. Parker, Yaniv Assaf, Frank Sengpiel, Shane M. O’Mara, Seralynne Denise Vann
Software Mentions: 5
Published: over 5 years ago

10.1186/s13321-018-0312-9

MER: a shell script and annotation server for minimal named entity recognition and linking
Cited by: 27
Author(s): Francisco M. Couto, André Lamúrias
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0235263

Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications
Cited by: 2
Author(s): George W. Preston, Liping Yang, David H. Phillips, Claudia S. Maier
Software Mentions: 4
Published: over 4 years ago

10.1186/s13062-018-0211-z

Profiling microbial strains in urban environments using metagenomic sequencing data
Cited by: 26
Author(s): Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett, Nicola Segata
Software Mentions: 4
Published: almost 7 years ago

10.3389/fphar.2018.01011

In silico Prioritization of Transporter–Drug Relationships From Drug Sensitivity Screens
Cited by: 21
Author(s): Adrián César-Razquin, Enrico Gottardi, Meizhu Yang, Marc Brehme, Julio Sáez-Rodríguez, Giulio Superti‐Furga
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-27979-w

Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea
Cited by: 22
Author(s): Himanshi Bhatia, Niraj Khemka, Mukesh Jain, Rohini Garg
Software Mentions: 4
Published: over 6 years ago

10.3390/ani10010002

Atmospheric Ammonia Affects Myofiber Development and Lipid Metabolism in Growing Pig Muscle
Cited by: 10
Author(s): Shouwei Tang, Jingjing Xie, Sheng Zhang, Weida Wu, Bao Yi, Hongfu Zhang
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2431-13-152

The swiss neonatal quality cycle, a monitor for clinical performance and tool for quality improvement
Cited by: 6
Author(s): Mark Adams, Tjade Claus Hoehre, Hans Ulrich Bucher
Software Mentions: 4
Published: about 11 years ago

10.3389/fmicb.2019.00170

Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater
Cited by: 18
Author(s): Florian Trigodet, Nicolas Larché, Hilary G. Morrison, Mohamed Jebbar, Dominique Thierry, Loïs Maignien
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-11-598

Initial steps towards a production platform for DNA sequence analysis on the grid
Cited by: 8
Author(s): Angela C. M. Luyf, Barbera D.C. van Schaik, Michèl de Vries, Frank Baas, Antoine H. C. van Kampen, Sílvia D. Olabarriaga
Software Mentions: 4
Published: about 14 years ago

10.3389/fonc.2021.653902

Fucoidan Inhibits the Progression of Hepatocellular Carcinoma via Causing lncRNA LINC00261 Overexpression
Cited by: 10
Author(s): Danhui Ma, Jiayi Wei, Sinuo Chen, Heming Wang, Ning Lv, Shihua Luo, Chieh-Lun Liu, Guangqi Song, Qunyan Yao
Software Mentions: 4
Published: over 3 years ago

10.1534/g3.120.401497

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (<i>Coregonus artedi)</i> Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids
Cited by: 13
Author(s): Danielle M. Blumstein, Matthew A. Campbell, Matthew C. Hale, Ben J. G. Sutherland, Garrett J. McKinney, Wendylee Stott, Wesley A. Larson
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2020.00736

Differential Expression of IgM and IgD Discriminates Two Subpopulations of Human Circulating IgM+IgD+CD27+ B Cells That Differ Phenotypically, Functionally, and Genetically
Cited by: 27
Author(s): Diana Bautista, Camilo Vásquez, Paola Ayala-Ramírez, Juan Téllez-Sosa, Elizabeth Ernestina Godoy-Lozano, Jesús Martínez-Barnetche, Manuel Franco, Juana Ángel
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.36828

Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptor
Cited by: 12
Author(s): Corinne L Pender, H. Robert Horvitz
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-6564-6

Transcriptome analysis of fungicide-responsive gene expression profiles in two Penicillium italicum strains with different response to the sterol demethylation inhibitor (DMI) fungicide prochloraz
Cited by: 15
Author(s): Tingfu Zhang, Qing Cao, Na Li, De Li Liu, Yongze Yuan
Software Mentions: 4
Published: almost 5 years ago

10.1155/2021/6672899

Comparative Transcriptome Analysis Reveals Relationship among mRNAs, lncRNAs, and circRNAs of Slow Transit Constipation
Cited by: 2
Author(s): Shuai Yan, Yinzi Yue, Mingming Sun, Yinghui Chen, Xiaopeng Wang, Haihua Qian
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2020.603454

Identifying Candidate Genes Involved in the Regulation of Early Growth Using Full-Length Transcriptome and RNA-Seq Analyses of Frontal and Parietal Bones and Vertebral Bones in Bighead Carp (Hypophthalmichthys nobilis)
Cited by: 6
Author(s): Weiwei Luo, Ying Zhou, Junru Wang, Xin Yu, Jingou Tong
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.39231

Expansion of the fatty acyl reductase gene family shaped pheromone communication in Hymenoptera
Cited by: 24
Author(s): Michal Tupec, Aleš Buček, Václav Janous̆ek, Heiko Vogel, Darina Prchalová, Jiří Kindl, Tereza Pavlíčková, Petra Wenzelová, Ullrich Jahn, Irena Valterová, Iva Pichová
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-59887-3

Genomic divergence reveals unique populations among Indian Yaks
Cited by: 8
Author(s): S. Jayakumar, M R Vineeth, Tarida Marlin Surya, Kritika Singh, S. P. Dixit, S. K. Niranjan, M. S. Tantia, I. D. Gupta, Dhanalakshmi Ravikumar
Software Mentions: 4
Published: almost 5 years ago

10.1093/database/baw168

KTCNlncDB—a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas
Cited by: 13
Author(s): Michał Wojciech Szcześniak, Michał Kabza, Justyna A. Karolak, Małgorzata Rydzanicz, Dorota Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafał Płoski, Jacek P. Szaflik, Marzena Gajęcka
Software Mentions: 4
Published: almost 8 years ago

10.1002/ece3.2134

Divergence and isolation of cryptic sympatric taxa within the annual legume <i>Amphicarpaea bracteata</i>
Cited by: 8
Author(s): Rebecca Y. Kartzinel, Daniel Spalink, Donald M. Waller, Thomas J. Givnish
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-14-331

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish
Cited by: 32
Author(s): Håvard Aanes, Oľga Østrup, Ingrid S. Andersen, Lars Fredrik Moen, Sinnakaruppan Mathavan, Philippe Collas, Peter Aleström
Software Mentions: 4
Published: over 11 years ago

10.1007/s12035-021-02296-y

The Coding and Small Non-coding Hippocampal Synaptic RNAome
Cited by: 9
Author(s): Robert Epple, Dennis M. Krüger, Tea Berulava, Gerrit Brehm, Momchil Ninov, Rezaul Islam, Sarah Köster, André Fischer
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1004660

Widespread Genome Reorganization of an Obligate Virus Mutualist
Cited by: 66
Author(s): Gaelen R. Burke, Kimberly K. O. Walden, James B. Whitfield, Hugh M. Robertson, Michael R. Strand
Software Mentions: 4
Published: over 10 years ago

10.3390/ijms22157834

Individual DNA Methylation Pattern Shifts in Nanoparticles-Exposed Workers Analyzed in Four Consecutive Years
Cited by: 6
Author(s): Andrea Rössnerová, K. Hoňková, Irena Chvojková, Daniela Pelclová, Vladimı́r Ždı́mal, Jaroslav A. Hubacek, Lucie Lischková, Štěpánka Vlčková, Jakub Ondráček, Štěpánka Dvořáčková, Jan Topinka, Pavel Rössner
Software Mentions: 4
Published: over 3 years ago

10.1098/rsos.160992

Mixing of porpoise ecotypes in southwestern UK waters revealed by genetic profiling
Cited by: 30
Author(s): Michaël C. Fontaine, Olivier Thatcher, Nicolas Ray, Sylvain Piry, Andrew Brownlow, Nicholas J. Davison, Paul D. Jepson, Rob Deaville, Simon J. Goodman
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2105-14-S7-S14

Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements
Cited by: 16
Author(s): Swaraj Basu, Ferenc Müller, Remo Sanges
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-015-1799-3

RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress
Cited by: 67
Author(s): Longxing Hu, Huiying Li, Liang Chen, Yanhong Lou, Erick Amombo, Jinmin Fu
Software Mentions: 4
Published: over 9 years ago

10.1128/MRA.00160-21

Delila-PY, a Pipeline for Utilizing the Delila Suite of Software to Identify Potential DNA Binding Motifs
Cited by: 1
Author(s): Kevin S. Myers, Michael Place, Jacek Kominek, Daniel R. Noguera, Timothy J. Donohue
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1002984

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences
Cited by: 142
Author(s): Olivier Arnaiz, Nathalie Mathy, Céline Baudry, Sophie Malinsky, Jean‐Marc Aury, Cyril Denby Wilkes, Olivier Garnier, Karine Labadie, Benjamin E. Lauderdale, Anne Le Mouël, Antoine Marmignon, Mariusz Nowacki, Julie Poulain, M Prajer, Patrick Wincker, Éric Meyer, Sandra Duharcourt, Laurent Duret, Mireille Bétermier, Linda Sperling
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0150094

Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens
Cited by: 8
Author(s): Jigna Shah, Prerak Desai, Ying Zhang, Sarah K. Scharber, Joshua A. Baller, Zheng Xing, Carol J. Cardona
Software Mentions: 4
Published: almost 9 years ago

10.3390/jcm8081158

Role of MYC-miR-29-B7-H3 in Medulloblastoma Growth and Angiogenesis
Cited by: 29
Author(s): Ian J. Purvis, Avilala Janardhan, Maheedhara R. Guda, Sujatha Venkataraman, Rajeev Vibhakar, Andrew J. Tsung, Kiran Kumar Velpula, Swapna Asuthkar
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008273

BCDIN3D regulates tRNAHis 3’ fragment processing
Cited by: 21
Author(s): Calder Reinsborough, Hélène Ipas, Nathan S. Abell, Ryan M. Nottingham, Jun Yao, Sravan K. Devanathan, Samantha B. Shelton, Alan M. Lambowitz, Blerta Xhemalçe
Software Mentions: 4
Published: over 5 years ago

10.1093/bib/bbw020

A review of bioinformatic pipeline frameworks
Cited by: 155
Author(s): Jeremy Leipzig
Software Mentions: 4
Published: over 8 years ago

10.1590/1678-4685-GMB-2017-0164

Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells
Cited by: 5
Author(s): Zhizhong Gong, Jianyun Liu, Xin Xie, Xiaoyuan Xu, Ping Wu, Huimin Li, Yaqin Wang, Weidong Li, Jianjun Xiong
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-017-1848-9

A machine learning approach for predicting methionine oxidation sites
Cited by: 26
Author(s): Juan Carlos Aledo, Francisco R. Cantón, Francisco J. Veredas
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0163106

Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants
Cited by: 21
Author(s): Micheline N. Ngaki, Bing Wang, Binod Bihari Sahu, Subodh Srivastava, Mohammad Samir Farooqi, Kondapalli Venkata Gowri Chandra Sekhar, Sundararaman Swaminathan, Madan K. Bhattacharyya
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-018-1437-x

Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency
Cited by: 63
Author(s): Scott I. Adamson, Lijun Zhan, Brenton R. Graveley
Software Mentions: 4
Published: over 6 years ago

10.3758/s13428-018-1046-3

Testing moderator hypotheses in meta-analytic structural equation modeling using subgroup analysis
Cited by: 33
Author(s): Suzanne Jak, Mike W.‐L. Cheung
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-11-583

Preprocessing of gene expression data by optimally robust estimators
Cited by: 15
Author(s): Matthias Kohl, Hans‐Peter Deigner
Software Mentions: 3
Published: about 14 years ago

10.3389/fpls.2021.720800

Disruption of Photomorphogenesis Leads to Abnormal Chloroplast Development and Leaf Variegation in Camellia sinensis
Cited by: 7
Author(s): Xizhi Gao, Chenyu Zhang, Cui Lu, Minghan Wang, Nianci Xie, Jianjiao Chen, Yunfei Li, Jiahao Chen, Chengwen Shen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0086976

Transcriptomic Analysis of Flower Development in Wintersweet (Chimonanthus praecox)
Cited by: 40
Author(s): Daofeng Liu, Shunzhao Sui, Jing Ma, Zhineng Li, Yanjun Guo, Dengpan Luo, Jingjing Yang, Mingyang Li
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-9-311

Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge
Cited by: 5
Author(s): Don Armstrong, Chaim O. Jacob, Raphael Zidovetzki
Software Mentions: 3
Published: over 16 years ago

10.1186/s13104-016-2069-4

Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus
Cited by: 4
Author(s): Matteo Buti, Daniel J. Sargent, Khethani Mhelembe, Pietro Delfino, K. R. Tobutt, Riccardo Velasco
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0199021

Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG
Cited by: 28
Author(s): Kejin Zhuang, Yujun Jiang, Xiaohan Feng, Li Li, Fangfang Dang, Wei Zhang, Chaoxin Man
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-017-4016-8

Characterization of mechanisms underlying degradation of sclerotia of Sclerotinia sclerotiorum by Aspergillus aculeatus Asp-4 using a combined qRT-PCR and proteomic approach
Cited by: 15
Author(s): Xiaojia Hu, Lü Qin, Daniel P. Roberts, Dilip K. Lakshman, Yiqin Gong, Jude E. Maul, Lin Xie, Chang Yeon Yu, Yinshui Li, Lei Hu, Liao Xiang-sheng, Lixin Xing
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2017.01009

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes
Cited by: 8
Author(s): Tam Tran, Sophie Mangenot, Ghislaine Magdelenat, Emilie Payen, Zoé Rouy, Hassiba Belahbib, Barry M. Grail, D. Barrie Johnson, Violaine Bonnefoy, Emmanuel Talla
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-020-02450-z

Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars
Cited by: 21
Author(s): Heng Zhou, Ying He, Yu Cheng Zhu, Meiyu Li, Shuang Song, Wenhao Bo, Yingyue Li, Xiaoming Pang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12866-019-1402-1

NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission
Cited by: 66
Author(s): Alexandra Dangel, Anja Berger, Regina Konrad, Andreas Sing
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-6512-5

Transcriptomic response to three osmotic stresses in gills of hybrid tilapia (Oreochromis mossambicus female × O. urolepis hornorum male)
Cited by: 44
Author(s): Huanhuan Su, Dongmei Ma, Hai‐Lei Zhu, Zhigang Liu, Fengying Gao
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2016.00636

Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure
Cited by: 17
Author(s): Yingjiao Zhang, Songcan Chen, Xiuli Hao, Jian‐Qiang Su, Xudong Xue, Yu Yan, Yan Zhu, Jun Ye
Software Mentions: 3
Published: over 8 years ago

10.1111/j.1467-7652.2011.00625.x

Large‐scale transcriptome analysis in chickpea ( <i>Cicer arietinum</i> L.), an orphan legume crop of the semi‐arid tropics of Asia and Africa
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Author(s): Pavana J Hiremath, Andrew Farmer, Steven B. Cannon, Jimmy E. Woodward, Himabindu Kudapa, Reetu Tuteja, Ashish Kumar, BhanuPrakash Amindala, Benjamin Mulaosmanovic, Neha Gujaria, L. Krishnamurthy, Pooran M. Gaur, Polavarapu B. KaviKishor, Trushar Shah, R. Srinivasan, Marc Lohse, Yongli Xiao, Christopher D. Town, Douglas R. Cook, Gregory D. May, Rajeev K. Varshney
Software Mentions: 3
Published: over 13 years ago

10.3389/fmicb.2016.01759

Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates
Cited by: 32
Author(s): Taya Forde, Karin Orsel, Ruth N. Zadoks, Roman Biek, Layne G. Adams, Sylvia Checkley, Tracy Davison, Jeroen De Buck, Mathieu Dumond, Brett Elkin, Laura Finnegan, Bryan Macbeth, Cait Nelson, Amanda Niptanatiak, Shane Sather, Helen Schwantje, Frank van der Meer, Susan Kutz
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2017.02485

Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors
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Author(s): Raymond Kiu, Shabhonam Caim, Sarah Alexander, Purnima Pachori, Lindsay J. Hall
Software Mentions: 3
Published: about 7 years ago