Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: q
https://packages.ecosyste.ms/registries/pypi.org/packages/q
Quick-and-dirty debugging output for tired programmers
13 versions
Latest release: over 2 years ago
4 dependent packages
21,509 downloads last month
Papers Mentioning q 39
10.1111/mec.14860
Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skinCited by: 43
Author(s): Robert Hooper, Jaelle C. Brealey, Tom van der Valk, Antton Alberdi, John W. Durban, Holly Fearnbach, Kelly M. Robertson, Robin W. Baird, M. Bradley Hanson, Paul R. Wade, M. Thomas P. Gilbert, Phillip A. Morin, Jochen B. W. Wolf, Andrew D. Foote, Katerina Guschanski
Software Mentions: 7
Published: about 6 years ago
10.1083/jcb.201612131
Nuclear phosphorylated Dicer processes double-stranded RNA in response to DNA damageCited by: 67
Author(s): Kaspar Burger, Margarita Schlackow, Martin Potts, Svenja Hester, Shabaz Mohammed, Monika Gullerová
Software Mentions: 6
Published: over 7 years ago
10.1186/s12864-019-5453-3
Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in JapanCited by: 15
Author(s): Maribet Gamboa, Kozo Watanabe
Software Mentions: 6
Published: almost 6 years ago
10.1186/s13326-019-0212-6
Exploring semantic deep learning for building reliable and reusable one health knowledge from PubMed systematic reviews and veterinary clinical notesCited by: 6
Author(s): Mercedes Arguello-Casteleiro, Robert Stevens, Julio Des-Diz, Chris Wroe, M.J. Fernandez-Prieto, Nava Maroto, Diego Maseda-Fernandez, George Demetriou, Simon Peters, P. J. W. Noble, Phil Jones, Joanna Dukes‐McEwan, Alan Radford, John Keane, Goran Nenadić
Software Mentions: 6
Published: about 5 years ago
10.1074/jbc.RA120.014598
The nuclear factor CECR2 promotes somatic cell reprogramming by reorganizing the chromatin structureCited by: 2
Author(s): Linlin Wu, Guoqing Zhao, Xu Shou, Jinqiang Kuang, Ming Jin, Guiying Wu, Tao Wang, Bo Wang, Ping Zhu, Duanqing Pei, Jing Liu
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pntd.0003853
The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until InfectionCited by: 46
Author(s): David Roquis, Julie M. J. Lepesant, Marion Picard, Michael Freitag, Hugues Parrinello, Marco Groth, Rémi Emans, Céline Cosseau, Christoph Grunau
Software Mentions: 5
Published: about 9 years ago
10.3389/fonc.2014.00251
Hidden Treasures in “Ancient†Microarrays: Gene-Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal TissueCited by: 14
Author(s): Konstantinos Kerkentzes, Vincenzo Lagani, Ioannis Tsamardinos, Mogens Vyberg, Oluf Dimitri Røe
Software Mentions: 5
Published: about 10 years ago
10.1002/mbo3.1231
Marine biofilms on different fouling control coating types reveal differences in microbial community composition and abundanceCited by: 16
Author(s): Maria Papadatou, Samuel Robson, Sergey Dobretsov, Joy E. M. Watts, Jennifer Longyear, Maria Salta
Software Mentions: 5
Published: over 3 years ago
10.1007/s00432-019-03078-9
Transcriptome analysis reveals overlap in fusion genes in a phase I clinical cohort of TNBC and HGSOC patients treated with buparlisib and olaparibCited by: 4
Author(s): Julia Eismann, Yujing J. Heng, Johannes M. Waldschmidt, Ioannis S. Vlachos, Kathryn P. Gray, Ursula A. Matulonis, Panagiotis A. Konstantinopoulos, Charles J. Murphy, Sheida Nabavi, Gerburg M. Wulf
Software Mentions: 4
Published: about 5 years ago
10.1007/s10577-020-09643-0
CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sitesCited by: 4
Author(s): Michi Miura, Honglin Chen
Software Mentions: 4
Published: about 4 years ago
10.1007/s10858-020-00327-9
NMR quality control of fragment libraries for screeningCited by: 18
Author(s): Sridhar Sreeramulu, Christian Richter, Till Kuehn, Kamal Azzaoui, Marcel J. J. Blommers, Rebecca Del Conte, Marco Fragai, Nils Trieloff, Peter Schmieder, Marc Nazaré, Edgar Specker, Vladimir N. Ivanov, Hartmut Oschkinat, Lucia Banci, Harald Schwalbe
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-017-3887-z
Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expressionCited by: 45
Author(s): Olivier Arnaiz, Erwin van Dijk, Mireille Bétermier, Maoussi Lhuillier-Akakpo, Augustin de Vanssay, Sandra Duharcourt, Erika Sallet, Jérôme Gouzy, Linda Sperling
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0136851
Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient OutcomesCited by: 52
Author(s): Priscilla F. McAuliffe, Kurt W. Evans, Argun Akçakanat, Ken Chen, Xiaofeng Zheng, Hao Zhao, Agda Karina Eterovic, Takafumi Sangai, Ashley M. Holder, Chandeshwar Sharma, Huiqin Chen, Kim Anh, Emily Tarco, Mihai Gagea, Katherine A. Naff, Ayşegül Şahin, Asha S. Multani, Dalliah M. Black, Elizabeth A. Mittendorf, Isabelle Bedrosian, Gordon B. Mills, Ana M. González-Angulo, Funda Meric‐Bernstam
Software Mentions: 3
Published: about 9 years ago
10.1002/cphg.105
The AD Knowledge Portal: A Repository for Multi‐Omic Data on Alzheimer's Disease and AgingCited by: 25
Author(s): Anna K. Greenwood, Kelsey S. Montgomery, Nicole Kauer, Kara Woo, Zoë Leanza, William L. Poehlman, Jake Gockley, Solveig K. Sieberts, Ljubomir Bradic, Benjamin A. Logsdon, Mette A. Peters, Larsson Omberg, Lara M. Mangravite
Software Mentions: 3
Published: about 4 years ago
10.1186/1471-2105-8-157
Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structuresCited by: 21
Author(s): Xin Lü, David L. Perkins
Software Mentions: 3
Published: over 17 years ago
10.1186/s12862-018-1275-1
Variable gene transcription underlies phenotypic convergence of hypoxia tolerance in sculpinsCited by: 5
Author(s): Milica Mandic, Marina L. Ramon, Aleeza C. Gerstein, Andrew Y. Gracey, Jeffrey G. Richards
Software Mentions: 3
Published: about 6 years ago
10.1016/j.isci.2021.102779
Copy number analyses of DNA repair genes reveal the role of poly(ADP-ribose) polymerase (PARP) in tree longevityCited by: 10
Author(s): Yuta Aoyagi Blue, Junko Kusumi, Akiko Satake
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2105-9-431
Probabilistic base calling of Solexa sequencing dataCited by: 91
Author(s): Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Félix Naef
Software Mentions: 2
Published: about 16 years ago
10.1242/bio.026393
Cloning, molecular evolution and functional characterization of ZmbHLH16, the maize ortholog of OsTIP2 (OsbHLH142)Cited by: 6
Author(s): Yongming Liu, Jia Li, Weihua Gui, Yonghao Sun, Yanli Lu, Hai Long, Chuan Li, Suzhi Zhang, Mengji Cao
Software Mentions: 2
Published: almost 8 years ago
10.1002/mnfr.201600372
Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized ratsCited by: 17
Author(s): Melissa N. Conley, Cooper Roberts, Thomas J. Sharpton, Urszula T. Iwaniec, Norman G. Hord
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pgen.1005990
Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned AutoimmunityCited by: 38
Author(s): Johannes Stuttmann, Nora Peine, Ana Victoria Torres García, Christine Wagner, Sayan Roy Choudhury, Yiming Wang, Geo Velikkakam James, Thomas Griebel, Rubén Alcázar, Kazuhiko Tsuda, Korbinian Schneeberger, Jane E. Parker
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0224858
Genetic susceptibility to angiotensin-converting enzyme-inhibitor induced angioedema: A systematic review and evaluation of methodological approachesCited by: 8
Author(s): Haivin Aziz Ali, Anne Fog Lomholt, Seyed Hamidreza Mahmoudpour, Thorbjørn Hermanrud, Anette Bygum, Christian von Buchwald, Marianne Antonius Jakobsen, Eva Rye Rasmussen
Software Mentions: 2
Published: about 5 years ago
10.1242/dev.157081
Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory networkCited by: 38
Author(s): Simon Scofield, Alex Murison, Angharad Jones, John A. Fozard, Mitsuhiro Aida, Leah R. Band, Malcolm J. Bennett, James A. H. Murray
Software Mentions: 2
Published: almost 7 years ago
10.1016/j.xpro.2021.100583
Protocol for single-cell ATAC sequencing using combinatorial indexing in mouse lung adenocarcinomaCited by: 8
Author(s): Isabella Del Priore, Sai Ma, Jonathan Strecker, Tyler Jacks, Lindsay M. LaFave, Jason D. Buenrostro
Software Mentions: 2
Published: over 3 years ago
10.3389/fpsyt.2020.564277
BDNF Gene's Role in Schizophrenia: From Risk Allele to Methylation ImplicationsCited by: 13
Author(s): Xiaoqian Fu, Jun Wang, Jianbin Du, Jing Sun, Ancha Baranova, Fuquan Zhang
Software Mentions: 1
Published: almost 4 years ago
10.1186/s13059-018-1560-8
Discovering in vivo cytokine-eQTL interactions from a lupus clinical trialCited by: 34
Author(s): Emma E Davenport, Tiffany Amariuta, María Gutiérrez‐Arcelus, Kamil Slowikowski, Harm Jan Westra, Yang Luo, Ciyue Shen, Deepak A. Rao, Ying Zhang, Stephen Pearson, David von Schack, Jean S. Beebe, Nan Bing, Sally John, Michael S. Vincent, Baohong Zhang, Soumya Raychaudhuri
Software Mentions: 1
Published: about 6 years ago
10.1172/jci.insight.98921
Repurposing sertraline sensitizes non–small cell lung cancer cells to erlotinib by inducing autophagyCited by: 47
Author(s): Xingwu Jiang, Weiqiang Lü, Xiaoyang Shen, Quan Wang, Jing Lv, Mingyao Liu, Feixiong Cheng, Zhongming Zhao, Xiufeng Pang
Software Mentions: 1
Published: over 6 years ago
10.1111/1462-2920.15095
Partial pathogenicity chromosomes in<i>Fusarium oxysporum</i>are sufficient to cause disease and can be horizontally transferredCited by: 23
Author(s): Jiming Li, Like Fokkens, Lee James Conneely, Martijn Rep
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0094185
Transcriptome Analysis of Integument Differentially Expressed Genes in the Pigment Mutant (quail) during Molting of Silkworm, Bombyx moriCited by: 22
Author(s): Hongyi Nie, Chun Li, Tingcai Cheng, Qiongyan Li, Yuqian Wu, Mengting Zhou, Yinxia Zhang, Qingyou Xia
Software Mentions: 1
Published: over 10 years ago
10.1155/2018/7943786
Prevalence and Antibiotic Resistance Patterns of<i>Campylobacter</i>spp. Isolated from Broiler Chickens in the North of TunisiaCited by: 33
Author(s): Manel Gharbi, Awatef Béjaoui, Cherif Ben Hamda, Ahlem Jouini, Kaïs Ghedira, Chahrazed Zrelli, Safa Hamrouni, Chedia Aouadhi, Ghaith Bessoussa, Abdeljelil Ghram, Abderrazak Maaroufi
Software Mentions: 1
Published: almost 6 years ago
10.1186/1471-2164-14-332
Structural and functional annotation of the porcine immunomeCited by: 151
Author(s): Harry Dawson, Jane Loveland, Géraldine Pascal, James Gilbert, Hirohide Uenishi, Katherine M. Mann, Yongming Sang, Jie Zhang, Denise Carvalho-Silva, Toby Hunt, Matthew P. Hardy, Zhi-Liang Hu, Shuzhen Zhao, Anna Anselmo, Hiroki Shinkai, Celine Chen, Bouabid Badaoui, Daniel Berman, Clara Amid, Mike Kay, D. M. Lloyd, Catherine Snow, Takeya Morozumi, Ryan Cheng, Megan Bystrom, Ronan Kapétanovic, John C. Schwartz, R. S. Kataria, Matthew Astley, Eric Fritz, Charles A. Steward, Mark Thomas, Laurens G. Wilming, Daisuke Toki, Alan Archibald, Bertrand Bed’Hom, Dario Beraldi, Ting Hua Huang, Tahar Aït-Ali, Frank Blecha, Sara Botti, Tom C. Freeman, Elisabetta Giuffra, David Hume, Joan K. Lunney, Michael P. Murtaugh, James M. Reecy, Jennifer Harrow, Claire Rogel‐Gaillard, Christopher K. Tuggle
Software Mentions: 1
Published: over 11 years ago
10.1186/s12864-016-3252-7
Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cellsCited by: 14
Author(s): Gi Young Jeong, Yeong-Hwan Lim, Young‐Kook Kim
Software Mentions: 1
Published: about 8 years ago
10.1111/jcmm.14095
MiR‐103 inhibiting cardiac hypertrophy through inactivation of myocardial cell autophagy via targeting <scp>TRPV</scp>3 channel in rat heartsCited by: 20
Author(s): Hanping Qi, Jing Ren, E Mingyao, Qianhui Zhang, Yonggang Cao, Lina Ba, Chao Song, Pilong Shi, Bowen Fu, Hai‐Ying Sun
Software Mentions: 1
Published: almost 6 years ago
10.1128/JCM.01249-17
Rapid Microarray-Based Detection of Rifampin, Isoniazid, and Fluoroquinolone Resistance in Mycobacterium tuberculosis by Use of a Single CartridgeCited by: 10
Author(s): Juliane Havlicek, Beatrice Dachsel, Peter Slickers, Sönke Andres, Patrick Beckert, Silke Feuerriegel, Stefan Niemann, Matthias Merker, Ines Labugger
Software Mentions: 1
Published: almost 7 years ago
10.1002/anie.201802080
Silyl‐Phosphino‐Carbene Complexes of Uranium(IV)Cited by: 38
Author(s): Erli Lu, Josef T. Boronski, Matthew Gregson, Ashley J. Wooles, Stephen T. Liddle
Software Mentions: 1
Published: over 6 years ago
10.1038/s41598-019-45235-7
Multidimensional diffusion MRI with spectrally modulated gradients reveals unprecedented microstructural detailCited by: 58
Author(s): Henrik Lundell, Markus Nilsson, Tim B. Dyrby, Geoffrey Parker, Penny L. Hubbard Cristinacce, Fenglei Zhou, Daniel Topgaard, Samo Lasič
Software Mentions: 1
Published: over 5 years ago
10.1186/s40246-018-0133-y
Identify Down syndrome transcriptome associations using integrative analysis of microarray database and correlation-interaction networkCited by: 15
Author(s): Min Chen, Jiayan Wang, Yingjun Luo, Kuo Cheng Huang, Xiaoshun Shi, Qing Liu, Jin Li, Zhengfei Lai, Shuya Xue, Haimei Gao, Allen Chen, Dunjin Chen
Software Mentions: 1
Published: almost 7 years ago
10.1038/s41396-019-0464-2
Diverse hydrogen production and consumption pathways influence methane production in ruminantsCited by: 108
Author(s): Chris Greening, Renae Geier, Cecilia Wang, Laura C. Woods, Sergio E. Morales, Michael J. McDonald, Rowena Rushton-Green, Xochitl C. Morgan, Satoshi Koike, Sinead C. Leahy, William J. Kelly, Isaac Cann, Graeme T. Attwood, Gregory M. Cook, Roderick I. Mackie
Software Mentions: 1
Published: over 5 years ago
10.3389/fphys.2019.01057
Comparison of Different Methods for Estimating Cardiac Timings: A Comprehensive Multimodal Echocardiography InvestigationCited by: 44
Author(s): Parastoo Dehkordi, Farzad Khosrow-Khavar, Marco Di Rienzo, Omer T. Inan, Samuel Schmidt, Andrew P. Blaber, Kasper Sørensen, Johannes Struijk, Vahid Zakeri, Prospero Lombardi, Md. Mobashir Hasan Shandhi, Mojtaba Borairi, John Zanetti, Kouhyar Tavakolian
Software Mentions: 1
Published: over 5 years ago