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: kallisto

https://packages.ecosyste.ms/registries/pypi.org/packages/kallisto

The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented.
9 versions
Latest release: about 1 year ago
2 dependent packages
282 downloads last month

Papers Mentioning kallisto 307

10.1038/s41598-020-78288-0
Common and personal target genes of the micronutrient vitamin D in primary immune cells from human peripheral blood
Cited by: 19
Author(s): Andrea Hanel, Antonio Neme, Marjo Malinen, Emmi Hämäläinen, Henna-Riikka Malmberg, Stéphane Etheve, Tomi‐Pekka Tuomainen, Jyrki K. Virtanen, Igor Bendik, Carsten Carlberg
Software Mentions: 5
Published: almost 4 years ago
10.3389/fonc.2020.01195
Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model
Cited by: 82
Author(s): Barbara Schrörs, Sebastian Boegel, Christian Albrecht, Thomas Bukur, Valesca Bukur, Christoph Holtsträter, Christoph Ritzel, Katja Manninen, Arbel D. Tadmor, Mathias Vormehr, Uğur Şahin, Martin Löwer
Software Mentions: 5
Published: over 4 years ago
10.1016/j.cell.2020.09.062
M. tuberculosis Reprograms Hematopoietic Stem Cells to Limit Myelopoiesis and Impair Trained Immunity
Cited by: 126
Author(s): Nargis Khan, Jeffrey Downey, Joaquín Sanz, Eva Kaufmann, Birte Blankenhaus, Alain Pacis, Erwan Pernet, Eisha Ahmed, Sílvia Cardoso, Anastasia Nijnik, Bruce Mazer, Christopher M. Sassetti, Marcel A. Behr, Miguel P. Soares, Luis B. Barreiro, Maziar Divangahi
Software Mentions: 5
Published: about 4 years ago
10.3389/fmicb.2016.00459
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
Cited by: 585
Author(s): Juan Jovel, Jordan Patterson, Weiwei Wang, Naomi Hotte, Sandra O’Keefe, Troy Mitchel, Troy Perry, Dina Kao, Andrew L. Mason, Karen Madsen, Gane Ka‐Shu Wong
Software Mentions: 5
Published: over 8 years ago
10.3390/biology10010039
Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets
Cited by: 11
Author(s): Adeel Malik, Chang-Bae Kim
Software Mentions: 5
Published: almost 4 years ago
10.1002/ps.6061
Toxicological and molecular profiling of insecticide resistance in a Brazilian strain of fall armyworm resistant to Bt Cry1 proteins
Cited by: 24
Author(s): Debora Boaventura, Benjamin Buer, Niklas Hamaekers, Frank Maiwald, Ralf Nauen
Software Mentions: 5
Published: about 4 years ago
10.3390/ijms21051720
Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana
Cited by: 27
Author(s): Stephanie Schaarschmidt, Axel Fischer, Ellen Zuther, Dirk K. Hincha
Software Mentions: 5
Published: over 4 years ago
10.1111/tpj.14699
Heating quinoa shoots results in yield loss by inhibiting fruit production and delaying maturity
Cited by: 18
Author(s): Jose C. Tovar, Carlos Quillatupa, Steven T. Callen, S. Elizabeth Castillo, Paige Pearson, Anastasia Shamin, Haley Schuhl, Noah Fahlgren
Software Mentions: 5
Published: over 4 years ago
10.3389/fmicb.2018.02382
Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing
Cited by: 23
Author(s): Blaire Steven, Jayne Belnap, Cheryl R. Kuske
Software Mentions: 5
Published: about 6 years ago
10.3390/v13020291
Metatranscriptome Analysis of Sympatric Bee Species Identifies Bee Virus Variants and a New Virus, Andrena-Associated Bee Virus-1
Cited by: 12
Author(s): Katie F. Daughenbaugh, Idan Kahnonitch, Charles C. Carey, Alexander J. McMenamin, Tanner Wiegand, Tal Erez, Naama Arkin, Brian T. Ross, Blake Wiedenheft, Asaf Sadeh, Nor Chejanovsky, Yael Mandelik, Michelle L. Flenniken
Software Mentions: 5
Published: almost 4 years ago
10.3390/plants9091176
Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
Cited by: 19
Author(s): Ivan Tsers, Vladimir Gorshkov, Natalia Gogoleva, Olga Parfirova, Olga Petrova, Alexander A. Kamnev
Software Mentions: 5
Published: about 4 years ago
10.1186/s13059-021-02386-z
BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
Cited by: 4
Author(s): Johan Gustafsson, Jonathan L. Robinson, Jens Nielsen, Lior Pachter
Software Mentions: 5
Published: over 3 years ago
10.1186/s13024-020-00415-2
Diabetic phenotype in mouse and humans reduces the number of microglia around β-amyloid plaques
Cited by: 16
Author(s): Teemu Natunen, Henna Martiskainen, Mikael Marttinen, Sami Gabbouj, Hennariikka Koivisto, Susanna Kemppainen, Satu Kaipainen, Mari Takalo, Hélèna Svobodova, Luukas Leppänen, Benjam Kemiläinen, Simo Ryhänen, Teemu Kuulasmaa, Eija Rahunen, Sisko Juutinen, Petra Mäkinen, Pasi Miettinen, Tuomas Rauramaa, Jussi Pihlajamäki, Annakaisa Haapasalo, Ville Leinonen, Heikki Tanila, Mikko Hiltunen
Software Mentions: 5
Published: about 4 years ago
10.18632/oncotarget.25330
Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Cited by: 14
Author(s): Michael Hamilton, Thomas Girke, Ernest Martinez
Software Mentions: 5
Published: over 6 years ago
10.1186/s13015-021-00181-w
Fast lightweight accurate xenograft sorting
Cited by: 8
Author(s): Jens Zentgraf, Sven Rahmann
Software Mentions: 4
Published: over 3 years ago
10.1186/s12859-019-2612-0
Barcode identification for single cell genomics
Cited by: 15
Author(s): Akshay Tambe, Lior Pachter
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12859-021-04147-y
Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes
Cited by: 1
Author(s): Michal R. Grzadkowski, Hannah D. Holly, Julia Somers, Emek Demir
Software Mentions: 4
Published: over 3 years ago
10.1186/s12859-020-3484-z
Short paired-end reads trump long single-end reads for expression analysis
Cited by: 13
Author(s): Adam H. Freedman, John Gaspar, Timothy B. Sackton
Software Mentions: 4
Published: over 4 years ago
10.1186/s12920-017-0295-9
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking
Cited by: 46
Author(s): Margaret M. Parker, Robert Chase, Andrew Lamb, Alejandro Reyes, Aabida Saferali, Jeong H. Yun, Blanca E. Himes, Edwin K. Silverman, Craig P. Hersh, Peter J. Castaldi
Software Mentions: 4
Published: about 7 years ago
10.1186/s12887-019-1564-x
Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation
Cited by: 22
Author(s): Najeeha Talat Iqbal, Sana Syed, Kamran Sadiq, Marium Khan, Junaid Iqbal, Z. Jennie, Fayaz Umrani, Sheraz Ahmed, Elizabeth A. Maier, Lee A. Denson, Yael Haberman, Monica McNeal, Kenneth D.R. Setchell, Xueheng Zhao, Shahida Qureshi, Lanlan Shen, Christopher A. Moskaluk, Ta‐Chiang Liu, Ömer H. Yılmaz, Donald E. Brown, Michael J. Barratt, Vanderlene L. Kung, Jeffrey I. Gordon, Sean R. Moore, Syed Asad Ali
Software Mentions: 4
Published: over 5 years ago
10.1186/s12870-021-02997-5
Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)
Cited by: 10
Author(s): J. Vladimir Torres-Rodríguez, M. Nancy Salazar-Vidal, Ricardo A. Chávez Montes, Julio A. Massange‐Sánchez, C. Stewart Gillmor, Ruairidh J. H. Sawers
Software Mentions: 4
Published: over 3 years ago
10.1186/s12870-021-03149-5
Pathogen and drought stress affect cell wall and phytohormone signaling to shape host responses in a sorghum COMT bmr12 mutant
Cited by: 6
Author(s): Maya Khasin, Lois F. Bernhardson, Patrick M. O’Neill, Nathan A. Palmer, Erin D. Scully, Scott E. Sattler, Deanna L. Funnell‐Harris
Software Mentions: 4
Published: over 3 years ago
10.1186/s13104-019-4471-1
Shiny-Seq: advanced guided transcriptome analysis
Cited by: 26
Author(s): Zenitha Sundararajan, Rainer Knoll, Peter Hombach, Matthias Becker, Joachim L. Schultze, Thomas Ulas
Software Mentions: 4
Published: over 5 years ago
10.1186/s40168-021-01048-3
Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements
Cited by: 28
Author(s): Dieter M. Tourlousse, Koji Narita, Takamasa Miura, Mitsuo Sakamoto, Akiko Ohashi, Keita Shiina, Masami Matsuda, Daisuke Miura, Mamiko Shimamura, Yoshifumi Ohyama, Atsushi Yamazoe, Yuichi Uchino, Keishi Kameyama, Shingo Arioka, Jiro Kataoka, Takayoshi Hisada, Kazuyuki Fujii, Shunsuke Takahashi, Miho Kuroiwa, Masatomo Rokushima, Mitsue Nishiyama, Yoshiki Tanaka, Takuya Fuchikami, Hitomi Aoki, Satoshi Kira, Ryo Koyanagi, Takeshi Naito, Morie Nishiwaki, Hirotaka Kumagai, Mikiko Konda, Keiji Kasahara, Moriya Ohkuma, Hiroko Kawasaki, Yuji Sekiguchi, Jun Terauchi
Software Mentions: 4
Published: over 3 years ago
10.3390/v13030433
Non-Metabolic Functions of PKM2 Contribute to Cervical Cancer Cell Proliferation Induced by the HPV16 E7 Oncoprotein
Cited by: 7
Author(s): Seoung-Ae Lee, Charles Ho, Madison Troxler, Chin-Yo Lin, Sang-Hyuk Chung
Software Mentions: 4
Published: over 3 years ago
10.7717/peerj.12087
SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization
Cited by: 6
Author(s): Mikio Shiga, Shigeto Seno, Makoto Onizuka, Hideo Matsuda
Software Mentions: 4
Published: about 3 years ago
10.1371/journal.pbio.3001306
Dynamic landscape of protein occupancy across the Escherichia coli chromosome
Cited by: 18
Author(s): Peter L. Freddolino, Haley M. Amemiya, Thomas J. Goss, Saeed Tavazoie
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pgen.1008189
Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia
Cited by: 66
Author(s): Guoxin Cui, Yi Jin Liew, Yong Li, Najeh M. Kharbatia, Noura Ibrahim Omar Zahran, Abdul‐Hamid Emwas, Vı́ctor M. Eguı́luz, Manuel Aranda
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pmed.1002309
Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis
Cited by: 231
Author(s): Alexandra Snyder, Tavi Nathanson, Samuel A. Funt, Arun Ahuja, Jacqueline L. Buros, Matthew D. Hellmann, Eliza Chang, Bülent Arman Aksoy, Hikmat Al‐Ahmadie, Erik Yusko, Marissa Vignali, Sharon Benzeno, Mariel Elena Boyd, Meredith Maisie Moran, Gopa Iyer, Harlan Robins, Elaine R. Mardis, Taha Merghoub, Jeff Hammerbacher, Jonathan E. Rosenberg, Dean F. Bajorin
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pone.0186794
A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health
Cited by: 16
Author(s): Vittoria Roncalli, Andrew E. Christie, Stephanie A. Sommer, Matthew Cieslak, Daniel K. Hartline, Petra H. Lenz
Software Mentions: 4
Published: about 7 years ago
10.1371/journal.pone.0247534
Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics
Cited by: 9
Author(s): Jessica A. Day, Christian Diener, Anne E. Otwell, Kourtney E. Tams, Brad M. Bebout, Angela M. Detweiler, Michael Lee, Madeline T. Scott, Wilson Ta, Monica Ha, Shienna A. Carreon, Kenny Tong, Abdirizak A. Ali, Sean M. Gibbons, Nitin S. Baliga
Software Mentions: 4
Published: over 3 years ago
10.1016/j.celrep.2021.109105
Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins
Cited by: 24
Author(s): Joseph Hiatt, Devin A. Cavero, Michael McGregor, Weihao Zheng, Jonathan M. Budzik, Theodore L. Roth, Kelsey M. Haas, David Wu, Ujjwal Rathore, Anke Meyer-Franke, Mohamed S. Bouzidi, Eric Shifrut, Youjin Lee, Vigneshwari Easwar Kumar, Eric V. Dang, David E. Gordon, Jason A. Wojcechowskyj, Judd F. Hultquist, Krystal A. Fontaine, Satish K. Pillai, Jeffery S. Cox, Joel D. Ernst, Nevan J. Krogan, Alexander Marson
Software Mentions: 4
Published: over 3 years ago
10.1186/s13072-019-0319-0
Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells
Cited by: 29
Author(s): Ryuichiro Nakato, Youichiro Wada, Ryo Nakaki, Genta Nagae, Yuki Katou, Sadami Tsutsumi, N. Nakajima, Hiroshi Fukuhara, Atsushi Iguchi, Takahide Kohro, Yasuharu Kanki, Yutaka Saitô, Mika Kobayashi, Akashi Izumi-Taguchi, Naoki Osato, Kenji Tatsuno, Asuka Kamio, Yoko Hayashi‐Takanaka, Hiromi Wada, Shinzo Ohta, Masamichi Aikawa, Hiroyuki Nakajima, Masaki Nakamura, Rebecca C. McGee, Kyle W. Heppner, Tatsuo Kawakatsu, Michiru Genno, Hiroshi Yanase, Haruki Kume, Takaaki Senbonmatsu, Yukio Homma, Shigeyuki Nishimura, Toutai Mitsuyama, Hiroyuki Aburatani, Hiroshi Kimurâ, Katsuhiko Shirahige
Software Mentions: 4
Published: almost 5 years ago
10.1111/eva.13142
Transcriptional frontloading contributes to cross‐tolerance between stressors
Cited by: 8
Author(s): Michael T. Collins, Melody S. Clark, John I. Spicer, Manuela Truebano
Software Mentions: 4
Published: about 4 years ago
10.3389/fgene.2020.00845
Comprehensive Analysis of mRNA and lncRNA Transcriptomes Reveals the Differentially Hypoxic Response of Preadipocytes During Adipogenesis
Cited by: 3
Author(s): Jinwei Zhang, Jideng Ma, Xiankun Zhou, Silu Hu, Liangpeng Ge, Jing Sun, Penghao Li, Keren Long, Long Jin, Qianzi Tang, Lingyan Liu, Xuewei Li, Surong Shuai, Mingzhou Li
Software Mentions: 4
Published: over 4 years ago
10.3389/fimmu.2017.01221
PI3Kδ Inhibition Enhances the Antitumor Fitness of Adoptively Transferred CD8+ T Cells
Cited by: 56
Author(s): Jacob S. Bowers, Kinga Majchrzak, Michelle H. Nelson, Bülent Arman Aksoy, Megan Wyatt, Aubrey S. Smith, Stefanie R. Bailey, Lillian R. Neal, Jeff Hammerbacher, Chrystal M. Paulos
Software Mentions: 4
Published: about 7 years ago
10.3389/fmicb.2021.641756
Chemotranscriptomic Profiling Defines Drug-Specific Signatures of the Glycopeptide Antibiotics Dalbavancin, Vancomycin and Chlorobiphenyl-Vancomycin in a VanB-Type-Resistant Streptomycete
Cited by: 0
Author(s): Andrew Hesketh, Giselda Bucca, Colin P. Smith, Hee‐Jeon Hong
Software Mentions: 4
Published: over 3 years ago
10.3389/fnins.2020.00774
Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala
Cited by: 19
Author(s): Marissa R Keever, Pan Zhang, Courtni R. Bolt, Adrienne M. Antonson, Haley E Rymut, Megan P. Caputo, Alexandra K Houser, Álvaro Gonzalez Hernández, Bruce R. Southey, Laurie A. Rund, Rodney W. Johnson, Sandra L. Rodriguez-Zas
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-017-1277-0
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
Cited by: 72
Author(s): Koen Van den Berge, Charlotte Soneson, Mark D. Robinson
Software Mentions: 4
Published: over 7 years ago
10.1186/s13073-020-00740-7
Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues
Cited by: 24
Author(s): Jean-David Larouche, Assya Trofimov, Leslie Hesnard, Grégory Ehx, Qingchuan Zhao, Krystel Vincent, Chantal Durette, Patrick Gendron, Jean‐Philippe Laverdure, Éric Bonneil, Caroline Côté, Sébastien Lemieux, Pierre Thibault, Claude Perreault
Software Mentions: 4
Published: over 4 years ago
10.1172/jci.insight.139932
Immunopathogenesis of hidradenitis suppurativa and response to anti–TNF-α therapy
Cited by: 61
Author(s): Margaret M. Lowe, Haley B. Naik, Sean Clancy, Mariela Pauli, Kathleen M. Smith, Yingtao Bi, Robert W. Dunstan, Johann E. Gudjonsson, Maia Paul, Hobart W. Harris, Esther Kim, Uk Sok Shin, Richard Ahn, Wilson Liao, Scott L. Hansen, Michael D. Rosenblum
Software Mentions: 4
Published: about 4 years ago
10.1016/j.jbc.2021.100335
Disturbed intramitochondrial phosphatidic acid transport impairs cellular stress signaling
Cited by: 9
Author(s): Akinori Eiyama, Mari J. Aaltonen, Hendrik Nolte, Takashi Tatsuta, Thomas Langer
Software Mentions: 4
Published: almost 4 years ago
10.1093/jxb/eraa036
The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions
Cited by: 14
Author(s): Matthew Haas, Axel Himmelbach, Martin Mascher
Software Mentions: 4
Published: almost 5 years ago
10.21203/rs.3.rs-141578/v1
COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone
Cited by: 14
Author(s): Aartik Sarma, Stephanie A. Christenson, Eran Mick, Thomas Deiss, Catherine DeVoe, Angela Oliveira Pisco, Rajani Ghale, Alejandra Jauregui, Ashley Byrne, Farzad Moazed, Natasha Spottiswoode, Pratik Sinha, Beth Shoshana Zha, Norma Neff, Michelle Tan, Paula Hayakawa Serpa, K. Mark Ansel, Jennifer G. Wilson, Aleksandra Leligdowicz, Emily Seigel, Marina Sirota, Joseph L. DeRisi, Michael A. Matthay, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Matthew F. Krummel, Prescott G. Woodruff, David J. Erle, Carolyn S. Calfee, Charles Langelier
Software Mentions: 4
Published: almost 4 years ago
10.1038/sdata.2017.33
Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines
Cited by: 102
Author(s): Jo Lynne Harenza, Maura Diamond, Rebecca N. Adams, Michael Song, Heather L. Davidson, Lori S. Hart, Maiah H. Dent, Paolo Fortina, C. Patrick Reynolds, John M. Maris
Software Mentions: 4
Published: over 7 years ago
10.1038/srep42110
Blubber transcriptome response to acute stress axis activation involves transient changes in adipogenesis and lipolysis in a fasting-adapted marine mammal
Cited by: 37
Author(s): Jane Khudyakov, Cory D. Champagne, Lorenzo Meneghetti, Daniel E. Crocker
Software Mentions: 4
Published: almost 8 years ago
10.1038/s41598-018-24243-z
Environment-dependent striatal gene expression in the BACHD rat model for Huntington disease
Cited by: 9
Author(s): Arianna Novati, Thomas Hentrich, Zinah Wassouf, Jonasz Jeremiasz Weber, Libo Yu-Taeger, Nicole Déglon, Huu Phuc Nguyen, Julia M. Schulze‐Hentrich
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-020-74598-5
Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19
Cited by: 36
Author(s): Anna A. Valyaeva, Anastasia A. Zharikova, Artem S. Kasianov, Yegor S. Vassetzky, Eugene V. Sheval
Software Mentions: 4
Published: about 4 years ago
10.1038/s41598-021-90540-9
Differential gene expression indicates modulated responses to chronic and intermittent hypoxia in corallivorous fireworms (Hermodice carunculata)
Cited by: 3
Author(s): Candace J. Grimes, Lene H. Petersen, Anja Schulze
Software Mentions: 4
Published: over 3 years ago
10.1128/mBio.00588-21
An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin
Cited by: 6
Author(s): Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa J. Cook, M. Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John T. Belisle, A Mortazavi, Alan G. Barbour
Software Mentions: 4
Published: over 3 years ago
10.1128/mSystems.00299-20
Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
Cited by: 44
Author(s): Elizabeth A. McDaniel, Brittany F. Peterson, Sarah Stevens, Patricia Q. Tran, Karthik Anantharaman, Katherine D. McMahon
Software Mentions: 4
Published: about 4 years ago
10.7554/eLife.52621
FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences
Cited by: 78
Author(s): Raeann Goering, Laura I. Hudish, Bryan B. Guzman, Nisha Raj, Gary J. Bassell, Holger A. Russ, Daniel Domínguez, J. Matthew Taliaferro
Software Mentions: 4
Published: over 4 years ago
10.7554/eLife.66417
Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19
Cited by: 56
Author(s): Courtney Tindle, MacKenzie Fuller, Ayden G. Fonseca, Sahar Taheri, Stella‐Rita Ibeawuchi, Nathan Beutler, Gajanan D. Katkar, Amanraj Claire, Vanessa Castillo, Moises Hernandez, Hana Russo, Jason Duran, Laura E. Crotty Alexander, Ann Tipps, Grace Lin, Patricia A. Thistlethwaite, Ranajoy Chattopadhyay, Thomas F. Rogers, Debashis Sahoo, Pradipta Ghosh, Soumita Das
Software Mentions: 4
Published: over 3 years ago
10.7554/eLife.62731
GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis
Cited by: 22
Author(s): Markus Terrey, Scott I. Adamson, Alana L. Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 4
Published: about 4 years ago
10.7554/eLife.49178
Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell
Cited by: 107
Author(s): Eran Mick, Denis V. Titov, Owen S. Skinner, Rohit Sharma, Alexis A. Jourdain, Vamsi K. Mootha
Software Mentions: 4
Published: over 4 years ago
10.7554/eLife.29132
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium
Cited by: 122
Author(s): David R. Hill, Sha Huang, Melinda S. Nagy, Veda K. Yadagiri, Courtney Fields, Dishari Mukherjee, Brooke Bons, Priya H. Dedhia, Alana M. Chin, Yu Hwai Tsai, Shrikar Thodla, Thomas M. Schmidt, Seth T. Walk, Vincent B. Young, Jason R. Spence
Software Mentions: 4
Published: about 7 years ago
10.7554/eLife.50901
A genetic, genomic, and computational resource for exploring neural circuit function
Cited by: 151
Author(s): Fred P. Davis, Aljoscha Nern, Serge Picard, Michael B. Reiser, Gerald M. Rubin, Sean R. Eddy, Gilbert L. Henry
Software Mentions: 4
Published: almost 5 years ago
10.3390/ijms20123101
Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation
Cited by: 29
Author(s): Saurabh Gupta, Yanni Dong, Paul P. Dijkwel, Bernd Mueller‐Roeber, Tsanko Gechev
Software Mentions: 4
Published: over 5 years ago
10.18632/oncotarget.16048
HLA class I loss in metachronous metastases prevents continuous T cell recognition of mutated neoantigens in a human melanoma model
Cited by: 26
Author(s): Barbara Schrörs, Silke Lübcke, Volker Lennerz, Martina Fatho, Anne Bicker, Catherine Wölfel, Patrick Derigs, Thomas Hankeln, Dirk Schadendorf, Annette Paschen, Thomas Wölfel
Software Mentions: 4
Published: over 7 years ago
10.1186/s12864-018-4488-1
Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes
Cited by: 38
Author(s): Mahsa Khorramdelazad, Ido Bar, Paul Whatmore, Gabrielle Smetham, Vijay Bhaaskaria, Yuedong Yang, Shahla Hosseini Bai, Nitin Mantri, Yaoqi Zhou, Rebecca Ford
Software Mentions: 3
Published: almost 7 years ago
10.3390/jcm10051057
Gene Expression Landscape of SDH-Deficient Gastrointestinal Stromal Tumors
Cited by: 9
Author(s): Valentina Indio, Angela Schipani, Margherita Nannini, Milena Urbini, Alessandro Rizzo, Antonio De Leo, Annalisa Altimari, Valerio Di Scioscio, Daria Messelodi, Giuseppe Tarantino, Annalisa Astolfi, Maria Abbondanza Pantaleo
Software Mentions: 3
Published: over 3 years ago
10.1093/jxb/erw105
The<i>Cer-cqu</i>gene cluster determines three key players in a β-diketone synthase polyketide pathway synthesizing aliphatics in epicuticular waxes
Cited by: 80
Author(s): Lizette M. Schneider, Nikolai M Adamski, Claus Bo Vöge Christensen, David Stuart, Sonia Vautrin, Mats Hansson, Cristóbal Uauy, Penny von Wettstein-Knowles
Software Mentions: 3
Published: over 8 years ago
10.1007/s41745-020-00178-1
Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art
Cited by: 9
Author(s): Justine Jia Wen Seow, Richard L. Wong, Rhea Pai, Ankur Sharma
Software Mentions: 3
Published: over 4 years ago
10.1038/s10038-020-00862-1
Practical guide for managing large-scale human genome data in research
Cited by: 26
Author(s): Tomoya Tanjo, Yosuke Kawai, Katsushi Tokunaga, Osamu Ogasawara, Masao Nagasaki
Software Mentions: 3
Published: about 4 years ago
10.1038/s41419-020-2303-9
Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia
Cited by: 32
Author(s): Yang Li, Joshua J. Gruber, Ulrike M. Litzenburger, Yiren Zhou, Yu Miao, Edward L. LaGory, Albert M. Li, Zhen Hu, Michaela Yip, Lori S. Hart, John M. Maris, Howard Y. Chang, Amato J. Giaccia, Jiangbin Ye
Software Mentions: 3
Published: almost 5 years ago
10.3390/microorganisms9081704
The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses
Cited by: 3
Author(s): Gabriel Quintanilha-Peixoto, Paula Luize Camargos Fonseca, Fábio Trigo Raya, Marina Püpke Marone, Dener Eduardo Bortolini, Piotr A. Mieczkowski, Roenick Proveti Olmo, Marcelo Falsarella Carazzolle, Christian A. Voigt, Ana Cristina Fermino Soares, Gonçalo Amarante Guimarães Pereira, Aristóteles Goés-Neto, Eric Roberto Guimarães Rocha Aguiar
Software Mentions: 3
Published: over 3 years ago
10.1084/jem.20202489
Germinal center–dependent and –independent memory B cells produced throughout the immune response
Cited by: 47
Author(s): Charlotte Viant, Tobias Wirthmiller, Mohamed ElTanbouly, Spencer Chen, Melissa Cipolla, Víctor Ramos, Thiago Y. Oliveira, Leonidas Stamatatos, Michel C. Nussenzweig
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1009305
Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level
Cited by: 21
Author(s): Suraj Kannan, Michael Farid, Brian L. Lin, Matthew Miyamoto, Chulan Kwon
Software Mentions: 3
Published: about 3 years ago
10.1101/2020.08.04.20167874
Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing
Cited by: 39
Author(s): Joshua S. Bloom, Laila Sathe, Chetan Munugala, Eric M. Jones, Molly Gasperini, Nathan B. Lubock, Fauna Yarza, Erin Thompson, Kyle M. Kovary, Jimin Park, Dawn Marquette, Stephania Kay, Mark Lucas, TreQuan Love, A. Sina Booeshaghi, Oliver F. Brandenberg, Longhua Guo, James Boocock, Myles Hochman, Scott W. Simpkins, Isabella Lin, Nathan LaPierre, Duke Hong, Yi Zhang, Gabriel Oland, Bianca Judy Choe, Sukantha Chandrasekaran, Evann E. Hilt, Manish J. Butte, Robert Damoiseaux, Clifford Kravit, Aaron Cooper, Yi Yin, Lior Pachter, Omai B. Garner, Jonathan Flint, Eleazar Eskin, Chongyuan Luo, Sriram Kosuri, Leonid Kruglyak, Valerie A. Arboleda
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pbio.2002399
Hippo signaling controls cell cycle and restricts cell plasticity in planarians
Cited by: 31
Author(s): Nídia de Sousa, Gustavo Rodríguez-Esteban, José Ignacio Rojo-Laguna, Emili Saló, Teresa Adell
Software Mentions: 3
Published: almost 7 years ago
10.3390/plants10071407
The Modification of Plant Cell Wall Polysaccharides in Potato Plants during Pectobacterium atrosepticum-Caused Infection
Cited by: 7
Author(s): Vladimir Gorshkov, Ivan Tsers, Bakhtiyar Islamov, Marina Ageeva, Natalia Gogoleva, Polina Mikshina, Olga Parfirova, Olga Gogoleva, Olga Petrova, Т. А. Горшкова, Alexander A. Kamnev
Software Mentions: 3
Published: over 3 years ago
10.1126/sciadv.aau8317
The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice
Cited by: 387
Author(s): Peng Zheng, Benhua Zeng, Meiling Liu, Jianjun Chen, Junxi Pan, Han Yu, Yiyun Liu, Ke Cheng, Chanjuan Zhou, Haiyang Wang, Xinyu Zhou, Siwen Gui, Seth W. Perry, Ma‐Li Wong, Júlio Licinio, Hong Wei, Peng Xie
Software Mentions: 3
Published: almost 6 years ago
10.1126/sciadv.aba2368
Actomyosin contractility confers mechanoprotection against TNFα-induced disruption of the intervertebral disc
Cited by: 19
Author(s): Paula Hernández, Timothy Jacobsen, Nadeen O. Chahine
Software Mentions: 3
Published: over 4 years ago
10.1186/s12870-019-1795-x
Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)
Cited by: 19
Author(s): Daniel R. Kohlhase, Jamie A. O’Rourke, Micheal D. K. Owen, Michelle A. Graham
Software Mentions: 3
Published: over 5 years ago
10.3390/ijms22158012
Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
Cited by: 3
Author(s): Rongxin Zhang, Yajun Li, Xingxing Zhang, Ke Xiao, Yue Hou, Hongde Liu, Xiao Sun
Software Mentions: 3
Published: over 3 years ago
10.3390/cells9020318
Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity
Cited by: 35
Author(s): Markus Wolfien, Anne-Marie Galow, Paula Müller, Madeleine Bartsch, Ronald M. Brunner, Tom Goldammer, Olaf Wolkenhauer, Andreas Hoeflich, Róbert Dávid
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12864-021-07934-2
CAMPAREE: a robust and configurable RNA expression simulator
Cited by: 1
Author(s): Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Antonijo Mrčela, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash, Gregory R. Grant
Software Mentions: 3
Published: about 3 years ago
10.3389/fpls.2021.641325
Genes That Mediate Starch Metabolism in Developing and Germinated Barley Grain
Cited by: 10
Author(s): Helen Collins, Natalie S. Betts, Christoph Dockter, Oliver Berkowitz, Ilka Braumann, José A. Cuesta-Seijo, Birgitte Skadhauge, James Whelan, Vincent Bulone, Geoffrey B. Fincher
Software Mentions: 3
Published: over 3 years ago
10.3389/fmicb.2019.01027
Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production
Cited by: 20
Author(s): Chee Kent Lim, Juan C. Villada, Annie Chalifour, Maria F. Duran, Hsu Feng Lu, Patrick K. H. Lee
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-018-23379-2
RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts
Cited by: 28
Author(s): C G Azar, Mark C. Valentine, Julie S. Trausch-Azar, Todd E. Druley, D. Michael Nelson, Alan L. Schwartz
Software Mentions: 3
Published: over 6 years ago
10.3390/nu13051457
Targeting Methylglyoxal in Diabetic Kidney Disease Using the Mitochondria-Targeted Compound MitoGamide
Cited by: 3
Author(s): Sih Min Tan, Runa Lindblom, Mark Ziemann, Adrienne Laskowski, Cesare Granata, Matthew Snelson, Vicki Thallas‐Bonke, Assam El‐Osta, Carlos D. Baeza-Garza, Stuart T. Caldwell, Richard C. Hartley, Thomas Krieg, Mark E. Cooper, Michael P. Murphy, Melinda T. Coughlan
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-018-25430-8
Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat
Cited by: 22
Author(s): Prabin Bajgain, Blake Russell, Mohsen Mohammadi
Software Mentions: 3
Published: over 6 years ago
10.1038/s41598-018-27912-1
Expression ratio of the TGFβ-inducible gene MYO10 is prognostic for overall survival of squamous cell lung cancer patients and predicts chemotherapy response
Cited by: 11
Author(s): Dmytro Dvornikov, Marc A. Schneider, Sebastian Ohse, Magdalena Szczygieł, I. Titkova, Marcus Rosenblatt, Thomas Muley, Arne Warth, Felix Herth, Hendrik Dienemann, Michael Thomas, Jens Timmer, Marcel Schilling, Hauke Busch, Melanie Boerries, Michael Meister, Ursula Klingmüller
Software Mentions: 3
Published: over 6 years ago
10.1128/mSystems.00668-20
Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways
Cited by: 9
Author(s): Shawn M. Doyle, Genmei Lin, Maya Morales‐McDevitt, Terry L. Wade, Antonietta Quigg, Jason B. Sylvan
Software Mentions: 3
Published: about 4 years ago
10.7554/eLife.61973
Improving oligo-conjugated antibody signal in multimodal single-cell analysis
Cited by: 27
Author(s): Terkild Brink Buus, Alberto Herrera, Ellie Ivanova, Eleni P. Mimitou, Anthony Cheng, Ramin S. Herati, Thales Papagiannakopoulos, Peter Smibert, Niels Ødum, Sergei B. Koralov
Software Mentions: 3
Published: over 3 years ago
10.1128/mSystems.00416-19
Genomewide Analysis of Mode of Action of the <i>S</i> -Adenosylmethionine Analogue Sinefungin in Leishmania infantum
Cited by: 13
Author(s): Arijit Bhattacharya, Meenakshi Sharma, Charles Packianathan, Barry P. Rosen, Philippe Leprohon, Marc Ouellette
Software Mentions: 3
Published: about 5 years ago
10.1128/mSphere.00477-17
The Candida albicans TOR-Activating GTPases Gtr1 and Rhb1 Coregulate Starvation Responses and Biofilm Formation
Cited by: 26
Author(s): Peter R. Flanagan, Ningning Liu, Darren J. Fitzpatrick, Karsten Hokamp, Julia R. Köhler, Gary P. Moran
Software Mentions: 3
Published: almost 7 years ago
10.1186/s12870-020-02590-2
Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum
Cited by: 11
Author(s): Javier Canales, Felipe Uribe, Carlos Henríquez-Valencia, Carlos Lovazzano, Joaquı́n Medina, Elena A. Vidal
Software Mentions: 3
Published: about 4 years ago
10.3390/ijms22094449
Transcriptome Analysis of Seed Weight Plasticity in Brassica napus
Cited by: 5
Author(s): Javier Canales, José Verdejo, Gabriela Carrasco‐Puga, Francisca M. Castillo, Anita Arenas‐M, Daniel F. Calderini
Software Mentions: 3
Published: over 3 years ago
10.3389/fimmu.2021.684015
Impaired Vitamin D Signaling in T Cells From a Family With Hereditary Vitamin D Resistant Rickets
Cited by: 6
Author(s): Fatima A. H. Al-Jaberi, Martin Kongsbak-Wismann, Alejandro Aguayo-Orozco, Nicolai Krogh, Terkild Brink Buus, Daniel Villalba Lopez, Anna K. O. Rode, Eva Gravesen, Klaus Ølgaard, Søren Brunak, Anders Woetmann, Niels Ødum, Charlotte M. Bonefeld, Carsten Geisler
Software Mentions: 3
Published: over 3 years ago
10.3389/fimmu.2021.632512
Enhanced Glycolysis Is Required for Antileishmanial Functions of Neutrophils Upon Infection With Leishmania donovani
Cited by: 12
Author(s): Mareike Ohms, Carolina Ferreira, Hauke Busch, Inken Wohlers, Ana Cristina Guerra Souza, Ricardo Silvestre, Tamás Laskay
Software Mentions: 3
Published: over 3 years ago
10.20411/pai.v5i1.348
Pharmacological Inhibition of PPAR&lt;sub&gt;y&lt;/sub&gt; Boosts HIV Reactivation and Th17 Effector Functions, while Preventing Progeny Virion Release and &lt;i&gt;de novo&lt;/i&gt; Infection
Cited by: 9
Author(s): Delphine Planas, Augustine Fert, Yuwei Zhang, Jean-Philippe Goulet, Jonathan Richard, Pradeep D. Uchil, María Julia Ruiz, Laurence Raymond Marchand, Debashree Chatterjee, Huicheng Chen, Tomas Raul Wiche Salinas, Annie Gosselin, Éric A. Cohen, Jean Pierre Routy, Nicolas Chomont, Petronela Ancuța
Software Mentions: 3
Published: about 4 years ago
10.1186/s12864-021-07523-3
Autosomal recessive loci contribute significantly to quantitative variation of male fertility in a dairy cattle population
Cited by: 15
Author(s): Maya Hiltpold, Naveen Kumar Kadri, F. Janett, Ulrich Witschi, F. Schmitz‐Hsu, Hubert Pausch
Software Mentions: 3
Published: over 3 years ago
10.1186/s13068-021-01946-6
Transcriptome analysis revealed the regulation of gibberellin and the establishment of photosynthetic system promote rapid seed germination and early growth of seedling in pearl millet
Cited by: 6
Author(s): Bingchao Wu, Min Sun, Huan Zhang, Dan Yang, Chuang Lin, İmran Khan, Xiaoshan Wang, Xinquan Zhang, Gang Nie, Guangyan Feng, Yanhong Yan, Li Zhou, Yan Peng, Linkai Huang
Software Mentions: 3
Published: over 3 years ago
10.3390/ijms22010296
Distinct Regulation of the Expression of Satellite DNAs in the Beetle Tribolium castaneum
Cited by: 4
Author(s): Antonio Sermek, Isidoro Feliciello, Đurđica Ugarković
Software Mentions: 3
Published: almost 4 years ago
10.1038/s42003-021-02331-7
Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics
Cited by: 13
Author(s): Christopher L. Anderson, Samodha C. Fernando
Software Mentions: 3
Published: over 3 years ago
10.1186/s12864-019-5438-2
Conserved regulation of RNA processing in somatic cell reprogramming
Cited by: 4
Author(s): Alexander Kanitz, Afzal Pasha Syed, Keisuke Kaji, Mihaela Zavolan
Software Mentions: 3
Published: almost 6 years ago
10.1016/j.omtm.2021.07.001
High throughput screening of novel AAV capsids identifies variants for transduction of adult NSCs within the subventricular zone
Cited by: 15
Author(s): Lukas P.M. Kremer, Santiago Cerrizuela, Sascha Dehler, Thomas Stiehl, Jonas Weinmann, Heike Abendroth, Susanne Kleber, Alexander Laure, Jihad El Andari, Simon Anders, Anna Marciniak‐Czochra, Dirk Grimm, Ana Martin‐Villalba
Software Mentions: 3
Published: almost 3 years ago
10.1128/mBio.00215-20
Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses
Cited by: 56
Author(s): Myra Hosmillo, Yasmin Chaudhry, Komal Nayak, Frédéric Sorgeloos, Bon‐Kyoung Koo, Alessandra Merenda, Reidun Lillestøl, Lydia N Drumright, Matthias Zilbauer, Ian Goodfellow
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0222325
Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana
Cited by: 13
Author(s): Johanna A. L. Goldman, Megan J. Schatz, Chris T. Berthiaume, Sacha Coesel, Mónica V. Orellana, E. Virginia Armbrust
Software Mentions: 3
Published: about 5 years ago