Publications by authors named "Daniel Putnam"

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Enhancement of sorghum biomass hydrolysis by addition of amylases to an ionic liquid-based deconstruction process.
Md Tahmid Islam, Venkataramana R Pidatala, Edward E K Baidoo, Paul Wolski, Hemant Choudhary, Daniel H Putnam

BMC Res Notes· December 2025

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CanID: A Robust and Accurate RNA-seq Expression-based Diagnostic Classification Scheme for Pediatric Malignancies.
Daniel K Putnam, Alexander M Gout, Delaram Rahbarinia, Meiling Jin, David Finkelstein

Genomics Proteomics Bioinformatics· November 2025

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Reimagining alfalfa as a flexible crop for water security in the Southwestern USA.
Emily Waring, Helen E Dahlke, John T Abatzoglou, Josué Medellín-Azuara, Matt A Yost, Daniel H Putnam

Sci Total Environ· August 2025

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CanID: a robust and accurate RNAseq Expression-based diagnostic classification scheme for pediatric malignancies.
Daniel K Putnam, Alexander M Gout, Delaram Rahbarinia, Meiling Jin, David Finkelstein

bioRxiv· August 2025

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Seq2Karyotype (S2K): A Method for Karyotyping Using Single-Sample Whole-Genome Sequencing Data.
Limeng Pu, Karol Szlachta, Virginia Valentine, Meiling Jin, Sivaraman Natarajan, Daniel Putnam

bioRxiv· August 2025

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Latent epigenetic programs in Müller glia contribute to stress and disease response in the retina.
Jackie L Norrie, Marybeth S Lupo, Danielle R Little, Abbas Shirinifard, Akhilesh Mishra, Daniel Putnam

Dev Cell· April 2025

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Engineered reduction of S-adenosylmethionine alters lignin in sorghum.
Yang Tian, Yu Gao, Halbay Turumtay, Emine Akyuz Turumtay, Yen Ning Chai, Daniel H Putnam

Biotechnol Biofuels Bioprod· October 2024

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Field performance of switchgrass plants engineered for reduced recalcitrance.
Aymerick Eudes, Chien-Yuan Lin, Christopher De Ben, Jasmine Ortega, Mi Yeon Lee, Daniel H Putnam

Front Plant Sci· May 2023

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A Guide to MethylationToActivity: A Deep Learning Framework That Reveals Promoter Activity Landscapes from DNA Methylomes in Individual Tumors.
Karissa Dieseldorff Jones, Daniel Putnam, Justin Williams, Xiang Chen

Methods Mol Biol· February 2023

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Engineering sorghum for higher 4-hydroxybenzoic acid content.
Chien-Yuan Lin, Yang Tian, Kimberly Nelson-Vasilchik, Joel Hague, Ramu Kakumanu, Daniel H Putnam

Metab Eng Commun· December 2022

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Correction to "Expression of Dehydroshikimate Dehydratase in Sorghum Improves Biomass Yield, Accumulation of Protocatechuate, and Biorefinery Economics".
Yang Tian, Minliang Yang, Chien-Yuan Lin, Joon-Hyun Park, Chuan-Yin Wu, Daniel H Putnam

ACS Sustain Chem Eng· October 2022

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Accurate genomic variant detection in single cells with primary template-directed amplification.
Veronica Gonzalez-Pena, Sivaraman Natarajan, Yuntao Xia, David Klein, Robert Carter, Daniel Putnam

Proc Natl Acad Sci U S A· June 2021

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MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors.
Justin Williams, Beisi Xu, Daniel Putnam, Andrew Thrasher, Chunliang Li

Genome Biol· January 2021

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Molecular Mechanism of Telomere Length Dynamics and Its Prognostic Value in Pediatric Cancers.
Zhaoming Wang, Stephen V Rice, Ti-Cheng Chang, Yu Liu, Qi Liu, Daniel K Putnam

J Natl Cancer Inst· July 2020

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Nucleome Dynamics during Retinal Development.
Jackie L Norrie, Marybeth S Lupo, Beisi Xu, Issam Al Diri, Marc Valentine, Daniel Putnam

Neuron· November 2019

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VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity.
Daniel K Putnam, Xiaotu Ma, Stephen V Rice, Yu Liu, Scott Newman

Sci Rep· July 2019

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The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment.
Samuel W Brady, Xiaotu Ma, Armita Bahrami, Gryte Satas, Gang Wu, Daniel K Putnam

Mol Cancer Res· April 2019

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The impact of lignin downregulation on alfalfa yield, chemical composition, and in vitro gas production.
Girma Getachew, Emilio A Laca, Daniel H Putnam, Dave Witte, Mark McCaslin

J Sci Food Agric· August 2018

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CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline.
Axel W Fischer, Sten Heinze, Daniel K Putnam, Bian Li, James C Pino

PLoS One· August 2016

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A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers.
Venu Gopal Vandavasi, Daniel K Putnam, Qiu Zhang, Loukas Petridis, William T Heller

Plant Physiol· January 2016

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Protein accumulation and rumen stability of wheat γ-gliadin fusion proteins in tobacco and alfalfa.
Xiaodong Sun, Cecilia L Chi-Ham, Tamar Cohen-Davidyan, Christopher DeBen, Girma Getachew, Daniel Putnam

Plant Biotechnol J· September 2015

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BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles.
Daniel K Putnam, Brian E Weiner, Nils Woetzel, Edward W Lowe, Jens Meiler

Proteins· August 2015

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CASP10-BCL::Fold efficiently samples topologies of large proteins.
Sten Heinze, Daniel K Putnam, Axel W Fischer, Tim Kohlmann, Brian E Weiner

Proteins· March 2015

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Reconstruction of SAXS Profiles from Protein Structures.
Daniel K Putnam, Edward W Lowe, Jens Meiler

Comput Struct Biotechnol J· June 2014

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Exploring schizophrenia drug-gene interactions through molecular network and pathway modeling.
Daniel K Putnam, Jingchun Sun, Zhongming Zhao

AMIA Annu Symp Proc· February 2013

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