This collection showcases the books, journal articles, book reviews, and other publications and presentations written by faculty and researchers of the Department of Biochemistry and Molecular Pharmacology.

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Publications from 2016

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Peak-Finding Algorithms, Jui-Hung Hung and Zhiping Weng

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Sequence Alignment and Homology Search, Jui-Hung Hung and Zhiping Weng

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Sequence Alignment and Homology Search with BLAST and ClustalW, Jui-Hung Hung and Zhiping Weng

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Visualizing Genomic Annotations with the UCSC Genome Browser, Jui-Hung Hung and Zhiping Weng

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Systematic Experimental Determination of Functional Constraints on Proteins and Adaptive Potential of Mutations: A Dissertation, Li Jiang

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A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance, Li Jiang, Ping Liu, Claudia Bank, Nicholas Renzette, Kristina L. Prachanronarong, L. Safak Yilmaz, Daniel R. Caffrey, Konstantin B. Zeldovich, Celia A. Schiffer, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Jennifer P. Wang, and Daniel N. Bolon

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Abrogation of collagen-induced arthritis by a peptidyl arginine deiminase inhibitor is associated with modulation of T cell-mediated immune responses, Joanna Kawalkowska, Anne-Marie Quirke, Fatemeh Ghari, Simon Davis, Venkataraman Subramanian, Paul R. Thompson, Richard O. Williams, Roman Fischer, Nicholas B. La Thangue, and Patrick J. Venables

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Understanding the Sequence-Specificity and RNA Target Recognition Properties of the Oocyte Maturation Factor, OMA-1, in Caenorhabditis elegans: A Dissertation, Ebru Kaymak

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NEAT1 is Required for Survival of Breast Cancer Cells Through FUS and miR-548, Hao Ke, Limin Zhao, Xu Feng, Haibo Xu, Li Zou, Qin Yang, Xiaosan Su, Lingtao Peng, and Baowei Jiao

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GnRH Stimulates Peptidylarginine Deiminase Catalyzed Histone Citrullination in Gonadotrope Cells, Shaihla A. Khan, Brian S. Edwards, Aaron Muth, Paul R. Thompson, Brian D. Cherrington, and Amy M. Navratil

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Endovascular reconstruction of unruptured intradural vertebral artery dissecting aneurysms with the Pipeline embolization device, Anna L. Kuhn, Peter Kan, Francesca Massi, Juan Diego Lozano, Samuel Y. Hou, Mary Howk, Matthew J. Gounis, Ajay K. Wakhloo, and Ajit S. Puri

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Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, Marc F. Lensink, Zhiping Weng, Thom Vreven, Brian G. Pierce, and Tyler M. Borrman

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Peptidylarginine Deiminase 3 (PAD3) Is Upregulated by Prolactin Stimulation of CID-9 Cells and Expressed in the Lactating Mouse Mammary Gland, Guangyuan Li, Isaac N. Hayward, Brittany R. Jenkins, Heather M. Rothfuss, Coleman H. Young, Marja T. Nevalainen, Aaron Muth, Paul R. Thompson, Amy M. Navratil, and Brian D. Cherrington

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Viral Proteases as Drug Targets and the Mechanisms of Drug Resistance: A Dissertation, Kuan-Hung Lin

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Dengue Protease Substrate Recognition: Binding of the Prime Side, Kuan-Hung Lin, Ellen A. Nalivaika, Kristina L. Prachanronarong, Nese Kurt Yilmaz, and Celia A. Schiffer

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Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites, Ce Feng Liu, Gabriel S. Brandt, Quyen Q. Hoang, Natalia Naumova, Vanja Lazarevic, Eun Sook Hwang, Job Dekker, Laurie H. Glimcher, Dagmar Ringe, and Gregory A. Petsko (Proceedings of the National Academy of Sciences of the United States of America, 10-25-2016)

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Oligosaccharyltransferase inhibition induces senescence in RTK-driven tumor cells, Cecilia Lopez-Sambrooks, Shiteshu Shrimal, Carol Khodier, Daniel P. Flaherty, Natalie Rinis, Jonathan C. Charest, Ningguo Gao, Peng Zhao, Lance Wells, Timothy A. Lewis, Mark A. Lehrman, Reid Gilmore, Jennifer E. Golden, and Joseph N. Contessa

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Ribosome*RelA structures reveal the mechanism of stringent response activation, Anna B. Loveland, Eugene Bah, Rohini Madireddy, Ying Zhang, Axel F. Brilot, Nikolaus Grigorieff, and Andrei A. Korostelev

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The Identification and Targeting of Partially-Folded Conformations on the Folding Free-Energy Landscapes of ALS-Linked Proteins for Therapeutic Intervention: A Dissertation, Brian C. Mackness

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CRISPR-Cas9 nuclear dynamics and target recognition in living cells, Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang, David Grünwald, and Thoru Pederson

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Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow, Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang, David Grünwald, and Thoru Pederson

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Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis, Matthew J. Markert, Ying Zhang, Metewo Selase Enuameh, Steven M. Reppert, Scot A. Wolfe, and Christine Merlin

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Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting, David Mavor, Benjamin P. Roscoe, Daniel N. Bolon, and James S. Fraser

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Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma, Michael J. McGeachie, Gaurav Jain, Amartya Sanyal, Ye Zhan, Bryan R. Lajoie, Job Dekker, Scott T. Weiss, and CAMP Research Group (The New England journal of medicine, 5-12-2016)

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Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma, Michael J. McGeachie, Bryan R. Lajoie, Job Dekker, and CAMP Research Group (American journal of respiratory and critical care medicine, 12-15-2016)

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A deep sequencing tool for partitioning clearance rates following antimalarial treatment in polyclonal infections, Nicole Mideo, Jeffrey A. Bailey, Nicholas J. Hathaway, Billy Ngasala, David L. Saunders, Chanthap Lon, Oksana Kharabora, Andrew Jamnik, Sujata Balasubramanian, Anders Bjorkman, Andreas Martensson, Steven R. Meshnick, Andrew F. Read, and Jonathan J. Juliano

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Systematic Mutant Analyses Elucidate General and Client-Specific Aspects of Hsp90 Function, Parul Mishra, Julia Flynn, Tyler N. Starr, and Daniel N. Bolon

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Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire, Lindsey Montefiori, Robert Wuerffel, Damian Roqueiro, Bryan R. Lajoie, Changying Guo, Tatiana Gerasimova, Supriyo De, William Wood, Kevin G. Becker, Job Dekker, Jie Liang, Ranjan Sen, and Amy L. Kenter (Cell reports, 2-2-2016)

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CTCF-mediated topological boundaries during development foster appropriate gene regulation, Varun Narendra, Milica Bulajic, Job Dekker, Esteban O. Mazzoni, and Danny Reinberg (Genes and development, 12-15-2016)

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WZB117 (2-Fluoro-6-(m-hydroxybenzoyloxy) Phenyl m-Hydroxybenzoate) Inhibits GLUT1-mediated Sugar Transport by Binding Reversibly at the Exofacial Sugar Binding Site, Ogooluwa A. Ojelabi, Kenneth P. Lloyd, Andrew Simon, Julie K. De Zutter, and Anthony Carruthers

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Neutrophil extracellular traps exacerbate Th1-mediated autoimmune responses in rheumatoid arthritis by promoting DC maturation, Garyfalia Papadaki, Konstantinos Kambas, Christiana Choulaki, Katerina Vlachou, Elias Drakos, George Bertsias, Konstantinos Ritis, Dimitrios T. Boumpas, Paul R. Thompson, Panayotis Verginis, and Prodromos Sidiropoulos

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Inhibition of APOBEC3G activity impedes double-stranded DNA repair, Ponnandy Prabhu, Shivender Shandilya, Elena Britan-Rosich, Adi Nagler, Celia A. Schiffer, and Moshe Kotler

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Understanding Drug Resistance and Antibody Neutralization Escape in Antivirals: A Dissertation, Kristina L. Prachanronarong

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Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase, Kristina L. Prachanronarong, Aysegul Ozen, Kelly Thayer, L. Safak Yilmaz, Konstantin B. Zeldovich, Daniel N. Bolon, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Jennifer P. Wang, Nese Kurt Yilmaz, and Celia A. Schiffer

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The Structural Basis for the Interdependence of Drug Resistance in the HIV-1 Protease, Debra A. Ragland

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Intergenerational Transfer of Epigenetic Information in Sperm, Oliver J. Rando

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A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces, Timothy P. Riley, Cory M. Ayres, Lance M. Hellman, Nishant K. Singh, Michael Cosiano, Jennifer M. Cimons, Michael J. Anderson, Kurt H. Piepenbrink, Brian G. Pierce, Zhiping Weng, and Brian M. Baker

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Computational Modeling of T Cell Receptor Complexes, Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Zhiping Weng, and Brian M. Baker

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Structural and molecular analysis of a protective epitope of Lyme disease antigen OspA and antibody interactions, Shivender Shandilya, Nese Kurt Yilmaz, Andrew Sadowski, Ejemel Monir, Zachary A. Schiller, William D. Thomas Jr., Mark S. Klempner, Celia A. Schiffer, and Yang Wang

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Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals, Upasna Sharma, Colin C. Conine, Jeremy Shea, Ana Boskovic, Alan G. Derr, Xin Y. Bing, Clemence Belleannee, Alper Kucukural, Ryan W. Serra, Fengyun Sun, Lina Song, Benjamin R. Carone, Emiliano P. Ricci, Xin Z. Li, Lucas Fauquier, Melissa J. Moore, Robert Sullivan, Craig C. Mello, Manuel Garber, and Oliver J. Rando

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Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus, Emily M. Smith, Bryan R. Lajoie, Gaurav Jain, and Job Dekker (American journal of human genetics, 1-7-2016)

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Genome-wide CRISPR Screen Identifies Regulators of MAPK as Suppressors of Liver Tumors in Mice, Chun-Qing Song, Yingxiang Li, Haiwei Mou, Jill Moore, Angela I. Park, Soren Hough, Zachary Kennedy, Andrew H. Fischer, Darryl Conte Jr., Zhiping Weng, and Wen Xue

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Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease, Djade I. Soumana, Nese Kurt Yilmaz, Akbar Ali, Kristina L. Prachanronarong, and Celia A. Schiffer

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Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172, Djade I. Soumana, Nese Kurt Yilmaz, Kristina L. Prachanronarong, Cihan Aydin, Akbar Ali, and Celia A. Schiffer

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The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans, Wen Tang, Shikui Tu, Heng-Chi Lee, Zhiping Weng, and Craig C. Mello

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MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory, Alex Tek, Andrei A. Korostelev, and Samuel Coulbourn Flores

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DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data, Junko Tsuji and Zhiping Weng

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TAD disruption as oncogenic driver, Anne-Laure Valton and Job Dekker (Current opinion in genetics and development, 2-1-2016)

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Interaction of tau with the RNA-Binding Protein TIA1 Regulates tau Pathophysiology and Toxicity, Tara Vanderweyde, John D. Leszyk, and Benjamin Wolozin

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Dynamics of Nucleosome Positioning Maturation following Genomic Replication, Pauline Vasseur, Saphia Tonazzini, Rahima Ziane, Alain Camasses, Oliver J. Rando, and Marta Radman-Livaja

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Performance of ZDOCK and IRAD in CAPRI rounds 28-34, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, and Zhiping Weng

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Regulation of X-linked gene expression during early mouse development by Rlim, Feng Wang, JongDae Shin, Jeremy Shea, Jun Yu, Ana Boskovic, Meg Byron, Xiaochun Zhu, Alex K. Shalek, Aviv Regev, Jeanne B. Lawrence, Eduardo M. Torres, Lihua J. Zhu, Oliver J. Rando, and Ingolf Bach

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Exploiting DNA Repair and ER Stress Response Pathways to Induce Apoptosis in Glioblastoma Multiforme: A Dissertation, Jessica L. Weatherbee

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ER stress in temozolomide-treated glioblastomas interferes with DNA repair and induces apoptosis, Jessica L. Weatherbee, Jean-Louis Kraus, and Alonzo H. Ross

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Dye-Sensitized Core/Active Shell Upconversion Nanoparticles for Optogenetics and Bioimaging Applications, Xiang Wu, Yuanwei Zhang, Kendra Takle, Osman Bilsel, Zhan Jun Li, Hyungseok Lee, Carlos Lois, Yang Xiang, and Gang Han

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Improving Viral Protease Inhibitors to Counter Drug Resistance, Nese Kurt Yilmaz, Ronald I. Swanstrom, and Celia A. Schiffer

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Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo, Hao Yin, Chun-Qing Song, Joseph R. Dorkin, Lihua Julie Zhu, Yingxiang Li, Qiongqiong Wu, Angela I. Park, Junghoon Yang, Sneha Suresh, Aizhan Bizhanova, Ankit Gupta, Mehmet Fatih Bolukbasi, Stephen Walsh, Roman L. Bogorad, Guangping Gao, Zhiping Weng, Yizhou Dong, Victor Koteliansky, Scot A. Wolfe, Robert Langer, Wen Xue, and Daniel G. Anderson

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Peptidylarginine deiminase 1-catalyzed histone citrullination is essential for early embryo development, Xiaoqian Zhang, Xiaoqiu Liu, Mei Zhang, Tingting Li, Aaron Muth, Paul R. Thompson, Scott A. Coonrod, and Xuesen Zhang

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Illuminating Cell Signaling with Near-Infrared Light-Responsive Nanomaterials, Yuanwei Zhang, Ling Huang, Zhan Jun Li, Guolin Ma, Yubin Zhou, and Gang Han

Publications from 2015

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The PsychENCODE project, Schahram Akbarian, Zhiping Weng, Eugenio Mattei, Michael Purcaro, Junko Tsuji, Geetha Senthil, Thomas Lehner, Pamela Sklar, Nenad Sestan, and PsychENCODE Consortium

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Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains, Guang Bai, Iris Cheung, Hennady P. Shulha, Joana E. Coelho, Ping Li, Xianjun Dong, Mira Jakovcevski, Yumei Wang, Anastasia Grigorenko, Yan Jiang, Andrew Hoss, Krupal Patel, Ming Zheng, Evgeny Rogaev, Richard H. Myers, Zhiping Weng, Schahram Akbarian, and Jiang-Fan Chen

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A systematic survey of an intragenic epistatic landscape, Claudia Bank, Ryan T. Hietpas, Jeffrey D. Jensen, and Daniel N. Bolon

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Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells, Ahmet Rasim Barutcu, Bryan R. Lajoie, Rachel Patton McCord, Coralee E. Tye, Deli Hong, Terri L. Messier, Gillian Browne, Andre J. van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano, and Gary S. Stein (Genome biology, 9-28-2015)

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A Simple Proteomics-Based Approach to Identification of Immunodominant Antigens from a Complex Pathogen: Application to the CD4 T Cell Response against Human Herpesvirus 6B, Aniuska Becerra-Artiles, Omar Dominguez-Amorocho, Lawrence J. Stern, and J. Mauricio Calvo-Calle

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Chromosome Conformation Capture (3C) in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 6-1-2015)

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Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 6-1-2015)

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Hi-C in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 7-1-2015)

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Measuring Chromatin Structure in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 7-1-2015)

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Randomized ligation control for chromosome conformation capture, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 6-1-2015)

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The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer, Jon-Matthew Belton, Bryan R. Lajoie, Sylvain Audibert, Sylvain Cantaloube, Imen Lassadi, Isabelle Goiffon, Davide Bau, Marc A. Marti-Renom, Kerstin Bystricky, and Job Dekker

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A docking interface in the cyclin Cln2 promotes multi-site phosphorylation of substrates and timely cell-cycle entry, Samyabrata Bhaduri, Ervin Valk, Matthew J. Winters, Brian Gruessner, Mart Loog, and Peter M. Pryciak

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Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets, David M. Blodgett, Anetta Nowosielska, Shaked Afik, Susanne Pechhold, Anthony J. Cura, Norman J. Kennedy, Soyoung Kim, Alper Kucukural, Roger J. Davis, Sally C. Kent, Dale L. Greiner, Manuel Garber, David M. Harlan, and Philip J. diLorio Jr.

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Gold nanoparticles stabilized with MPEG-grafted poly(l-lysine): in vitro and in vivo evaluation of a potential theranostic agent, Alexei A. Bogdanov, Suresh Gupta, Nadezhda Koshkina, Stuart J. Corr, Surong Zhang, Steven A. Curley, and Gang Han

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Gold nanoparticles stabilized with MPEG-grafted poly(l-lysine): in vitro and in vivo evaluation of a potential theranostic agent, Alexei A. Bogdanov Jr., Suresh Gupta, Nadezhda Koshkina, Stuart J. Corr, Surong Zhang, Steven A. Curley, and Gang Han

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REdiii: a pipeline for automated structure solution, Markus-Frederik Bohn and Celia A. Schiffer

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The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization, Markus-Frederik Bohn, Shivender Shandilya, Tania V. Silvas, Ellen A. Nalivaika, Takahide Kouno, Brian Kelch, Sean P. Ryder, Nese Kurt Yilmaz, Mohan Somasundaran, and Celia A. Schiffer

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DNA-binding-domain fusions enhance the targeting range and precision of Cas9, Mehmet Fatih Bolukbasi, Ankit Gupta, Sarah Oikemus, Alan G. Derr, Manuel Garber, Michael H. Brodsky, Lihua Julie Zhu, and Scot A. Wolfe

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Structural basis for mutation-induced destabilization of profilin 1 in ALS, Sivakumar Boopathy, Tania V. Silvas, Maeve Tischbein, Silvia Jansen, Shivender Shandilya, Jill A. Zitzewitz, John E. Landers, Bruce L. Goode, Celia A. Schiffer, and Daryl A. Bosco

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Systematic Dissection of Roles for Chromatin Regulators in Dynamics of Transcriptional Response to Stress in Yeast: A Dissertation, Hsiuyi V. Chen

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R loops regulate promoter-proximal chromatin architecture and cellular differentiation, Poshen B. Chen, Hsiuyi V. Chen, Diwash Acharya, Oliver J. Rando, and Thomas G. Fazzio

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Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs, Min-Te Chou, Bo W. Han, Chiung-Po Hsiao, Phillip D. Zamore, Zhiping Weng, and Jui-Hung Hung

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Condensin-driven remodelling of X chromosome topology during dosage compensation, Emily Crane, Qian Bian, Rachel Patton McCord, Bryan R. Lajoie, Bayly S. Wheeler, Edward J. Ralston, Satoru Uzawa, Job Dekker, and Barbara J. Meyer (Nature, 7-9-2015)

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Structural and functional diversity of Topologically Associating Domains, Job Dekker and Edith Heard (FEBS letters, 10-7-2015)

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Structural and functional diversity of Topologically Associating Domains, Job Dekker and Edith Heard (FEBS letters, 10-7-2015)

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Long-Range Chromatin Interactions, Job Dekker and Tom Misteli (Cold Spring Harbor perspectives in biology, 10-1-2015)

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The Lipid Droplet Protein Hypoxia-inducible Gene 2 Promotes Hepatic Triglyceride Deposition by Inhibiting Lipolysis, Marina T. DiStefano, Laura V. Danai, Rachel J. Roth Flach, Anil K. Chawla, David J. Pedersen, Adilson L. Guilherme, and Michael P. Czech

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The Exocyst Subunit Sec6 Interacts with Assembled Exocytic Snare Complexes: A Dissertation, Michelle L. Dubuke

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The Exocyst Subunit Sec6 Interacts with Assembled Exocytic SNARE Complexes, Michelle L. Dubuke, Stephanie Maniatis, Scott A. Shaffer, and Mary Munson

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POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA, Ahmed M. Elewa, Masaki Shirayama, Ebru Kaymak, Paul F. Harrison, David R. Powell, Zhuo Du, Christopher D. Chute, Hannah Woolf, Dongni Yi, Takao Ishidate, Jagan Srinivasan, Zhirong Bao, Traude H. Beilharz, Sean P. Ryder, and Craig C. Mello

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Exploring New Strategies to Overcome Resistance in Glioblastoma Multiforme: A Dissertation, Yulian P. Ellis

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Epigenomics and the structure of the living genome, Nir Friedman and Oliver J. Rando

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Chemical Biology of Protein Arginine Modifications in Epigenetic Regulation, Jakob Fuhrmann, Kathleen W. Clancy, and Paul R. Thompson

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Synthesis and Use of a Phosphonate Amidine to Generate an Anti-Phosphoarginine-Specific Antibody, Jakob Fuhrmann, Venkataraman Subramanian, and Paul R. Thompson

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Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements, Ming Gao, Travis Thomson, T Michael Creed, Shikui Tu, Sudan N. Loganathan, Christina A. Jackson, Patrick McCluskey, Yanyan Lin, Scott E. Collier, Zhiping Weng, Paul Lasko, Melanie D. Ohi, and Alexey L. Arkov

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A Single Injection of Recombinant Adeno-Associated Virus into the Lumbar Cistern Delivers Transgene Expression Throughout the Whole Spinal Cord, Yansu Guo, Dan Wang, Tao Qiao, Chunxing Yang, Qin Su, Guangping Gao, and Zuoshang Xu

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Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF, Sarah J. Hainer, Weifeng Gu, Benjamin R. Carone, Benjamin D. Landry, Oliver J. Rando, Craig C. Mello, and Thomas G. Fazzio

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Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production, Bo W. Han, Wei Wang, Chengjian Li, Zhiping Weng, and Phillip D. Zamore

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piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing, Bo W. Han, Wei Wang, Phillip D. Zamore, and Zhiping Weng

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Near-infrared photoactivatable control of Ca signaling and optogenetic immunomodulation, Lian He, Yuanwei Zhang, Guolin Ma, Peng Tan, Zhan Jun Li, Shengbing Zhang, Xiang Wu, Ji Jing, Shaohai Fang, Lijuan Zhou, Youjun Wang, Yun Huang, Patrick Hogan, Gang Han, and Yubin Zhou

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An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments, Erin E. Heyer, Hakan Ozadam, Emiliano P. Ricci, Can Cenik, and Melissa J. Moore