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Biology and Biochemistry

D-Index
47
Citations
18741
World Ranking
18536
National Ranking
7568

Overview

Stephanie Malfatti is affiliated with Lawrence Livermore National Laboratory in the United States, conducting research primarily in the fields of biochemistry, genetics, and molecular biology. Their work spans several subfields including molecular biology, ecology, plant science, and cell biology.

Their research focuses on several main topics:

  • Genomics and Phylogenetic Studies
  • RNA and protein synthesis mechanisms
  • Bacteriophages and microbial interactions
  • Machine Learning in Bioinformatics
  • Plant-Microbe Interactions and Immunity
  • Plant Pathogens and Fungal Diseases

Stephanie Malfatti has contributed to multiple research papers published in scientific venues such as G3 Genes Genomes Genetics, Microorganisms, bioRxiv (Cold Spring Harbor Laboratory), and UNC Libraries. Notable papers include:

  • MultiPhATE2: code for functional annotation and comparison of phage genomes, 2021, G3 Genes Genomes Genetics
  • Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes, 2021, Microorganisms
  • MultiPhATE2: Code for Functional Annotation and Comparison of Bacteriophage Genomes, 2020, bioRxiv (Cold Spring Harbor Laboratory)
  • Defining the core Arabidopsis thaliana root microbiome, 2020, UNC Libraries

Malfatti has frequently collaborated with several coauthors, with multiple joint publications involving Carol Zhou, Robert A. Edwards, Brian Souza, Jeffrey A. Kimbrel, and Katelyn McNair. These collaborations reflect a broad intersection of expertise spanning computational biology, microbial genomics, and bioinformatics.

Their publication record indicates an emphasis on computational tools for genomic analysis, especially in relation to bacteriophages and microbial communities. Their work on MultiPhATE2, a software solution for functional annotation of phage genomes, illustrates this focus. Additionally, studies on protein-coding gene identification and core root microbiomes highlight interdisciplinary applications of molecular biology techniques.

Best Publications

  • Defining the core Arabidopsis thaliana root microbiome

    Derek S. Lundberg;Sarah L. Lebeis;Sur Herrera Paredes;Scott Yourstone

  • Insights into the phylogeny and coding potential of microbial dark matter

    Christian Rinke;Patrick Schwientek;Alexander Sczyrba;Alexander Sczyrba;Natalia N. Ivanova

  • Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

    Gabrielle Rocap;Frank W. Larimer;Frank W. Larimer;Jane Lamerdin;Stephanie Malfatti

  • Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

    Sarah L. Lebeis;Sarah L. Lebeis;Sur Herrera Paredes;Derek S. Lundberg;Natalie Breakfield

  • Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

    Frank W Larimer;Patrick S. G. Chain;Patrick S. G. Chain;Loren John Hauser;Loren John Hauser;Jane Lamerdin

  • The genome of a motile marine Synechococcus

    B. Palenik;B. Brahamsha;F. W. Larimer;F. W. Larimer;M. Land;M. Land

  • Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

    Olivia U. Mason;Olivia U. Mason;Terry C. Hazen;Terry C. Hazen;Sharon Borglin;Patrick S. G. Chain;Patrick S. G. Chain

  • The complete genome sequence of Francisella tularensis, the causative agent of tularemia.

    Pär Larsson;Petra C F Oyston;Patrick Chain;May C Chu

  • Genome Project Standards in a New Era of Sequencing

    P. S. G. Chain;D. V. Grafham;R. S. Fulton;M. G. FitzGerald

  • The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes

    Mark W. J. van Passel;Ravi Kant;Erwin G. Zoetendal;Caroline M. Plugge

  • Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

    Patrick S. G. Chain;Vincent J. Denef;Konstantinos T. Konstantinidis;Konstantinos T. Konstantinidis;Lisa M. Vergez;Lisa M. Vergez

  • The DNA sequence and biology of human chromosome 19

    Jane Grimwood;Laurie A. Gordon;Laurie A. Gordon;Anne Olsen;Anne Olsen;Astrid Terry

  • Tackling soil diversity with the assembly of large, complex metagenomes

    Adina Chuang Howe;Janet K. Jansson;Janet K. Jansson;Stephanie A. Malfatti;Susannah G. Tringe

  • Deep‐sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill

    Jacob Bælum;Sharon Borglin;Romy Chakraborty;Julian L. Fortney

  • Pathogenomic Sequence Analysis of Bacillus cereus and Bacillus thuringiensis Isolates Closely Related to Bacillus anthracis

    Cliff S. Han;Gary Xie;Jean F. Challacombe;Michael R. Altherr

  • Whole-Genome Analyses of Speciation Events in Pathogenic Brucellae

    Patrick S. G. Chain;Diego J. Comerci;Marcelo E. Tolmasky;Frank W. Larimer

  • Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.

    Stefan M Sievert;Kathleen M Scott;Martin G Klotz;Patrick S. G. Chain;Patrick S. G. Chain

  • Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

    Matthew L. Bendall;Sarah L.R. Stevens;Leong Keat Chan;Stephanie Malfatti

  • Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255

    Shawn R. Starkenburg;Patrick S. G. Chain;Patrick S. G. Chain;Luis A. Sayavedra-Soto;Loren Hauser

  • Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

    P. B. Pope;S. E. Denman;M. Jones;S. G. Tringe

Frequent Co-Authors

Patrick S. G. Chain
Patrick S. G. Chain Los Alamos National Laboratory
Miriam Land
Miriam Land Oak Ridge National Laboratory
Susannah G. Tringe
Susannah G. Tringe Joint Genome Institute
Frank W. Larimer
Frank W. Larimer Oak Ridge National Laboratory
Loren Hauser
Loren Hauser Digital Infuzion (United States)
Tijana Glavina del Rio
Tijana Glavina del Rio Joint Genome Institute
Alex Copeland
Alex Copeland Joint Genome Institute
Susan Lucas
Susan Lucas Joint Genome Institute
Natalia Ivanova
Natalia Ivanova Lawrence Berkeley National Laboratory
David Bruce
David Bruce Pebble Labs

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